Alexandria Boehm

All Publications

• Detection and quantification of human immunodeficiency virus-1 (HIV-1) total nucleic acids in wastewater settled solids from two California communities. Applied and environmental microbiology Wolfe, M. K., Varkila, M. R., Zulli, A., Parsonnet, J., Boehm, A. B. 2024: e0147724

  Abstract

  Wastewater surveillance for infectious agents has proved useful in identifying the circulation of viruses within populations. We investigated the presence and concentration of human immunodeficiency virus (HIV)-1 total nucleic acids (including both viral RNA and proviral DNA) in wastewater solids. We retrospectively measured HIV-1 nucleic acids in two samples per week for 26 months at two wastewater treatment plants serving populations with different prevalences of HIV infections in San Francisco and Santa Clara County, California, USA. We detected HIV nucleic acids in a majority of samples with concentrations ranging from non-detect to 3.9 × 105 cp/g (N = 459 samples total). Concentrations of HIV-1 were significantly higher in samples from the wastewater treatment plant serving a population with a higher prevalence of people living with HIV than in the plant serving a population with a lower prevalence. The HIV-1 nucleic acids amplified were primarily DNA and thus represented proviral DNA shedding into wastewater. Additionally, we found that HIV-1 nucleic acid concentrations in wastewater solids were orders of magnitude higher than those in liquid wastewater indicating that the HIV-1 target preferentially sorbs to solids. Whether concentrations of HIV-1 in wastewater solids can be used to identify the number of incident cases remains unknown. Additional work on HIV-1 shedding from individuals with viremia and people living with HIV is needed to translate wastewater measurements into quantitative information on infections. Additional work may also be needed to document non-human sources of HIV-1 nucleic acids in wastewater.Human immunodeficiency virus (HIV)-1 has infected nearly 100 million people since it emerged in the 1980s. Antiretroviral therapy prevents transmission of HIV and also allows infected individuals to live healthy lives with normal life expectancy. Consequently, identifying unrecognized cases of HIV is of paramount importance. Since wastewater represents a composite biological sample from a community, it may provide valuable information on HIV-1 prevalence that can be used to inform HIV testing and outreach.

  View details for DOI 10.1128/aem.01477-24

  View details for PubMedID 39526804

• Detection of Hepatovirus A (HAV) in wastewater indicates widespread national distribution and association with socioeconomic indicators of vulnerability. mSphere Zulli, A., Chan, E. M., Boehm, A. B. 2024: e0064524

  Abstract

  Wastewater-based epidemiology, which seeks to assess disease occurrence in communities through measurements of infectious disease biomarkers in wastewater, may represent a valuable tool for understanding the occurrence of hepatitis A infections in communities. In this study, we measured concentrations of Hepatovirus A (HAV) RNA, in samples from 191 wastewater treatment plants spanning 40 US states and the District of Columbia from September 2023 to June 2024 and compared the measurements with traditional measures of disease occurrence. Nationally, 13.76% of the 21,079 wastewater samples were positive for HAV RNA, and both concentrations and positivity rates were associated with NNDSS hepatitis A case data nationally (Kendall rank correlation coefficient = 0.20, concentrations; and 0.33, positivity rate; both P < 0.05). We further demonstrated that higher rates of wastewater HAV detection were positively associated with socioeconomic indicators of vulnerability including homelessness and drug overdose deaths (both P < 0.0001). Areas with above average levels of homelessness were 48% more likely to have HAV wastewater detections, while areas with above average levels of drug overdose deaths were 14% more likely to have HAV wastewater detections. Using more granular case data, we present a case study in the state of Maine that reinforces these results and suggests a potential lead time for wastewater over clinical case detection and exposure events. The ability to detect HAV RNA in wastewater before clinical cases emerge could allow public health officials to implement targeted interventions like vaccination campaigns.IMPORTANCEDespite the existence of a highly effective vaccine for hepatitis A, outbreaks in vulnerable populations remain common. The disease can be asymptomatic or subclinical, and disproportionately impacts populations with inadequate access to healthcare, leading to a severe underestimation of the occurrence of this viral infection. This study investigates the potential for wastewater measurements of biomarkers of the causative agent of hepatitis A (HAV RNA) to provide insights into disease occurrence. Results highlight the potential for wastewater-based epidemiology to be a complementary tool to traditional surveillance for monitoring and controlling HAV transmission.

  View details for DOI 10.1128/msphere.00645-24

  View details for PubMedID 39475316

• Environmental Machine Learning, Baseline Reporting, and Comprehensive Evaluation: The EMBRACE Checklist. Environmental science & technology Zhu, J. J., Boehm, A. B., Ren, Z. J. 2024

  View details for DOI 10.1021/acs.est.4c09611

  View details for PubMedID 39469888

• Moving beyond Wastewater: Perspectives on Environmental Surveillance of Infectious Diseases for Public Health Action in Low-Resource Settings. Environment & health (Washington, D.C.) Delgado Vela, J., Philo, S. E., Brown, J., Taniuchi, M., Cantrell, M., Kossik, A., Ramaswamy, M., Ajjampur, S. S., Guerfali, F. Z., Holm, R. H., Meschke, J. S., Otero, M. C., Pickering, A. J., Rahman, M., Shaw, A. G., Shrestha, A., Sirikanchana, K., Tevuzula, V. M., Halden, R. U., Boehm, A. B., Bibby, K. 2024; 2 (10): 684-687

  View details for DOI 10.1021/envhealth.4c00119

  View details for PubMedID 39474434

  View details for PubMedCentralID PMC11503661

• Human pathogen nucleic acids in wastewater solids from 191 wastewater treatment plants in the United States. Scientific data Boehm, A. B., Wolfe, M. K., Bidwell, A. L., Zulli, A., Chan-Herur, V., White, B. J., Shelden, B., Duong, D. 2024; 11 (1): 1141

  Abstract

  We measured concentrations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants, influenza A and B viruses, respiratory syncytial virus, human metapneumovirus, enterovirus D68, human parainfluenza types 1, 2, 3, 4a, and 4b in aggregate, norovirus genotype II, rotavirus, Candida auris, hepatitis A virus, human adenovirus, mpox virus, H5 influenza A virus, and pepper mild mottle virus nucleic acids in wastewater solids prospectively at 191 wastewater treatment plants in 40 states across the United States plus Washington DC. Measurements were made two to seven times per week from 1 January 2022 to 30 June 2024, depending on wastewater treatment plant staff availability. Measurements were made using droplet digital (reverse-transcription-) polymerase chain reaction (ddRT-PCR) following best practices for making environmental molecular biology measurements. These data can be used to better understand disease occurrence in communities contributing to the wastewater.

  View details for DOI 10.1038/s41597-024-03969-8

  View details for PubMedID 39420189

  View details for PubMedCentralID 10312197

• Call for Papers for a Special Issue on "Ocean Health" ENVIRONMENTAL SCIENCE & TECHNOLOGY Dachs, J., Boehm, A., Sunderland, E., Deiner, K., Martin, J. W., Schlenk, D., Brooks, B. 2024; 58 (40): 17523

  View details for DOI 10.1021/acs.est.4c10143

  View details for Web of Science ID 001331418600001

• Call for Papers for a Special Issue on "Ocean Health" ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS Dachs, J., Boehm, A., Sunderland, E., Deiner, K., Martin, J. W., Schlenk, D., Brooks, B. 2024; 11 (10): 1016

  View details for DOI 10.1021/acs.estlett.4c00791

  View details for Web of Science ID 001331286800001

• You can bring plankton to fecal indicator organisms, but you cannot make the plankton graze: particle contribution toE. coliand MS2 inactivation in surface waters. mSphere Kennedy, L. C., Mattis, A. M., Boehm, A. B. 2024: e0065624

  Abstract

  Organisms that are associated with feces ("fecal indicator organisms") are monitored to assess the potential for fecal contamination of surface water bodies in the United States. However, the effect of the complex mixtures of chemicals and the natural microbial community within surface water ("particles") on fecal indicator organism persistence is not well characterized. We aimed to better understand how particles, including biological (e.g., potential grazers) and inert (e.g., minerals) types, affect the fecal indicator organisms Escherichia coli K-12 ("E. coli") and bacteriophage MS2 in surface waters. A gradient of particles captured by a 0.2-m-pore-size filter ("large particles") was generated, and the additional particles and dissolved constituents that passed through the filter were deemed "small particles." We measured the ratio of MS2 and E. coli that survived over a 24-h incubation period for each condition (0%-1,000% large-particle concentration in raw water) and completed a linear regression that included large- and small-particle coefficients. Particles were characterized by quantifying plankton, total bacterial cells, and total solids. E. coli and MS2 persistence was not significantly affected by large particles, but small particles had an effect in most waters. Small particles in higher-salinity waters had the largest, negative effect on E. coli and MS2 survival ratios: Significant small-particle coefficients ranged from -1.7 to -5.5 day-1 in the marine waters and -0.89 to -3.2 day-1 in the fresh and estuarine waters. This work will inform remediation efforts for impaired surface water bodies.IMPORTANCEMany surface water bodies in the United States have organisms associated with fecal contamination that exceed regulatory standards and prevent safe recreation. The process to remediate impaired water bodies is complicated because these fecal indicator organisms are affected by the local environmental conditions. For example, the effect of particles in surface water on fecal indicator concentrations are difficult to quantify in a way that is comparable between studies and water bodies. We applied a method that overcomes this limitation to assess the effects of large particles, including natural plankton that could consume the seeded fecal indicator organisms. Even in environmental water samples with diverse communities of plankton present, no effect of large particles on fecal indicator concentrations was observed. These findings have implications for the interpretation and design of future studies, including that particle characterization of surface water may be necessary to assess the fate of fecal indicators.

  View details for DOI 10.1128/msphere.00656-24

  View details for PubMedID 39360835

• Persistence of respiratory, enteric, and fecal indicator viruses in fecal sludge from on-site sanitation in Dakar, Senegal JOURNAL OF WATER SANITATION AND HYGIENE FOR DEVELOPMENT Grijalva, L., Seck, A., Roldan-Hernandez, L., Graham, K. E., Boehm, A. B., Tarpeh, W. A. 2024

  View details for DOI 10.2166/washdev.2024.011

  View details for Web of Science ID 001325915700001

• Wastewater Surveillance for Influenza A Virus and H5 Subtype Concurrent with the Highly Pathogenic Avian Influenza A(H5N1) Virus Outbreak in Cattle and Poultry and Associated Human Cases - United States, May 12-July 13, 2024. MMWR. Morbidity and mortality weekly report Louis, S., Mark-Carew, M., Biggerstaff, M., Yoder, J., Boehm, A. B., Wolfe, M. K., Flood, M., Peters, S., Stobierski, M. G., Coyle, J., Leslie, M. T., Sinner, M., Nims, D., Salinas, V., Lustri, L., Bojes, H., Shetty, V., Burnor, E., Rabe, A., Ellison-Giles, G., Yu, A. T., Bell, A., Meyer, S., Lynfield, R., Sutton, M., Scholz, R., Falender, R., Matzinger, S., Wheeler, A., Ahmed, F. S., Anderson, J., Harris, K., Walkins, A., Bohra, S., O'Dell, V., Guidry, V. T., Christensen, A., Moore, Z., Wilson, E., Clayton, J. L., Parsons, H., Kniss, K., Budd, A., Mercante, J. W., Reese, H. E., Welton, M., Bias, M., Webb, J., Cornforth, D., Santibanez, S., Soelaeman, R. H., Kaur, M., Kirby, A. E., Barnes, J. R., Fehrenbach, N., Olsen, S. J., Honein, M. A. 2024; 73 (37): 804-809

  Abstract

  As part of the response to the highly pathogenic avian influenza A(H5N1) virus outbreak in U.S. cattle and poultry and the associated human cases, CDC and partners are monitoring influenza A virus levels and detection of the H5 subtype in wastewater. Among 48 states and the District of Columbia that performed influenza A testing of wastewater during May 12-July 13, 2024, a weekly average of 309 sites in 38 states had sufficient data for analysis, and 11 sites in four states reported high levels of influenza A virus. H5 subtype testing was conducted at 203 sites in 41 states, with H5 detections at 24 sites in nine states. For each detection or high level, CDC and state and local health departments evaluated data from other influenza surveillance systems and partnered with wastewater utilities and agriculture departments to investigate potential sources. Among the four states with high influenza A virus levels detected in wastewater, three states had corresponding evidence of human influenza activity from other influenza surveillance systems. Among the 24 sites with H5 detections, 15 identified animal sources within the sewershed or adjacent county, including eight milk-processing inputs. Data from these early investigations can help health officials optimize the use of wastewater surveillance during the upcoming respiratory illness season.

  View details for DOI 10.15585/mmwr.mm7337a1

  View details for PubMedID 39298357

• Prospective study of Candida auris nucleic acids in wastewater solids in 190 wastewater treatment plants in the United States suggests widespread occurrence. mBio Zulli, A., Chan, E. M., Shelden, B., Duong, D., Xu, X. S., White, B. J., Wolfe, M. K., Boehm, A. B. 2024: e0090824

  Abstract

  Candida auris is an emerging, multidrug-resistant fungal pathogen that poses a significant public health threat in healthcare settings. Despite yearly clinical cases rapidly increasing from 77 to 8,131 in the last decade, surveillance data on its distribution and prevalence remain limited. We implemented a novel assay for C. auris detection on a nationwide scale prospectively from September 2023 to March 2024, analyzing a total of 13,842 samples from 190 wastewater treatment plants across 41 U.S. states. Assays were extensively validated through comparison to other known assays and internal controls. Of these 190 wastewater treatment plants, C. auris was detected in the wastewater solids of 65 of them (34.2%) with 1.45% of all samples having detectable levels of C. auris nucleic-acids. Detections varied seasonally, with 2.00% of samples positive in autumn vs 1.01% in winter (P < 0.0001). The frequency of detection in wastewater was significantly associated with states having older populations (P < 0.001), sewersheds containing more hospitals (P < 0.0001), and sewersheds containing more nursing homes (P < 0.001). These associations are in agreement with known C. auris epidemiology. This nationwide study demonstrates the viability of wastewater surveillance for C. auris surveillance and further highlights the value of wastewater surveillance when clinical testing is constrained.This study highlights the viability of wastewater surveillance when dealing with emerging pathogens. By leveraging an existing framework of wastewater surveillance, we reveal the widespread presence of C. auris in the United States. We further demonstrate that these wastewater detections are consistent with demographic factors relevant to C. auris epidemiology like age and number of hospitals or nursing homes. As C. auris and other pathogens continue to emerge, the low-cost and rapid nature of wastewater surveillance will provide public health officials with the information necessary to enact targeted prevention and control strategies.

  View details for DOI 10.1128/mbio.00908-24

  View details for PubMedID 39041799

• Spatial and temporal variation in respiratory syncytial virus (RSV) subtype RNA in wastewater and relation to clinical specimens. mSphere Zambrana, W., Huang, C., Solis, D., Sahoo, M. K., Pinsky, B. A., Boehm, A. B. 2024: e0022424

  Abstract

  Respiratory syncytial virus (RSV) causes a large burden of respiratory illness globally. It has two subtypes, RSV A and RSV B, but little is known regarding the predominance of these subtypes during different seasons and their impact on morbidity and mortality. Using molecular methods, we quantified RSV A and RSV B RNA in wastewater solids across multiple seasons and metropolitan areas to gain insight into the predominance of RSV subtypes. We determined the predominant subtype for each group using the proportion of RSV A to total RSV (RSV A + RSV B) in each wastewater sample (PA,WW) and conducted a comparative analysis temporally, spatially, and against clinical specimens. A median PA,WW of 0.00 in the first season and 0.58 in the second season indicated a temporal shift in the predominant subtype. Spatially, while we observed dominance of the same subtype, PA,WW was higher in some areas (PA,WW = 0.58-0.88). The same subtype predominated in wastewater and clinical samples, but clinical samples showed higher levels of RSV A (RSV A positivity in clinical samples = 0.79, median PA,WW = 0.58). These results suggest that wastewater, alongside clinical data, holds promise for enhanced subtype surveillance.IMPORTANCERespiratory syncytial virus (RSV) causes a large burden of respiratory illness globally. It has two subtypes, RSV A and RSV B, but little is known regarding the predominance of these subtypes during different seasons and their impact on morbidity and mortality. The study illustrates that information on subtype predominance can be gleaned from wastewater. As a biological composite sample from the entire contributing population, wastewater monitoring of RSV A and B can complement clinical surveillance of RSV.

  View details for DOI 10.1128/msphere.00224-24

  View details for PubMedID 38926903

• Advances in Wastewater-Based Epidemiology in the ES&T Family of Journals. Environmental science & technology Julian, T. R., Boehm, A. B. 2024

  View details for DOI 10.1021/acs.est.4c04913

  View details for PubMedID 38885441

• Advances in Wastewater-Based Epidemiology in the <i>ES&T</i> Family of Journals ACS ES&T WATER Julian, T. R., Boehm, A. B. 2024

  View details for DOI 10.1021/acsestwater.4c00459

  View details for Web of Science ID 001249602700001

• Advances in Wastewater-Based Epidemiology in the <i>ES&T</i> Family of Journals ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS Julian, T. R., Boehm, A. B. 2024

  View details for DOI 10.1021/acs.estlett.4c00406

  View details for Web of Science ID 001249613000001

• Detection of Hemagglutinin H5 Influenza A Virus Sequence in Municipal Wastewater Solids at Wastewater Treatment Plants with Increases in Influenza A in Spring, 2024 ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS Wolfe, M. K., Duong, D., Shelden, B., Chan, E. G., Chan-Herur, V., Hilton, S., Paulos, A., Xu, X. S., Zulli, A., White, B. J., Boehm, A. B. 2024

  View details for DOI 10.1021/acs.estlett.4c00331

  View details for Web of Science ID 001228030300001

• Maximizing the Impact of Research Featuring Nucleic-Acid Sequencing Methods inEnvironmental Science & TechnologyandEnvironmental Science & Technology Letters. Environmental science & technology Boehm, A. B., Raskin, L., Alvarez, P., Hong, P. 2024; 58 (19): 8115-8116

  View details for DOI 10.1021/acs.est.4c03765

  View details for PubMedID 38741572

• Maximizing the Impact of Research Featuring Nucleic-Acid Sequencing Methods in <i>Environmental Science & Technology</i> and <i>Environmental Science & Technology Letters</i> ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS Boehm, A. B., Raskin, L., Alvarez, P., Hong, P. 2024; 11 (5): 382-383

  View details for DOI 10.1021/acs.estlett.4c00295

  View details for Web of Science ID 001226384500001

• Solid-liquid partitioning of dengue, West Nile, Zika, hepatitis A, influenza A, and SARS-CoV-2 viruses in wastewater from across the USA ENVIRONMENTAL SCIENCE-WATER RESEARCH & TECHNOLOGY Roldan-Hernandez, L., Van Oost, C., Boehm, A. B. 2024

  View details for DOI 10.1039/d4ew00225c

  View details for Web of Science ID 001219701900001

• Observations of Respiratory Syncytial Virus (RSV) Nucleic Acids in Wastewater Solids Across the United States in the 2022-2023 Season: Relationships with RSV Infection Positivity and Hospitalization Rates. ACS ES&T water Zulli, A., Varkila, M. R., Parsonnet, J., Wolfe, M. K., Boehm, A. B. 2024; 4 (4): 1657-1667

  Abstract

  Respiratory syncytial virus (RSV) is a leading cause of respiratory illness and hospitalization, but clinical surveillance detects only a minority of cases. Wastewater surveillance could determine the onset and extent of RSV circulation in the absence of sensitive case detection, but to date, studies of RSV in wastewater are few. We measured RSV RNA concentrations in wastewater solids from 176 sites during the 2022-2023 RSV season and compared those to publicly available RSV infection positivity and hospitalization rates. Concentrations ranged from undetectable to 107 copies per gram. RSV RNA concentration aggregated at state and national levels correlated with infection positivity and hospitalization rates. RSV season onset was determined using both wastewater and clinical positivity rates using independent algorithms for 14 states where both data were available at the start of the RSV season. In 4 of 14 states, wastewater and clinical surveillance identified RSV season onset during the same week; in 3 states, wastewater onset preceded clinical onset, and in 7 states, wastewater onset occurred after clinical onset. Wastewater concentrations generally peaked in the same week as hospitalization rates but after case positivity rates peaked. Differences in onset and peaks in wastewater versus clinical data may reflect inherent differences in the surveillance approaches.

  View details for DOI 10.1021/acsestwater.3c00725

  View details for PubMedID 38633368

  View details for PubMedCentralID PMC11019535

• A mixed-effects model to predict COVID-19 hospitalizations using wastewater surveillance JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING Daza-Torres, M. L., Montesinos-Lopez, J., Bischel, H. N., Naughton, C. C., Desai, A. N., Wolfe, M. K., Boehm, A. B., Nuno, M. 2024; 12 (2)

  View details for DOI 10.1016/j.jece.2024.112485

  View details for Web of Science ID 001221070900001

• Persistence and free chlorine disinfection of human coronaviruses and their surrogates in water. Applied and environmental microbiology Zhang, M., Leong, M. W., Mitch, W. A., Blish, C. A., Boehm, A. 2024: e0005524

  Abstract

  The coronavirus disease 2019 pandemic illustrates the importance of understanding the behavior and control of human pathogenic viruses in the environment. Exposure via water (drinking, bathing, and recreation) is a known route of transmission of viruses to humans, but the literature is relatively void of studies on the persistence of many viruses, especially coronaviruses, in water and their susceptibility to chlorine disinfection. To fill that knowledge gap, we evaluated the persistence and free chlorine disinfection of human coronavirus OC43 (HCoV-OC43) and its surrogates, murine hepatitis virus (MHV) and porcine transmissible gastroenteritis virus (TGEV), in drinking water and laboratory buffer using cell culture methods. The decay rate constants of human coronavirus and its surrogates in water varied, depending on virus and water matrix. In drinking water without disinfectant addition, MHV showed the largest decay rate constant (estimate ± standard error, 2.25 ± 0.09 day-1) followed by HCoV-OC43 (0.99 ± 0.12 day-1) and TGEV (0.65 ± 0.06 day-1), while in phosphate buffer without disinfectant addition, HCoV-OC43 (0.51 ± 0.10 day-1) had a larger decay rate constant than MHV (0.28 ± 0.03 day-1) and TGEV (0.24 ± 0.02 day-1). Upon free chlorine disinfection, the inactivation rates of coronaviruses were independent of free chlorine concentration and were not affected by water matrix, though they still varied between viruses. TGEV showed the highest susceptibility to free chlorine disinfection with the inactivation rate constant of 113.50 ± 7.50 mg-1 min-1 L, followed by MHV (81.33 ± 4.90 mg-1 min-1 L) and HCoV-OC43 (59.42 ± 4.41 mg-1 min-1 L).This study addresses an important knowledge gap on enveloped virus persistence and disinfection in water. Results have immediate practical applications for shaping evidence-based water policies, particularly in the development of disinfection strategies for pathogenic virus control.

  View details for DOI 10.1128/aem.00055-24

  View details for PubMedID 38511945

• Persistence of human respiratory viral RNA in wastewater-settled solids. Applied and environmental microbiology Zhang, M., Roldan-Hernandez, L., Boehm, A. 2024: e0227223

  Abstract

  Wastewater-based epidemiology has emerged as a valuable tool for monitoring respiratory viral diseases within communities by analyzing concentrations of viral nucleic-acids in wastewater. However, little is known about the fate of respiratory virus nucleic-acids in wastewater. Two important fate processes that may modulate their concentrations in wastewater as they move from household drains to the point of collection include sorption or partitioning to wastewater solids and degradation. This study investigated the decay kinetics of genomic nucleic-acids of seven human respiratory viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), respiratory syncytial virus (RSV), human coronavirus (HCoV)-OC43, HCoV-229E, HCoV-NL63, human rhinovirus (HRV), and influenza A virus (IAV), as well as pepper mild mottle virus (PMMoV) in wastewater solids. Viruses (except for PMMoV) were spiked into wastewater solids and their concentrations were followed for 50 days at three different temperatures (4°C, 22°C, and 37°C). Viral genomic RNA decayed following first-order kinetics with decay rate constants k from 0 to 0.219 per day. Decay rate constants k were not different from 0 for all targets in solids incubated at 4°C; k values were largest at 37°C and at this temperature, k values were similar across nucleic-acid targets. Regardless of temperature, there was limited viral RNA decay, with an estimated 0% to 20% reduction, over the typical residence times of sewage in the piped systems between input and collection point (<1 day). The k values reported herein can be used directly in fate and transport models to inform the interpretation of measurements made during wastewater surveillance.IMPORTANCEUnderstanding whether or not the RNA targets quantified for wastewater-based epidemiology (WBE) efforts decay during transport between drains and the point of sample collection is critical for data interpretation. Here we show limited decay of viral RNA targets typically measured for respiratory disease WBE.

  View details for DOI 10.1128/aem.02272-23

  View details for PubMedID 38501669

• Is detection of enteropathogens and human or animal faecal markers in the environment associated with subsequent child enteric infections and growth: an individual participant data meta-analysis. The Lancet. Global health Mertens, A., Arnold, B. F., Benjamin-Chung, J., Boehm, A. B., Brown, J., Capone, D., Clasen, T., Fuhrmeister, E. R., Grembi, J. A., Holcomb, D., Knee, J., Kwong, L. H., Lin, A., Luby, S. P., Nala, R., Nelson, K., Njenga, S. M., Null, C., Pickering, A. J., Rahman, M., Reese, H. E., Steinbaum, L., Stewart, J. R., Thilakaratne, R., Cumming, O., Colford, J. M., Ercumen, A. 2024; 12 (3): e433-e444

  Abstract

  Quantifying contributions of environmental faecal contamination to child diarrhoea and growth faltering can illuminate causal mechanisms behind modest health benefits in recent water, sanitation, and hygiene (WASH) trials. We aimed to assess associations between environmental detection of enteropathogens and human or animal microbial source tracking markers (MSTM) and subsequent child health outcomes.In this individual participant data meta-analysis we searched we searched PubMed, Embase, CAB Direct Global Health, Agricultural and Environmental Science Database, Web of Science, and Scopus for WASH intervention studies with a prospective design and concurrent control that measured enteropathogens or MSTM in environmental samples, or both, and subsequently measured enteric infections, diarrhoea, or height-for-age Z-scores (HAZ) in children younger than 5 years. We excluded studies that only measured faecal indicator bacteria. The initial search was done on Jan 19, 2021, and updated on March 22, 2023. One reviewer (AM) screened abstracts, and two independent reviewers (AM and RT) examined the full texts of short-listed articles. All included studies include at least one author that also contributed as an author to the present Article. Our primary outcomes were the 7-day prevalence of caregiver-reported diarrhoea and HAZ in children. For specific enteropathogens in the environment, primary outcomes also included subsequent child infection with the same pathogen ascertained by stool testing. We estimated associations using covariate-adjusted regressions and pooled estimates across studies.Data from nine published reports from five interventions studies, which included 8603 children (4302 girls and 4301 boys), were included in the meta-analysis. Environmental pathogen detection was associated with increased infection prevalence with the same pathogen and lower HAZ (ΔHAZ -0·09 [95% CI -0·17 to -0·01]) but not diarrhoea (prevalence ratio 1·22 [95% CI 0·95 to 1·58]), except during wet seasons. Detection of MSTM was not associated with diarrhoea (no pooled estimate) or HAZ (ΔHAZ -0·01 [-0·13 to 0·11] for human markers and ΔHAZ -0·02 [-0·24 to 0·21] for animal markers). Soil, children's hands, and stored drinking water were major transmission pathways.Our findings support a causal chain from pathogens in the environment to infection to growth faltering, indicating that the lack of WASH intervention effects on child growth might stem from insufficient reductions in environmental pathogen prevalence. Studies measuring enteropathogens in the environment should subsequently measure the same pathogens in stool to further examine theories of change between WASH, faecal contamination, and health. Given that environmental pathogen detection was predictive of infection, programmes targeting specific pathogens (eg, vaccinations and elimination efforts) can environmentally monitor the pathogens of interest for population-level surveillance instead of collecting individual biospecimens.The Bill & Melinda Gates Foundation and the UK Foreign and Commonwealth Development Office.

  View details for DOI 10.1016/S2214-109X(23)00563-6

  View details for PubMedID 38365415

• Environmental DNA metabarcoding differentiates between micro-habitats within the rocky intertidal ENVIRONMENTAL DNA Shea, M. M., Boehm, A. B. 2024; 6 (2)

  View details for DOI 10.1002/edn3.521

  View details for Web of Science ID 001307393100010

• Observations of Respiratory Syncytial Virus (RSV) Nucleic Acids in Wastewater Solids Across the United States in the 2022-2023 Season: Relationships with RSV Infection Positivity and Hospitalization Rates ACS ES&T WATER Zulli, A., Varkila, M. J., Parsonnet, J., Wolfe, M. K., Boehm, A. B. 2024

  View details for DOI 10.1021/acsestwater.3c00725

  View details for Web of Science ID 001178631400001

• A retrospective longitudinal study of adenovirus group F, norovirus GI and GII, rotavirus, and enterovirus nucleic acids in wastewater solids at two wastewater treatment plants: solid-liquid partitioning and relation to clinical testing data. mSphere Boehm, A. B., Shelden, B., Duong, D., Banaei, N., White, B. J., Wolfe, M. K. 2024: e0073623

  Abstract

  Enteric infections are important causes of morbidity and mortality, yet clinical surveillance is limited. Wastewater-based epidemiology (WBE) has been used to study community circulation of individual enteric viruses and panels of respiratory diseases, but there is limited work studying the concurrent circulation of a suite of important enteric viruses. A retrospective WBE study was carried out at two wastewater treatment plants located in California, United States. Using digital droplet polymerase chain reaction (PCR), we measured concentrations of human adenovirus group F, enteroviruses, norovirus genogroups I and II, and rotavirus nucleic acids in wastewater solids two times per week for 26 months (n = 459 samples) between February 2021 and mid-April 2023. A novel probe-based PCR assay was developed and validated for adenovirus. We compared viral nucleic acid concentrations to positivity rates for viral infections from clinical specimens submitted to a local clinical laboratory to assess concordance between the data sets. We detected all viral targets in wastewater solids. At both wastewater treatment plants, human adenovirus group F and norovirus GII nucleic acids were detected at the highest concentrations (median concentrations greater than 105 copies/g), while rotavirus RNA was detected at the lowest concentrations (median on the order of 103 copies/g). Rotavirus, adenovirus group F, and norovirus nucleic acid concentrations were positively associated with clinical specimen positivity rates. Concentrations of tested viral nucleic acids exhibited complex associations with SARS-CoV-2 and other respiratory viral nucleic acids in wastewater, suggesting divergent transmission patterns.IMPORTANCEThis study provides evidence for the use of wastewater solids for the sensitive detection of enteric virus targets in wastewater-based epidemiology programs aimed to better understand the spread of enteric disease at a localized, community level without limitations associated with testing many individuals. Wastewater data can inform clinical, public health, and individual decision-making aimed to reduce the transmission of enteric disease.

  View details for DOI 10.1128/msphere.00736-23

  View details for PubMedID 38411118

• Strengthening the academic pipeline for underrepresented students via early exposure to graduate education Chem Fernandez, S., Anderson, C. E., Boehm, A. B., Congreve, D. N. 2024; 10 (6): 1609-1619

  View details for DOI 10.1016/j.chempr.2024.05.001

• Wastewater surveillance for bacterial targets: current challenges and future goals. Applied and environmental microbiology Philo, S. E., De Leon, K. B., Noble, R. T., Zhou, N. A., Alghafri, R., Bar-Or, I., Darling, A., D'Souza, N., Hachimi, O., Kaya, D., Kim, S., Gaardbo Kuhn, K., Layton, B. A., Mansfeldt, C., Oceguera, B., Radniecki, T. S., Ram, J. L., Saunders, L. P., Shrestha, A., Stadler, L. B., Steele, J. A., Stevenson, B. S., Bibby, K., Boehm, A. B., Halden, R. U., Delgado Vela, J. 2023: e0142823

  Abstract

  IMPORTANCE: Wastewater surveillance was a useful tool to elucidate the burden and spread of SARS-CoV-2 during the pandemic. Public health officials and researchers are interested in expanding these surveillance programs to include bacterial targets, but many questions remain. The NSF-funded Research Coordination Network for Wastewater Surveillance of SARS-CoV-2 and Emerging Public Health Threats held a workshop to identify barriers and research gaps to implementing bacterial wastewater surveillance programs.

  View details for DOI 10.1128/aem.01428-23

  View details for PubMedID 38099657

• Temperature and particles interact to affect human norovirus and MS2 persistence in surface water. Environmental science. Processes & impacts Kennedy, L. C., Lowry, S. A., Boehm, A. B. 2023

  Abstract

  Modeling the fate and transport of viruses and their genetic material in surface water is necessary to assess risks associated with contaminated surface waters and to inform environmental surveillance efforts. Temperature has been identified as a key variable affecting virus persistence in surface waters, but the effects of the presence of biological and inert particles and of their interaction with temperature have not been well characterized. We assessed these effects on the persistence of human norovirus (HuNoV) genotype II.4 purified from stool and MS2 in surface water. Raw or filter-sterilized creek water microcosms were inoculated and incubated in the dark at 10 °C, 15 °C, and 20 °C. HuNoV (i.e., genome segments and intact capsids) and MS2 (i.e., infectious MS2, genome segments, and intact capsids) concentrations were followed over 36 days. The range in positive, significant first-order decay rate constants for HuNoV in this study was 0.14 to 0.69 day-1 compared with 0.026 to 0.71 day-1 for that of MS2. Decay rate constants for HuNoV genome segments and infectious MS2 were largest in creek water that included biological and inert particles and incubated at higher temperatures. In addition, for HuNoV and MS2 incubated in raw or filter-sterilized creek water at 15 °C, capsid damage was not identified as a dominant inactivation mechanism. Environmental processes and events that affect surface water biological and inert particles, temperature, or both could lead to variable virus decay rate constants. Incorporating the effects of particles, temperature, and their interaction could enhance models of virus fate and transport in surface water.

  View details for DOI 10.1039/d3em00357d

  View details for PubMedID 38078556

• Wastewater Detection of Emerging Arbovirus Infections: Case Study of Dengue in the United States ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS Wolfe, M. K., Paulos, A., Zulli, A., Duong, D., Shelden, B., White, B. J., Boehm, A. B. 2023; 11 (1): 9-15

  View details for DOI 10.1021/acs.estlett.3c00769

  View details for Web of Science ID 001139444900001

• Sunlight Inactivation of Enveloped Viruses in Clear Water. Environmental science & technology Anderson, C. E., Boehm, A. B. 2023

  Abstract

  Enveloped virus fate in the environment is not well understood; there are no quantitative data on sunlight inactivation of enveloped viruses in water. Herein, we measured the sunlight inactivation of two enveloped viruses (Phi6 and murine hepatitis virus, MHV) and a nonenveloped virus (MS2) over time in clear water with simulated sunlight exposure. We attenuated UV sunlight wavelengths using long-pass 50% cutoff filters at 280, 305, and 320 nm. With the lowest UV attenuation tested, all decay rate constants (corrected for UV light screening, k̂) were significantly different from dark controls; the MS2 k̂ was equal to 4.5 m2/MJ, compared to 16 m2/MJ for Phi6 and 52 m2/MJ for MHV. With the highest UV attenuation tested, only k̂ for MHV (6.1 m2/MJ) was different from the dark control. Results indicate that the two enveloped viruses decay faster than the nonenveloped virus studied, and k̂ are significantly impacted by UV attenuation. Differences in k̂ may be due to the presence of viral envelopes but may also be related to other differing intrinsic properties of the viruses, including genome length and composition. Reported k̂ values can inform strategies to reduce the risk from exposure to enveloped viruses in the environment.

  View details for DOI 10.1021/acs.est.3c06680

  View details for PubMedID 38062652

• The National Wastewater Surveillance System's Centers of Excellence Contributions to Public Health Action During the Respiratory Virus MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT Valencia, D., Yu, A., Wheeler, A., Hopkins, L., Pray, I., Horter, L., Vugia, D. J., Matzinger, S., Stadler, L., Kloczko, N., Welton, M., Bertsch-Merbach, S., Domakonda, K., Antkiewicz, D., Turner, H., Crain, C., Mulenga, A., Shafer, M., Owiti, J., Schneider, R., Janssen, K. H., Wolfe, M. K., Mcclellan, S. L., Boehm, A. B., Roguet, A., White, B., Schussman, M. K., Rane, M. S., Hemming, J., Collins, C., Abram, A., Burnor, E., Westergaard, R., Ricaldi, J. N., Person, J., Fehrenbach, N. 2023; 72 (48): 1309-1312

  View details for Web of Science ID 001115488000001

  View details for PubMedID 38032883

  View details for PubMedCentralID PMC10718204

• United States Influenza 2022-2023 Season Characteristics as Inferred from Wastewater Solids, Influenza Hospitalization, and Syndromic Data. Environmental science & technology Schoen, M. E., Bidwell, A. L., Wolfe, M. K., Boehm, A. B. 2023

  Abstract

  Influenza A virus (IAV) causes significant morbidity and mortality in the United States and has pandemic potential. Identifying IAV epidemic patterns is essential to inform the timing of vaccinations and nonpharmaceutical interventions. In a prospective, longitudinal study design, we measured IAV RNA in wastewater settled solids at 163 wastewater treatment plants across 33 states to characterize the 2022-2023 influenza season at the state, health and human services (HHS) regional, and national scales. Influenza season onset, offset, duration, peak, and intensity using IAV RNA in wastewater were compared with those determined using laboratory-confirmed influenza hospitalization rates and outpatient visits for influenza-like illness (ILI). The onset for HHS regions as determined by IAV RNA in wastewater roughly corresponded with those determined using ILI when the annual geometric mean of IAV RNA concentration was used as a baseline (i.e., the threshold that triggers onset), although offsets between the two differed. IAV RNA in wastewater provided early warning of onset, compared to the ILI estimate, when the baseline was set at twice the limit of IAV RNA detection in wastewater. Peak when determined by IAV RNA in wastewater generally preceded peak determined by IAV hospitalization rate by 2 weeks or less. IAV RNA in wastewater settled solids is an IAV-specific indicator that can be used to augment clinical surveillance for seasonal influenza epidemic timing and intensity.

  View details for DOI 10.1021/acs.est.3c07526

  View details for PubMedID 38014848

• Rebuttal to Correspondence on "The Environmental Microbiology Minimum Information (EMMI) Guidelines: qPCR and dPCR Quality and Reporting for Environmental Microbiology". Environmental science & technology Borchardt, M. A., Boehm, A. B., Salit, M., Spencer, S. K., Wigginton, K. R., Noble, R. T. 2023

  View details for DOI 10.1021/acs.est.3c08824

  View details for PubMedID 37932026

• Correction to "SARS-CoV-2 RNA in Wastewater Settled Solids Is Associated with COVID-19 Cases in a Large Urban Sewershed". Environmental science & technology Graham, K. E., Loeb, S., Roldan-Hernandez, L., Kim, S., Wigginton, K. R., Boehm, A. 2023

  View details for DOI 10.1021/acs.est.3c07132

  View details for PubMedID 37755703

• Occurrence of Human Viruses on Fomites in the Environment: A Systematic Review and Meta-analysis. ACS environmental Au Zambrana, W., Boehm, A. B. 2023; 3 (5): 277-294

  Abstract

  Documenting the occurrence of viruses on fomites is crucial in determining the significance of fomite-mediated transmission and the potential use of fomites for environmental disease surveillance. We conducted a systematic review and meta-analysis to compile information on the occurrence of human viruses on fomites in the environment; we identified 134 peer-reviewed papers. We compiled sampling and measurement methods, results, quality control information, and whether virus data were compared with community health data from the papers. We conducted univariate and multivariate analyses to investigate if presence of virus on fomites was associated with virus type (enveloped, nonenveloped), sampling location (healthcare setting, nonhealthcare temporary setting, nonhealthcare nontemporary setting), and area of fomite swabbed (<50, 50-100, >100 cm2). Across 275 data sets from the 134 papers, there was the most data available for Coronaviridae and from fomites at hospitals. Positivity rates, defined as the percent positive fomite samples, were low (median = 6%). Data were available on viruses from 16 different viral families, but data on viruses from 9 families had few (n < 5) data sets. Many human virus families were not identified in this review (11 families). Less than 15% of the data sets reported virus concentrations in externally valid units (viruses per area of surface), and 16% provided a quantitative comparison between virus and health data. Virus type and area swabbed were significant predictors of virus presence on fomites, and the positivity rate of data sets collected from healthcare settings and nonhealthcare nontemporary settings (e.g., individual housing) were significantly higher than those collected in nonhealthcare temporary settings (e.g., restaurants). Data from this review indicates that viruses may be present on fomites, that fomite-mediated virus transmission may occur, and that fomites may provide information on circulation of infectious diseases in the community. However, more quantitative data on diverse viruses are needed, and method reporting needs significant improvements.

  View details for DOI 10.1021/acsenvironau.3c00025

  View details for PubMedID 37743950

  View details for PubMedCentralID PMC10515712

• Adsorption of Respiratory Syncytial Virus, Rhinovirus, SARS-CoV-2, and F+ Bacteriophage MS2 RNA onto Wastewater Solids from Raw Wastewater. Environmental science & technology Roldan-Hernandez, L., Boehm, A. B. 2023

  Abstract

  Despite the widespread adoption of wastewater surveillance, more research is needed to understand the fate and transport of viral genetic markers in wastewater. This information is essential for optimizing monitoring strategies and interpreting wastewater surveillance data. In this study, we examined the solid-liquid partitioning behavior of four viruses in wastewater: SARS-CoV-2, respiratory syncytial virus (RSV), rhinovirus (RV), and F+ coliphage/MS2. We used two approaches: (1) laboratory partitioning experiments using lab-grown viruses and (2) distribution experiments using endogenous viruses in raw wastewater. Partition experiments were conducted at 4 and 22 °C. Wastewater samples were spiked with varying concentrations of each virus, solids and liquids were separated via centrifugation, and viral RNA concentrations were quantified using reverse-transcription-digital droplet PCR (RT-ddPCR). For the distribution experiments, wastewater samples were collected from six wastewater treatment plants and processed without spiking exogenous viruses; viral RNA concentrations were measured in wastewater solids and liquids. In both experiments, RNA concentrations were higher in the solid fraction than the liquid fraction by approximately 3-4 orders of magnitude. Partition coefficients (KF) ranged from 2000-270,000 mL·g-1 across viruses and temperature conditions. Distribution coefficients (Kd) were consistent with results from partitioning experiments. Further research is needed to understand how virus and wastewater characteristics might influence the partitioning of viral genetic markers in wastewater.

  View details for DOI 10.1021/acs.est.3c03376

  View details for PubMedID 37647137

• The Environmental Microbiology Minimum Information (EMMI) Guidelines: qPCR and dPCR Quality and Reporting for Environmental Microbiology (vol 55, pg 10210, 2021) ENVIRONMENTAL SCIENCE & TECHNOLOGY Borchardt, M. A., Boehm, A. B., Salit, M., Spencer, S. K., Wigginton, K. R., Noble, R. T. 2023: 12931

  View details for DOI 10.1021/acs.est.3c06441

  View details for Web of Science ID 001052004000001

  View details for PubMedID 37594384

• More than a Tripledemic: Influenza A Virus, Respiratory Syncytial Virus, SARS-CoV-2, and Human Metapneumovirus in Wastewater during Winter 2022-2023. Environmental science & technology letters Boehm, A. B., Wolfe, M. K., White, B. J., Hughes, B., Duong, D., Bidwell, A. 2023; 10 (8): 622-627

  Abstract

  Wastewater monitoring can provide insights into respiratory disease occurrence in communities that contribute to the wastewater system. Using daily measurements of RNA of influenza A (IAV), respiratory syncytial virus (RSV), and human metapneumovirus (HMPV), as well as SARS-CoV-2 in wastewater solids from eight publicly owned treatment works in the Greater San Francisco Bay Area of California between July 2022 and early July 2023, we identify a "tripledemic" when concentrations of IAV, RSV, and SARS-CoV-2 peaked at approximately the same time. HMPV was also widely circulating. We designed novel hydrolysis probe RT-PCR assays for different IAV subtype markers to discern that the dominant circulating IAV subtype was H3N2. We show that wastewater data can be used to identify the onset and offset of wastewater disease occurrence events. This information can provide insight into disease epidemiology and timely, localized information to inform hospital staffing and clinical decision making to respond to circulating viruses. Whereas RSV and IAV wastewater events were mostly regionally coherent, HMPV events displayed localized occurrence patterns.

  View details for DOI 10.1021/acs.estlett.3c00385

  View details for PubMedID 37577361

  View details for PubMedCentralID PMC10413932

• Human norovirus (HuNoV) GII RNA in wastewater solids at 145 United States wastewater treatment plants: comparison to positivity rates of clinical specimens and modeled estimates of HuNoV GII shedders. Journal of exposure science & environmental epidemiology Boehm, A. B., Wolfe, M. K., White, B. J., Hughes, B., Duong, D., Banaei, N., Bidwell, A. 2023

  Abstract

  BACKGROUND: Human norovirus (HuNoV) is a leading cause of disease globally, yet actual incidence is unknown. HuNoV infections are not reportable in the United States, and surveillance is limited to tracking severe illnesses or outbreaks. Wastewater monitoring for HuNoV has been done previously and results indicate it is present in wastewater influent and concentrations are associated with HuNoV infections in the communities contributing to wastewater. However, work has mostly been limited to monthly samples of liquid wastewater at one or a few wastewater treatment plants (WWTPs).OBJECTIVE: The objectives of this study are to investigate whether HuNoV GII preferentially adsorbs to wastewater solids, investigate concentrations of HuNoV GII in wastewater solids in wastewater treatment plants across the county, and explore how those relate to clinical measures of disease occurrence. In addition, we aim to develop and apply a mass-balance model that predicts the fraction of individuals shedding HuNoV in their stool based on measured concentrations in wastewater solids.METHODS: We measured HuNoV GII RNA in matched wastewater solids and liquid influent in 7 samples from a WWTP. We also applied the HuNoV GII assay to measure viral RNA in over 6000 wastewater solids samples from 145 WWTPs from across the United States daily to three times per week for up to five months. Measurements were made using digital droplet RT-PCR.RESULTS: HuNoV GII RNA preferentially adsorbs to wastewater solids where it is present at 1000 times the concentration in influent. Concentrations of HuNoV GII RNA correlate positively with clinical HuNoV positivity rates. Model output of the fraction of individuals shedding HuNoV is variable and uncertain, but consistent with indirect estimates of symptomatic HuNoV infections in the United States.IMPACT STATEMENT: Illness caused by HuNoV is not reportable in the United States so there is limited data on disease occurrence. Wastewater monitoring can provide information about the community spread of HuNoV. Data from wastewater can be available within 24h of sample receipt at a laboratory. Wastewater is agnostic to whether individuals seek medical care, are symptomatic, and the severity of illness. Knowledge gleaned from wastewater may be used by public health professionals to make recommendations on hand washing, surface disinfection, or other behaviors to reduce transmission of HuNoV, or medical doctors to inform clinical decision making.

  View details for DOI 10.1038/s41370-023-00592-4

  View details for PubMedID 37550566

• Occurrence of Human Viruses on Fomites in the Environment: A Systematic Review and Meta-analysis ACS ENVIRONMENTAL AU Zambrana, W., Boehm, A. B. 2023

  View details for DOI 10.1021/acsenvironau.3c00025

  View details for Web of Science ID 001035674500001

• More than a Tripledemic: Influenza A Virus, Respiratory Syncytial Virus, SARS-CoV-2, and Human Metapneumovirus in Wastewater during Winter 2022-2023 ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS Boehm, A. B., Wolfe, M. K., White, B. L., Hughes, B., Duong, D., Bidwell, A. 2023

  View details for DOI 10.1021/acs.estlett.3c00385

  View details for Web of Science ID 001033081300001

• The Tomato Brown Rugose Fruit Virus Movement Protein Gene Is a Novel Microbial Source Tracking Marker. Applied and environmental microbiology Natarajan, A., Fremin, B. J., Schmidtke, D. T., Wolfe, M. K., Zlitni, S., Graham, K. E., Brooks, E. F., Severyn, C. J., Sakamoto, K. M., Lacayo, N. J., Kuersten, S., Koble, J., Caves, G., Kaplan, I., Singh, U., Jagannathan, P., Rezvani, A. R., Bhatt, A. S., Boehm, A. B. 2023: e0058323

  Abstract

  Microbial source tracking (MST) identifies sources of fecal contamination in the environment using host-associated fecal markers. While there are numerous bacterial MST markers that can be used herein, there are few such viral markers. Here, we designed and tested novel viral MST markers based on tomato brown rugose fruit virus (ToBRFV) genomes. We assembled eight nearly complete genomes of ToBRFV from wastewater and stool samples from the San Francisco Bay Area in the United States. Next, we developed two novel probe-based reverse transcription-PCR (RT-PCR) assays based on conserved regions of the ToBRFV genome and tested the markers' sensitivities and specificities using human and non-human animal stool as well as wastewater. The ToBRFV markers are sensitive and specific; in human stool and wastewater, they are more prevalent and abundant than a commonly used viral marker, the pepper mild mottle virus (PMMoV) coat protein (CP) gene. We used the assays to detect fecal contamination in urban stormwater samples and found that the ToBRFV markers matched cross-assembly phage (crAssphage), an established viral MST marker, in prevalence across samples. Taken together, these results indicate that ToBRFV is a promising viral human-associated MST marker. IMPORTANCE Human exposure to fecal contamination in the environment can cause transmission of infectious diseases. Microbial source tracking (MST) can identify sources of fecal contamination so that contamination can be remediated and human exposures can be reduced. MST requires the use of host-associated MST markers. Here, we designed and tested novel MST markers from genomes of tomato brown rugose fruit virus (ToBRFV). The markers are sensitive and specific to human stool and highly abundant in human stool and wastewater samples.

  View details for DOI 10.1128/aem.00583-23

  View details for PubMedID 37404180

• Expansion of wastewater-based disease surveillance to improve health equity in California's Central Valley: sequential shifts in case-to-wastewater and hospitalization-to-wastewater ratios. Frontiers in public health Kadonsky, K. F., Naughton, C. C., Susa, M., Olson, R., Singh, G. L., Daza-Torres, M. L., Montesinos-López, J. C., Garcia, Y. E., Gafurova, M., Gushgari, A., Cosgrove, J., White, B. J., Boehm, A. B., Wolfe, M. K., Nuño, M., Bischel, H. N. 2023; 11: 1141097

  Abstract

  Over a third of the communities (39%) in the Central Valley of California, a richly diverse and important agricultural region, are classified as disadvantaged-with inadequate access to healthcare, lower socio-economic status, and higher exposure to air and water pollution. The majority of racial and ethnic minorities are also at higher risk of COVID-19 infection, hospitalization, and death according to the Centers for Disease Control and Prevention. Healthy Central Valley Together established a wastewater-based disease surveillance (WDS) program that aims to achieve greater health equity in the region through partnership with Central Valley communities and the Sewer Coronavirus Alert Network. WDS offers a cost-effective strategy to monitor trends in SARS-CoV-2 community infection rates.In this study, we evaluated correlations between public health and wastewater data (represented as SARS-CoV-2 target gene copies normalized by pepper mild mottle virus target gene copies) collected for three Central Valley communities over two periods of COVID-19 infection waves between October 2021 and September 2022. Public health data included clinical case counts at county and sewershed scales as well as COVID-19 hospitalization and intensive care unit admissions. Lag-adjusted hospitalization:wastewater ratios were also evaluated as a retrospective metric of disease severity and corollary to hospitalization:case ratios.Consistent with other studies, strong correlations were found between wastewater and public health data. However, a significant reduction in case:wastewater ratios was observed for all three communities from the first to the second wave of infections, decreasing from an average of 4.7 ± 1.4 over the first infection wave to 0.8 ± 0.4 over the second.The decline in case:wastewater ratios was likely due to reduced clinical testing availability and test seeking behavior, highlighting how WDS can fill data gaps associated with under-reporting of cases. Overall, the hospitalization:wastewater ratios remained more stable through the two waves of infections, averaging 0.5 ± 0.3 and 0.3 ± 0.4 over the first and second waves, respectively.

  View details for DOI 10.3389/fpubh.2023.1141097

  View details for PubMedID 37457240

  View details for PubMedCentralID PMC10348812

• Human viral nucleic acids concentrations in wastewater solids from Central and Coastal California USA. Scientific data Boehm, A. B., Wolfe, M. K., Wigginton, K. R., Bidwell, A., White, B. J., Hughes, B., Duong, D., Chan-Herur, V., Bischel, H. N., Naughton, C. C. 2023; 10 (1): 396

  Abstract

  We measured concentrations of SARS-CoV-2, influenza A and B virus, respiratory syncytial virus (RSV), mpox virus, human metapneumovirus, norovirus GII, and pepper mild mottle virus nucleic acids in wastewater solids at twelve wastewater treatment plants in Central California, USA. Measurements were made daily for up to two years, depending on the wastewater treatment plant. Measurements were made using digital droplet (reverse-transcription-) polymerase chain reaction (RT-PCR) following best practices for making environmental molecular biology measurements. These data can be used to better understand disease occurrence in communities contributing to the wastewater.

  View details for DOI 10.1038/s41597-023-02297-7

  View details for PubMedID 37349355

• Longitudinal and quantitative fecal shedding dynamics of SARS-CoV-2, pepper mild mottle virus, and crAssphage. mSphere Arts, P. J., Kelly, J. D., Midgley, C. M., Anglin, K., Lu, S., Abedi, G. R., Andino, R., Bakker, K. M., Banman, B., Boehm, A. B., Briggs-Hagen, M., Brouwer, A. F., Davidson, M. C., Eisenberg, M. C., Garcia-Knight, M., Knight, S., Peluso, M. J., Pineda-Ramirez, J., Diaz Sanchez, R., Saydah, S., Tassetto, M., Martin, J. N., Wigginton, K. R. 2023: e0013223

  Abstract

  Wastewater-based epidemiology (WBE) emerged during the coronavirus disease 2019 (COVID-19) pandemic as a scalable and broadly applicable method for community-level monitoring of infectious disease burden. The lack of high-resolution fecal shedding data for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) limits our ability to link WBE measurements to disease burden. In this study, we present longitudinal, quantitative fecal shedding data for SARS-CoV-2 RNA, as well as for the commonly used fecal indicators pepper mild mottle virus (PMMoV) RNA and crAss-like phage (crAssphage) DNA. The shedding trajectories from 48 SARS-CoV-2-infected individuals suggest a highly individualized, dynamic course of SARS-CoV-2 RNA fecal shedding. Of the individuals that provided at least three stool samples spanning more than 14 days, 77% had one or more samples that tested positive for SARS-CoV-2 RNA. We detected PMMoV RNA in at least one sample from all individuals and in 96% (352/367) of samples overall. CrAssphage DNA was detected in at least one sample from 80% (38/48) of individuals and was detected in 48% (179/371) of all samples. The geometric mean concentrations of PMMoV and crAssphage in stool across all individuals were 8.7 × 104 and 1.4 × 104 gene copies/milligram-dry weight, respectively, and crAssphage shedding was more consistent for individuals than PMMoV shedding. These results provide us with a missing link needed to connect laboratory WBE results with mechanistic models, and this will aid in more accurate estimates of COVID-19 burden in sewersheds. Additionally, the PMMoV and crAssphage data are critical for evaluating their utility as fecal strength normalizing measures and for source-tracking applications. IMPORTANCE This research represents a critical step in the advancement of wastewater monitoring for public health. To date, mechanistic materials balance modeling of wastewater-based epidemiology has relied on SARS-CoV-2 fecal shedding estimates from small-scale clinical reports or meta-analyses of research using a wide range of analytical methodologies. Additionally, previous SARS-CoV-2 fecal shedding data have not contained sufficient methodological information for building accurate materials balance models. Like SARS-CoV-2, fecal shedding of PMMoV and crAssphage has been understudied to date. The data presented here provide externally valid and longitudinal fecal shedding data for SARS-CoV-2, PMMoV, and crAssphage which can be directly applied to WBE models and ultimately increase the utility of WBE.

  View details for DOI 10.1128/msphere.00132-23

  View details for PubMedID 37338211

• Respiratory virus concentrations in human excretions that contribute to wastewater: a systematic review and meta-analysis. Journal of water and health Lowry, S. A., Wolfe, M. K., Boehm, A. B. 2023; 21 (6): 831-848

  Abstract

  Concentrations of nucleic acids from a range of respiratory viruses in wastewater solids collected from wastewater treatment plants correlate to clinical data on disease occurrence in the community contributing to the wastewater. Viral nucleic acids enter wastewater from excretions deposited in toilets or drains. To relate measured concentrations in wastewater at a treatment plant to the number of community infections, viral nucleic-acid concentrations in human excretions are needed as inputs to a mass balance model. Here, we carried out a systematic review and meta-analysis to characterize the concentrations and presence of influenza A and B, respiratory syncytial virus, metapneumovirus, parainfluenza virus, rhinovirus, and seasonal coronaviruses in stool, urine, mucus, sputum, and saliva. We identified 220 data sets from 50 articles and reported viral concentrations and presence in these excretions. Data were unevenly distributed across virus type (with the most available for influenza) and excretion type (with the most available for respiratory excretions). Most articles only reported the presence or absence of the virus in a cross-sectional study design. There is a need for more concentration data, including longitudinal data, across all respiratory virus and excretion types. Such data would allow quantitatively linking virus wastewater concentrations to numbers of infected individuals.

  View details for DOI 10.2166/wh.2023.057

  View details for PubMedID 37387346

• Respiratory virus concentrations in human excretions that contribute to wastewater: a systematic review and meta-analysis JOURNAL OF WATER AND HEALTH Lowry, S. A., Wolfe, M. K., Boehm, A. 2023

  View details for DOI 10.2166/wh.2023.057

  View details for Web of Science ID 000989043600001

• Enveloped and non-enveloped virus survival on microfiber towels. PeerJ Anderson, C. E., Wolfe, M. K., Boehm, A. B. 2023; 11: e15202

  Abstract

  Handwashing is an important intervention which can reduce indirect disease transmission, however soap and water for handwashing purposes is not available in some low-resource regions. When handwashing with soap and water is not possible, individuals may use alternatives such as the Supertowel (a microfiber towel with an antimicrobial coating). Testing of viral inactivation as a result of antimicrobial treatment on the Supertowel, however, has been limited. The goal of this study is to provide information about the performance of the Supertowel's antimicrobial treatment against viruses, which will help inform the use of the towels as handwashing alternatives.We seeded the Supertowel and a regular microfiber towel with two bacteriophages (enveloped Phi6 and non-enveloped MS2) and monitored viral inactivation over time. Additionally, we assessed if temperature, humidity, whether the towel was initially wet or dry, or virus type had an effect on viral decay rate constants. Virus concentrations were measured repeatedly over 24 h.We found that neither towel type (whether the towel was a Supertowel or a regular microfiber towel) nor humidity were significant variables in our model of decay rate constants (P = 0.06 and P = 0.22, respectively). We found that the variables of temperature, whether towels were initially wet versus dry, and virus type were significantly different from 0, suggesting that these variables explained variance in the decay rate constant (P = 6.55 × 10-13, P = 0.001, and P < 2 × 10-16, respectively). Higher temperatures, dry towels, and enveloped viruses all resulted in increases in the decay rate constant.Viruses seeded onto a Supertowel decay similar to viruses seeded onto a regular towel indicating that the virucidal potential of the Supertowel is minimal.

  View details for DOI 10.7717/peerj.15202

  View details for PubMedID 37073274

  View details for PubMedCentralID PMC10106082

• Systematic review of marine environmental DNA metabarcoding studies: toward best practices for data usability and accessibility. PeerJ Shea, M. M., Kuppermann, J., Rogers, M. P., Smith, D. S., Edwards, P., Boehm, A. B. 2023; 11: e14993

  Abstract

  The emerging field of environmental DNA (eDNA) research lacks universal guidelines for ensuring data produced are FAIR-findable, accessible, interoperable, and reusable-despite growing awareness of the importance of such practices. In order to better understand these data usability challenges, we systematically reviewed 60 peer reviewed articles conducting a specific subset of eDNA research: metabarcoding studies in marine environments. For each article, we characterized approximately 90 features across several categories: general article attributes and topics, methodological choices, types of metadata included, and availability and storage of sequence data. Analyzing these characteristics, we identified several barriers to data accessibility, including a lack of common context and vocabulary across the articles, missing metadata, supplementary information limitations, and a concentration of both sample collection and analysis in the United States. While some of these barriers require significant effort to address, we also found many instances where small choices made by authors and journals could have an outsized influence on the discoverability and reusability of data. Promisingly, articles also showed consistency and creativity in data storage choices as well as a strong trend toward open access publishing. Our analysis underscores the need to think critically about data accessibility and usability as marine eDNA metabarcoding studies, and eDNA projects more broadly, continue to proliferate.

  View details for DOI 10.7717/peerj.14993

  View details for PubMedID 36992947

  View details for PubMedCentralID PMC10042160

• Wastewater concentrations of human influenza, metapneumovirus, parainfluenza, respiratory syncytial virus, rhinovirus, and seasonal coronavirus nucleic-acids during the COVID-19 pandemic: a surveillance study. The Lancet. Microbe Boehm, A. B., Hughes, B., Duong, D., Chan-Herur, V., Buchman, A., Wolfe, M. K., White, B. J. 2023

  Abstract

  Respiratory disease is a major cause of morbidity and mortality; however, surveillance for circulating respiratory viruses is passive and biased. Wastewater-based epidemiology has been used to understand SARS-CoV-2, influenza A, and respiratory syncytial virus (RSV) infection rates at a community level but has not been used to investigate other respiratory viruses. We aimed to use wastewater-based epidemiology to understand community viral respiratory infection occurrence.A retrospective wastewater-based epidemiology surveillance study was carried out at a large wastewater treatment plant located in California, USA. Using droplet digital RT-PCR, we measured RNA concentrations of influenza A and influenza B viruses, RSV A and RSV B, parainfluenza (1-4) viruses, rhinovirus, seasonal coronaviruses, and metapneumovirus in wastewater solids three times per week for 17 months (216 samples) between Feb 1, 2021, and June 21, 2022. Novel probe-based RT-PCR assays for non-influenza viral targets were developed and validated. We compared viral RNA concentrations to positivity rates for viral infections from clinical specimens submitted to California Sentinel Clinical Laboratories (sentinel laboratories) to assess concordance between the two datasets.We detected RNA from all tested viruses in wastewater solids. Human rhinovirus (median concentration 4300 [0-9500] copies per gram dry weight) and seasonal human coronaviruses (35 000 [17 000-56 000]) were found at the highest concentrations. Concentrations of viral RNA correlated significantly and positively with positivity rates of associated viral diseases from sentinel laboratories (tau 0·32-0·57, p<0·0009); the only exceptions were influenza B and RSV A, which were rarely detected in wastewater solids. Measurements from wastewater indicated coronavirus OC43 dominated the seasonal human coronavirus infections whereas parainfluenza 3 dominated among parainfluenza infections during the study period. Concentrations of all tested viral RNA decreased noticeably after the omicron BA.1 surge suggesting a connection between changes in human behaviour during the surge and transmission of all respiratory viruses.Wastewater-based epidemiology can be used to obtain information on circulation of respiratory viruses at a localised, community level without the need to test many individuals because a single sample of wastewater represents the entire contributing community. Results from wastewater can be available within 24 h of sample collection, generating real time information to inform public health responses, clinical decision making, and individual behaviour modifications.CDC Foundation.

  View details for DOI 10.1016/S2666-5247(22)00386-X

  View details for PubMedID 36965504

  View details for PubMedCentralID PMC10032662

• Wastewater monitoring of SARS-CoV-2 RNA at K-12 schools: comparison to pooled clinical testing data. PeerJ Kim, S., Boehm, A. B. 2023; 11: e15079

  Abstract

  Wastewater measurements of SARS-CoV-2 RNA have been extensively used to supplement clinical data on COVID-19. Most examples in the literature that describe wastewater monitoring for SARS-CoV-2 RNA use samples from wastewater treatment plants and individual buildings that serve as the primary residence of community members. However, wastewater surveillance can be an attractive supplement to clinical testing in K-12 schools where individuals only spend a portion of their time but interact with others in close proximity, increasing risk of potential transmission of disease.Wastewater samples were collected from two K-12 schools in California and divided into solid and liquid fractions to be processed for detection of SARS-CoV-2. The resulting detection rate in each wastewater fraction was compared to each other and the detection rate in pooled clinical specimens.Most wastewater samples were positive for SARS-CoV-2 RNA when clinical testing was positive (75% for solid samples and 100% for liquid samples). Wastewater samples continued to test positive for SARS-CoV-2 RNA when clinical testing was negative or in absence of clinical testing (83% for both solid and liquid samples), indicating presence of infected individuals in the schools. Wastewater solids had a higher concentration of SARS-CoV-2 than wastewater liquids on an equivalent mass basis by three orders of magnitude.

  View details for DOI 10.7717/peerj.15079

  View details for PubMedID 36967994

  View details for PubMedCentralID PMC10035418

• Effects of water, sanitation, and hygiene interventions on detection of enteropathogens and host-specific faecal markers in the environment: a systematic review and individual participant data meta-analysis. The Lancet. Planetary health Mertens, A., Arnold, B. F., Benjamin-Chung, J., Boehm, A. B., Brown, J., Capone, D., Clasen, T., Fuhrmeister, E., Grembi, J. A., Holcomb, D., Knee, J., Kwong, L. H., Lin, A., Luby, S. P., Nala, R., Nelson, K., Njenga, S. M., Null, C., Pickering, A. J., Rahman, M., Reese, H. E., Steinbaum, L., Stewart, J., Thilakaratne, R., Cumming, O., Colford, J. M., Ercumen, A. 2023; 7 (3): e197-e208

  Abstract

  Water, sanitation, and hygiene (WASH) improvements are promoted to reduce diarrhoea in low-income countries. However, trials from the past 5 years have found mixed effects of household-level and community-level WASH interventions on child health. Measuring pathogens and host-specific faecal markers in the environment can help investigate causal pathways between WASH and health by quantifying whether and by how much interventions reduce environmental exposure to enteric pathogens and faecal contamination from human and different animal sources. We aimed to assess the effects of WASH interventions on enteropathogens and microbial source tracking (MST) markers in environmental samples.We did a systematic review and individual participant data meta-analysis, which included searches from Jan 1, 2000, to Jan 5, 2023, from PubMed, Embase, CAB Direct Global Health, Agricultural and Environmental Science Database, Web of Science, and Scopus, of prospective studies with water, sanitation, or hygiene interventions and concurrent control group that measured pathogens or MST markers in environmental samples and measured child anthropometry, diarrhoea, or pathogen-specific infections. We used covariate-adjusted regression models with robust standard errors to estimate study-specific intervention effects and pooled effect estimates across studies using random-effects models.Few trials have measured the effect of sanitation interventions on pathogens and MST markers in the environment and they mostly focused on onsite sanitation. We extracted individual participant data on nine environmental assessments from five eligible trials. Environmental sampling included drinking water, hand rinses, soil, and flies. Interventions were consistently associated with reduced pathogen detection in the environment but effect estimates in most individual studies could not be distinguished from chance. Pooled across studies, we found a small reduction in the prevalence of any pathogen in any sample type (pooled prevalence ratio [PR] 0·94 [95% CI 0·90-0·99]). Interventions had no effect on the prevalence of MST markers from humans (pooled PR 1·00 [95% CI 0·88-1·13]) or animals (pooled PR 1·00 [95% CI 0·97-1·03]).The small effect of these sanitation interventions on pathogen detection and absence of effects on human or animal faecal markers are consistent with the small or null health effects previously reported in these trials. Our findings suggest that the basic sanitation interventions implemented in these studies did not contain human waste and did not adequately reduce exposure to enteropathogens in the environment.Bill and Melinda Gates Foundation and the UK Foreign and Commonwealth Development Office.

  View details for DOI 10.1016/S2542-5196(23)00028-1

  View details for PubMedID 36889861

• Effects of water, sanitation, and hygiene interventions on detection of enteropathogens and host-specific faecal markers in the environment: a systematic review and individual participant data meta-analysis LANCET PLANETARY HEALTH Mertens, A., Arnold, B. F., Benjamin-Chung, J., Boehm, A. B., Brown, J., Capone, D., Clasen, T., Fuhrmeister, E., Grembi, J. A., Holcomb, D., Knee, J., Kwong, L. H., Lin, A., Luby, S. P., Nala, R., Nelson, K., Njenga, S. M., Null, C., Pickering, A. J., Rahman, M., Reese, H. E., Steinbaum, L., Stewart, J., Thilakaratne, R., Cumming, O., Colford, J. M., Ercumen, A. 2023; 7 (3): E197-E208

  View details for Web of Science ID 000995850000001

• Persistence of Human Norovirus (GII) in Surface Water: Decay Rate Constants and Inactivation Mechanisms. Environmental science & technology Kennedy, L. C., Costantini, V. P., Huynh, K. A., Loeb, S. K., Jennings, W. C., Lowry, S., Mattioli, M. C., Vinje, J., Boehm, A. B. 2023

  Abstract

  Human norovirus (HuNoV) is an important cause of acute gastroenteritis and can be transmitted by water exposures, but its persistence in water is not well understood. Loss of HuNoV infectivity in surface water was compared with persistence of intact HuNoV capsids and genome segments. Surface water from a freshwater creek was filter-sterilized, inoculated with HuNoV (GII.4) purified from stool, and incubated at 15 or 20 °C. We measured HuNoV infectivity via the human intestinal enteroid system and HuNoV persistence via reverse transcription-quantitative polymerase chain reaction assays without (genome segment persistence) or with (intact viral capsid persistence) enzymatic pretreatment to digest naked RNA. For infectious HuNoV, results ranged from no significant decay to a decay rate constant ("k") of 2.2 day-1. In one creek water sample, genome damage was likely a dominant inactivation mechanism. In other samples from the same creek, loss of HuNoV infectivity could not be attributed to genome damage or capsid cleavage. The range in k and the difference in the inactivation mechanism observed in water from the same site could not be explained, but variable constituents in the environmental matrix could have contributed. Thus, a single k may be insufficient for modeling virus inactivation in surface waters.

  View details for DOI 10.1021/acs.est.2c09637

  View details for PubMedID 36812385

• Investigating the Efficacy of Various Handwashing Methods against Enveloped and Non-Enveloped Viruses. The American journal of tropical medicine and hygiene E Anderson, C., Tong, J., Zambrana, W., B Boehm, A., K Wolfe, M. 2023

  Abstract

  Respiratory and diarrheal diseases are leading causes of death worldwide. Handwashing may reduce disease; however, recommended methods (soap and water for 20 seconds) are not always possible, particularly in low-resource settings. The aim of this study is to evaluate handwashing when recommended methods are not feasible, including washing with water only, washing with soapy water, washing for a short duration, using alcohol-based hand sanitizer (ABHS), and cleaning hands with towels. To evaluate laboratory efficacy, we seeded MS2 (a non-enveloped virus) and Phi6 (an enveloped virus) onto the hands of volunteers who then washed their hands. Viruses remaining were recovered and quantified using culture-based and molecular methods to determine the log reduction value (LRV) after washing. Results indicated that washing with water only and with soapy water were similar to washing with soap and water for 20 seconds for both viruses (median LRV for MS2 = 2.8; Phi6 = 3.2). Most towel alternative conditions had LRVs significantly smaller than LRVs from washing with soap and water for either virus. LRVs of ABHS and soap and water for 5 seconds were similar to soap and water for 20 seconds for Phi6 but less for MS2 (median MS2 LRV differences = 2.5 and 0.51 for ABHS and soap and water for 5 seconds, respectively). Additionally, LRVs determined using molecular methods were in agreement with those obtained using culture-based methods. These results suggest some handwashing alternatives were as effective as recommended methods whereas others were not, and inform recommendations and future research on handwashing alternatives in low-resource settings.

  View details for DOI 10.4269/ajtmh.22-0287

  View details for PubMedID 36780893

• Use of Wastewater for Mpox Outbreak Surveillance in California. The New England journal of medicine Wolfe, M. K., Yu, A. T., Duong, D., Rane, M. S., Hughes, B., Chan-Herur, V., Donnelly, M., Chai, S., White, B. J., Vugia, D. J., Boehm, A. B. 2023

  View details for DOI 10.1056/NEJMc2213882

  View details for PubMedID 36652340

• Tomato brown rugose fruit virus Mo gene is a novel microbial source tracking marker. bioRxiv : the preprint server for biology Natarajan, A., Fremin, B. J., Schmidtke, D. T., Wolfe, M. K., Zlitni, S., Graham, K. E., Brooks, E. F., Severyn, C. J., Sakamoto, K. M., Lacayo, N. J., Kuersten, S., Koble, J., Caves, G., Kaplan, I., Singh, U., Jagannathan, P., Rezvani, A. R., Bhatt, A. S., Boehm, A. B. 2023

  Abstract

  Microbial source tracking (MST) identifies sources of fecal contamination in the environment using fecal host-associated markers. While there are numerous bacterial MST markers, there are few viral markers. Here we design and test novel viral MST markers based on tomato brown rugose fruit virus (ToBRFV) genomes. We assembled eight nearly complete genomes of ToBRFV from wastewater and stool samples from the San Francisco Bay Area in the United States of America. Next, we developed two novel probe-based RT-PCR assays based on conserved regions of the ToBRFV genome, and tested the markers’ sensitivities and specificities using human and non-human animal stool as well as wastewater. TheToBRFV markers are sensitive and specific; in human stool and wastewater, they are more prevalent and abundant than a currently used marker, the pepper mild mottle virus (PMMoV) coat protein (CP) gene. We applied the assays to detect fecal contamination in urban stormwater samples and found that the ToBRFV markers matched cross-assembly phage (crAssphage), an established viral MST marker, in prevalence across samples. Taken together, ToBRFV is a promising viral human-associated MST marker.Human exposure to fecal contamination in the environment can cause transmission of infectious diseases. Microbial source tracking (MST) can identify sources of fecal contamination so that contamination can be remediated and human exposures can be reduced. MST requires the use of fecal host-associated MST markers. Here we design and test novel MST markers from genomes of tomato brown rugose fruit virus (ToBRFV). The markers are sensitive and specific to human stool, and highly abundant in human stool and wastewater samples.

  View details for DOI 10.1101/2023.01.09.523366

  View details for PubMedID 36712100

  View details for PubMedCentralID PMC9882089

• Trends of Enterovirus D68 Concentrations in Wastewater, California, USA, February 2021-April 2023. Emerging infectious diseases Boehm, A. B., Wadford, D. A., Hughes, B., Duong, D., Chen, A., Padilla, T., Wright, C., Moua, L., Bullick, T., Salas, M., Morales, C., White, B. J., Glaser, C. A., Vugia, D. J., Yu, A. T., Wolfe, M. K. 2023; 29 (11): 2362-2365

  Abstract

  In this retrospective study, we measured enterovirus D68 (EV-D68) genomic RNA in wastewater solids longitudinally at 2 California, USA, wastewater treatment plants twice per week for 26 months. EV-D68 RNA was undetectable except when concentrations increased from mid-July to mid-December 2022, which coincided with a peak in confirmed EV-D68 cases.

  View details for DOI 10.3201/eid2911.231080

  View details for PubMedID 37877593

• Divergence of wastewater SARS-CoV-2 and reported laboratory-confirmed COVID-19 incident case data coincident with wide-spread availability of at-home COVID-19 antigen tests. PeerJ Boehm, A. B., Wolfe, M. K., White, B., Hughes, B., Duong, D. 2023; 11: e15631

  Abstract

  Concentrations of SARS-CoV-2 RNA in wastewater settled solids from publicly owned treatment works (POTWs) historically correlated strongly with laboratory confirmed incident COVID-19 case data. With the increased availability of at-home antigen tests since late 2021 and early 2022, laboratory test availability and test seeking behavior has decreased. In the United States, the results from at-home antigen tests are not typically reportable to public health agencies and thus are not counted in case reports. As a result, the number of reported laboratory-confirmed incident COVID-19 cases has decreased dramatically, even during times of increased test positivity rates and wastewater concentrations of SARS-CoV-2 RNA. Herein, we tested whether the correlative relationship between wastewater concentrations of SARS-CoV-2 RNA and reported laboratory-confirmed COVID-19 incidence rate has changed since 1 May 2022, a point in time immediately before the onset of the BA.2/BA.5 surge, the first surge to begin after at-home antigen test availability was high in the region. We used daily data from three POTWs in the Greater San Francisco Bay Area of California, USA for the analysis. We found that although there is a significant positive association between wastewater measurements and incident rate data collected after 1 May 2022, the parameters describing the relationship are different than those describing the relationship between the data collected prior to 1 May 2022. If laboratory test seeking or availability continues to change, the relationship between wastewater and reported case data will continue to change. Our results suggest, assuming SARS-CoV-2 RNA shedding remains relatively stable among those infected with the virus as different variants emerge, that wastewater concentrations of SARS-CoV-2 RNA can be used to estimate COVID-19 cases as they would have been during the time when laboratory testing availability and test seeking behavior were at a high (here, before 1 May 2022) using the historical relationship between SARS-CoV-2 RNA and COVID-19 case data.

  View details for DOI 10.7717/peerj.15631

  View details for PubMedID 37397016

• High-frequency fecal indicator bacteria (FIB) observations to assess water quality drivers at an enclosed beach. PloS one Searcy, R. T., Phaneuf, J. R., Boehm, A. B. 2023; 18 (6): e0286029

  Abstract

  Fecal indicator bacteria (FIB) are monitored at beaches to assess water quality and associated health risk from recreational exposure. However, monitoring is generally conducted infrequently (i.e. weekly or less often), potentially leading to inaccurate assessment of water quality at a beach at the time of use. While some work has shown that FIB in marine environments can vary over short (e.g. subhourly) time scales, that work has been mainly focused on 'open' beaches. 'Enclosed' beaches-those that are partially barriered from exchange with offshore water and thus have different residence times and mixing dynamics in the nearshore environment-have been less studied. Here we present results from a high-frequency (once per 30 minutes) FIB sampling event conducted within a Central California, USA, harbor over 48 hours. FIB concentrations at this enclosed site were more variable at high-frequencies than what has been reported at open beach sites. Correlation and regression analyses showed FIB concentrations were most strongly associated with chlorophyll a concentration, turbidity, wind speed, and tide level. Results indicate the importance of measuring FIB concentrations and explanatory environmental parameters at appropriate temporal resolutions when conducting water quality monitoring or source tracking studies. Overall, this work highlights how high-frequency sampling can effectively provide information about water quality dynamics at beaches of interest.

  View details for DOI 10.1371/journal.pone.0286029

  View details for PubMedID 37267238

• Quantifying the Viral Reduction Achieved Using Ash and Sand as Handwashing Agents. The American journal of tropical medicine and hygiene Zambrana, W., Tong, J., E Anderson, C., B Boehm, A., Wolfe, M. K. 2022

  Abstract

  The WHO recommends handwashing with soap and water for 20-40 seconds. In settings where soap is not available, ash or sand is used for handwashing, yet their efficacy as handwashing materials is underresearched. The purpose of this study was to quantify the removal of viruses using ash and sand as handwashing agents, and compare their efficacy to commonly recommended handwashing methods. We performed a volunteer study to estimate the log reduction value (LRV) of model viruses Phi6 and MS2 on hands after six handwashing conditions: two handwashing agents (ash and water, and sand and water) with two time points (5 and 20 seconds), and two handwashing agents (soap and water, and water only) with one time point (20 seconds). Plaque assays were used to measure infectious virus reduction. Handwashing with any of the handwashing agents for 20 seconds resulted in a greater LRV than the 2-log reduction U.S. Food and Drug Administration criteria for both viruses. Soap and water resulted in a significantly greater LRV (2.7-4.8) than washing with ash and water (2.0-2.8) or sand and water (1.8-2.7) for 5 seconds for both viruses, and water only resulted in a significantly higher LRV (2.8) than all ash (2.0-2.6) and sand (1.8-2.4) conditions for MS2 only. These results suggest that using ash or sand as handwashing agents can be efficacious in reducing viruses but may be less efficacious than soap, especially when used for shorter durations. Further research should investigate the use of ash and sand as handwashing agents in real-world settings.

  View details for DOI 10.4269/ajtmh.22-0581

  View details for PubMedID 36535259

• Know Before You Go: Data-Driven Beach Water Quality Forecasting. Environmental science & technology Searcy, R. T., Boehm, A. B. 2022

  Abstract

  Forecasting environmental hazards is critical in preventing or building resilience to their impacts on human communities and ecosystems. Environmental data science is an emerging field that can be harnessed for forecasting, yet more work is needed to develop methodologies that can leverage increasingly large and complex data sets for decision support. Here, we design a data-driven framework that can, for the first time, forecast bacterial standard exceedances at marine beaches with 3 days lead time. Using historical data sets collected at two California sites, we train nearly 400 forecast models using statistical and machine learning techniques and test forecasts against predictions from both a naive "persistence" model and a baseline nowcast model. Overall, forecast models are found to have similar sensitivities and specificities to the persistence model, but significantly higher areas under the ROC curve (a metric distinguishing a model's ability to effectively parse classes across decision thresholds), suggesting that forecasts can provide enhanced information beyond past observations alone. Forecast model performance at all lead times was similar to that of nowcast models. Together, results suggest that integrating the forecasting framework developed in this study into beach management programs can enable better public notification and aid in proactive pollution and health risk management.

  View details for DOI 10.1021/acs.est.2c05972

  View details for PubMedID 36472482

• SARS-CoV-2 RNA Wastewater Settled Solids Surveillance Frequency and Impact on Predicted COVID-19 Incidence Using a Distributed Lag Model. ACS ES&T water Schoen, M. E., Wolfe, M. K., Li, L., Duong, D., White, B. J., Hughes, B., Boehm, A. B. 2022; 2 (11): 2167-2174

  Abstract

  Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concentrations in wastewater settled solids correlate well with coronavirus disease 2019 (COVID-19) incidence rates (IRs). Here, we develop distributed lag models to estimate IRs using concentrations of SARS-CoV-2 RNA from wastewater solids and investigate the impact of sampling frequency on model performance. SARS-CoV-2 N gene and pepper mild mottle virus (PMMoV) RNA concentrations were measured daily at four wastewater treatment plants in California. Artificially reduced data sets were produced for each plant with sampling frequencies of once every 2, 3, 4, and 7 days. Sewershed-specific models that related daily N/PMMoV to IR were fit for each sampling frequency with data from mid-November 2020 through mid-July 2021, which included the period of time during which Delta emerged. Models were used to predict IRs during a subsequent out-of-sample time period. When sampling occurred at least once every 4 days, the in- and out-of-sample root-mean-square error changed by <7 cases/100 000 compared to daily sampling across sewersheds. This work illustrates that real-time, daily predictions of IR are possible with small errors, despite changes in circulating variants, when sampling frequency is once every 4 days or more. However, reduced sampling frequency may not serve other important wastewater surveillance use cases.

  View details for DOI 10.1021/acsestwater.2c00074

  View details for PubMedID 36380770

• Persistence of Endogenous SARS-CoV-2 and Pepper Mild Mottle Virus RNA in Wastewater-Settled Solids. ACS ES&T water Roldan-Hernandez, L., Graham, K. E., Duong, D., Boehm, A. B. 2022; 2 (11): 1944-1952

  Abstract

  Limited information is available on the decay rate of endogenous SARS-CoV-2 and pepper mild mottle virus (PMMoV) RNA in wastewater and primary settled solids, potentially limiting an understanding of how transit or holding times within wastewater infrastructure might impact RNA measurements and their relationship to community COVID-19 infections. In this study, primary settled solids samples were collected from two wastewater treatment plants in the San Francisco Bay Area. Samples were thoroughly mixed, aliquoted into subsamples, and stored at 4, 22, and 37 °C for 10 days. The concentrations of SARS-CoV-2 (N1 and N2 targets) and PMMoV RNA were measured using an RT-ddPCR. Limited decay (<1 log10 reduction) was observed in the detection of viral RNA targets at all temperature conditions, suggesting that SARS-CoV-2 and PMMoV RNA can be highly persistent in solids. First-order decay rate constants ranged from 0.011 to 0.098 day-1 for SARS-CoV-2 RNA and from 0.010 to 0.091 day-1 for PMMoV RNA depending on the temperature conditions. A slower decay was observed for SARS-CoV-2 RNA in primary settled solids compared to previously reported decay in wastewater influent. Further research is needed to understand if solid content and wastewater characteristics might influence the persistence of viral RNA targets.

  View details for DOI 10.1021/acsestwater.2c00003

  View details for PubMedID 36380769

• Prevalence of Positive Rapid Antigen Tests After 7-Day Isolation Following SARS-CoV-2 Infection in College Athletes During Omicron Variant Predominance. JAMA network open Tsao, J., Kussman, A., Segovia, N. A., Abrams, G. D., Boehm, A. B., Hwang, C. E. 2022; 5 (10): e2237149

  Abstract

  Importance: The US Centers for Disease Control and Prevention shortened the recommended isolation period for SARS-CoV-2 infection from 10 days to 5 days in December 2021. It is unknown whether an individual with the infection may still have a positive result to a rapid antigen test and potentially be contagious at the end of this shortened isolation period.Objective: To estimate the proportion of individuals with SARS-CoV-2 infection whose rapid antigen test is still positive starting 7 days postdiagnosis.Design, Setting, and Participants: This case series analyzed student athletes at a National Collegiate Athletic Association Division I university campus who tested positive for SARS-CoV-2 between January 3 and May 6, 2022. Individuals underwent rapid antigen testing starting 7 days postdiagnosis to determine whether they could end their isolation period.Exposures: Rapid antigen testing 7 days after testing positive for SARS-CoV-2.Main Outcomes and Measures: Rapid antigen test results, symptom status, and SARS-CoV-2 variant identification via campus wastewater analysis.Results: A total of 264 student athletes (140 [53%] female; mean [SD] age, 20.1 [1.2] years; range, 18-25 years) representing 268 infections (177 [66%] symptomatic, 91 [34%] asymptomatic) were included in the study. Of the 248 infections in individuals who did a day 7 test, 67 (27%; 95% CI, 21%-33%) tests were still positive. Patients with symptomatic infections were significantly more likely to test positive on day 7 vs those who were asymptomatic (35%; 95% CI, 28%-43% vs 11%; 95% CI, 5%-18%; P<.001). Patients with the BA.2 variant were also significantly more likely to test positive on day 7 compared with those with the BA.1 variant (40%; 95% CI, 29%-51% vs 21%; 95% CI, 15%-27%; P=.007).Conclusions and Relevance: In this case series, rapid antigen tests remained positive in 27% of the individuals after 7 days of isolation, suggesting that the Centers for Disease Control and Prevention-recommended 5-day isolation period may be insufficient in preventing ongoing spread of disease. Further studies are needed to determine whether these findings are present in a more heterogeneous population and in subsequent variants.

  View details for DOI 10.1001/jamanetworkopen.2022.37149

  View details for PubMedID 36255722

• Interlaboratory performance and quantitative PCR data acceptance metrics for NIST SRM 2917. Water research Sivaganesan, M., Willis, J. R., Karim, M., Babatola, A., Catoe, D., Boehm, A. B., Wilder, M., Green, H., Lobos, A., Harwood, V. J., Hertel, S., Klepikow, R., Howard, M. F., Laksanalamai, P., Roundtree, A., Mattioli, M., Eytcheson, S., Molina, M., Lane, M., Rediske, R., Ronan, A., D'Souza, N., Rose, J. B., Shrestha, A., Hoar, C., Silverman, A. I., Faulkner, W., Wickman, K., Kralj, J. G., Servetas, S. L., Hunter, M. E., Jackson, S. A., Shanks, O. C. 2022; 225: 119162

  Abstract

  Surface water quality quantitative polymerase chain reaction (qPCR) technologies are expanding from a subject of research to routine environmental and public health laboratory testing. Readily available, reliable reference material is needed to interpret qPCR measurements, particularly across laboratories. Standard Reference Material 2917 (NIST SRM 2917) is a DNA plasmid construct that functions with multiple water quality qPCR assays allowing for estimation of total fecal pollution and identification of key fecal sources. This study investigates SRM 2917 interlaboratory performance based on repeated measures of 12 qPCR assays by 14 laboratories (n=1008 instrument runs). Using a Bayesian approach, single-instrument run data are combined to generate assay-specific global calibration models allowing for characterization of within- and between-lab variability. Comparable data sets generated by two additional laboratories are used to assess new SRM 2917 data acceptance metrics. SRM 2917 allows for reproducible single-instrument run calibration models across laboratories, regardless of qPCR assay. In addition, global models offer multiple data acceptance metric options that future users can employ to minimize variability, improve comparability of data across laboratories, and increase confidence in qPCR measurements.

  View details for DOI 10.1016/j.watres.2022.119162

  View details for PubMedID 36191524

• Our Selections for the Best ES&T Letters Papers in 2021 ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS Brooks, B. W., Arnold, W. A., Boehm, A. B., Hamilton, J. F., Martin, J. W., Mihelcic, J. R., Mitrano, D. M., Ren, Z., Schlenk, D., Wang, S. 2022; 9 (8): 658-659

  View details for DOI 10.1021/acs.estlett.2c00500

  View details for Web of Science ID 000840729300001

• Modeling infection from SARS-CoV-2 wastewater concentrations: promise, limitations, and future directions. Journal of water and health Soller, J., Jennings, W., Schoen, M., Boehm, A., Wigginton, K., Gonzalez, R., Graham, K. E., McBride, G., Kirby, A., Mattioli, M. 2022; 20 (8): 1197-1211

  Abstract

  Estimating total infection levels, including unreported and asymptomatic infections, is important for understanding community disease transmission. Wastewater can provide a pooled community sample to estimate total infections that is independent of case reporting biases toward individuals with moderate to severe symptoms and by test-seeking behavior and access. We derive three mechanistic models for estimating community infection levels from wastewater measurements based on a description of the processes that generate SARS-CoV-2 RNA signals in wastewater and accounting for the fecal strength of wastewater through endogenous microbial markers, daily flow, and per-capita wastewater generation estimates. The models are illustrated through two case studies of wastewater data collected during 2020-2021 in Virginia Beach, VA, and Santa Clara County, CA. Median simulated infection levels generally were higher than reported cases, but at times, were lower, suggesting a discrepancy between the reported cases and wastewater data, or inaccurate modeling results. Daily simulated infection estimates showed large ranges, in part due to dependence on highly variable clinical viral fecal shedding data. Overall, the wastewater-based mechanistic models are useful for normalization of wastewater measurements and for understanding wastewater-based surveillance data for public health decision-making but are currently limited by lack of robust SARS-CoV-2 fecal shedding data.

  View details for DOI 10.2166/wh.2022.094

  View details for PubMedID 36044189

  View details for PubMedCentralID wh_2022_094

• Wastewater surveillance for rapid identification of infectious diseases in prisons LANCET MICROBE Hassard, F., Smith, T. R., Boehm, A. B., Nolan, S., O'Mara, O., Di Cesare, M., Graham, D. 2022; 3 (8): E556-E557

  View details for DOI 10.1016/2666-5247(22)00154-9

  View details for Web of Science ID 000931001000003

• Modeling infection from SARS-CoV-2 wastewater concentrations: promise, limitations, and future directions JOURNAL OF WATER AND HEALTH Soller, J., Jennings, W., Schoen, M., Boehm, A., Wigginton, K., Gonzalez, R., Graham, K. E., McBride, G., Kirby, A., Mattioli, M. 2022

  View details for DOI 10.2166/wh.2022.094

  View details for Web of Science ID 000823175300001

• Differential Overlap in Human and Animal Fecal Microbiomes and Resistomes in Rural versus Urban Bangladesh APPLIED AND ENVIRONMENTAL MICROBIOLOGY Swarthout, J. M., Fuhrmeister, E. R., Hamzah, L., Harris, A. R., Ahmed, M. A., Gurley, E. S., Satter, S. M., Boehm, A. B., Pickering, A. J. 2022

  View details for DOI 10.1128/aem.00759-22

  View details for Web of Science ID 000823787800001

• Wastewater-Based Detection of Two Influenza Outbreaks ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS Wolfe, M. K., Duong, D., Bakker, K. M., Ammerman, M., Mortenson, L., Hughes, B., Arts, P., Lauring, A. S., Fitzsimmons, W. J., Bendall, E., Hwang, C. E., Martin, E. T., White, B. J., Boehm, A. B., Wigginton, K. R. 2022

  View details for DOI 10.1021/acs.estlett.2c00350

  View details for Web of Science ID 000826900900001

• Data Science for Advancing Environmental Science, Engineering, and Technology: Upcoming Special and Virtual Issues in ES&T and ES&T Letters ENVIRONMENTAL SCIENCE & TECHNOLOGY V. Lowry, G., Boehm, A. B., Brooks, B. W., Gago-Ferrero, P., Jiang, G., Jones, G. D., Liu, Q., Ren, Z. J., Wang, S., Zimmerman, J. 2022

  View details for DOI 10.1021/acs.est.2c03735

  View details for Web of Science ID 000820429900001

• Regional Replacement of SARS-CoV-2 Variant Omicron BA.1 with BA.2 as Observed through Wastewater Surveillance. Environmental science & technology letters Boehm, A. B., Hughes, B., Wolfe, M. K., White, B. J., Duong, D., Chan-Herur, V. 2022; 9 (6): 575-580

  Abstract

  Greater knowledge of circulating SARS-CoV-2 variants can inform pandemic response, vaccine development, disease epidemiology, and use of monoclonal antibody treatments. We developed custom assays targeting characteristic mutations in SARS-CoV-2 variants Omicron BA.1 and BA.2 and confirmed their sensitivity and specificity in silico and in vitro. We then applied these assays to daily wastewater solid samples from eight publicly owned treatment works in the greater Bay Area of California, United States, over four months to obtain a spatially and temporally intensive data set. We documented regional replacement of BA.1 with BA.2 in agreement with, and ahead of, clinical sequencing data. This study highlights the utility of wastewater surveillance for real-time tracking of SARS-CoV-2 sublineage circulation. The results suggest that concerted efforts to design RT-PCR assays that target variant and variant sublineage characteristic mutations for wide-scale wastewater monitoring implementation will be informative for pandemic response.

  View details for DOI 10.1021/acs.estlett.2c00266

  View details for PubMedID 35711323

• Data Science for Advancing Environmental Science, Engineering, and Technology: Upcoming Special and Virtual Issues in ES&T and ES&T Letters ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS Lowry, G. V., Boehm, A. B., Brooks, B. W., Gago-Ferrero, P., Jiang, G., Jones, G. D., Liu, Q., Ren, Z. J., Wang, S., Zimmerman, J. 2022

  View details for DOI 10.1021/acs.estlett.2c00345

  View details for Web of Science ID 000818983200001

  View details for PubMedID 35713615

• Integrating Environmental Dimensions of "One Health" to Combat Antimicrobial Resistance: Essential Research Needs. Environmental science & technology Jin, L., Pruden, A., Boehm, A. B., Alvarez, P. J., Raskin, L., Kohn, T., Li, X. 2022

  View details for DOI 10.1021/acs.est.2c01651

  View details for PubMedID 35678702

• Wastewater surveillance for rapid identification of infectious diseases in prisons. The Lancet. Microbe Hassard, F., Smith, T. R., Boehm, A. B., Nolan, S., O'Mara, O., Di Cesare, M., Graham, D. 2022

  View details for DOI 10.1016/S2666-5247(22)00154-9

  View details for PubMedID 35688168

• SARS-CoV-2 RNA and N Antigen Quantification via Wastewater at the Campus Level, Building Cluster Level, and Individual-Building Level ACS ES&T WATER Zambrana, W., Catoe, D., Coffman, M. M., Kim, S., Anand, A., Solis, D., Sahoo, M. K., Pinsky, B. A., Bhatt, A. S., Boehm, A. B., Wolfe, M. K. 2022

  View details for DOI 10.1021/acsestwater.2c00050

  View details for Web of Science ID 000820376800001

• SARS-CoV-2 RNA and N Antigen Quantification via Wastewater at the Campus Level, Building Cluster Level, and Individual-Building Level. ACS ES&T water Zambrana, W., Catoe, D., Coffman, M. M., Kim, S., Anand, A., Solis, D., Sahoo, M. K., Pinsky, B. A., Bhatt, A. S., Boehm, A. B., Wolfe, M. K. 2022; 2 (11): 2025-33

  Abstract

  Monitoring wastewater for SARS-CoV-2 from populations smaller than those served by wastewater treatment plants may help identify small spatial areas (subsewersheds) where COVID-19 infections are present. We sampled wastewater from three nested locations with different sized populations within the same sewer network at a university campus and quantified SARS-CoV-2 RNA using reverse transcriptase droplet digital polymerase chain reaction (PCR). SARS-CoV-2 RNA concentrations and/or concentrations normalized by PMMoV were positively associated with laboratory-confirmed COVID-19 cases for both the sewershed level and the subsewershed level. We also used an antigen-based assay to detect the nucleocapsid (N) antigen from SARS-CoV-2 in wastewater samples at the sewershed level. The N antigen was regularly detected at the sewershed level, but the results were not associated with either laboratory-confirmed COVID-19 cases or SARS-CoV-2 RNA concentrations. The results of this study indicate that wastewater monitoring based on quantification of SARS-CoV-2 RNA using PCR-based methods is associated with COVID-19 cases at multiple geographic scales within the subsewershed level and can serve to aid the public health response.

  View details for DOI 10.1021/acsestwater.2c00050

  View details for PubMedID 37552722

  View details for PubMedCentralID PMC9128006

• Highly variable removal of pathogens, antibiotic resistance genes, conventional fecal indicators and human-associated fecal source markers in a pilot-scale stormwater biofilter operated under realistic stormflow conditions. Water research Rugh, M. B., Grant, S. B., Hung, W., Jay, J. A., Parker, E. A., Feraud, M., Li, D., Avasarala, S., Holden, P. A., Liu, H., Rippy, M. A., Werfhorst, L. C., Kefela, T., Peng, J., Shao, S., Graham, K. E., Boehm, A. B., Choi, S., Mohanty, S. K., Cao, Y. 2022; 219: 118525

  Abstract

  Green stormwater infrastructure systems, such as biofilters, provide many water quality and other environmental benefits, but their ability to remove human pathogens and antibiotic resistance genes (ARGs) from stormwater runoff is not well documented. In this study, a field scale biofilter in Southern California (USA) was simultaneously evaluated for the breakthrough of a conservative tracer (bromide), conventional fecal indicators, bacterial and viral human-associated fecal source markers (HF183, crAssphage, and PMMoV), ARGs, and bacterial and viral pathogens. When challenged with a 50:50 mixture of untreated sewage and stormwater (to mimic highly contaminated storm flow) the biofilter significantly removed (p < 0.05) 14 of 17 microbial markers and ARGsin descending order of concentration reduction: ermB (2.5 log(base 10) reduction) > Salmonella (2.3) > adenovirus (1.9) > coliphage (1.5) > crAssphage (1.2) > E. coli (1.0) 16S rRNA genes (1.0) fecal coliform (1.0) intl1 (1.0) > Enterococcus (0.9) MRSA (0.9) sul1 (0.9) > PMMoV (0.7) > Entero1A (0.5). No significant removal was observed for GenBac3, Campylobacter, and HF183. From the bromide data, we infer that 0.5 log-units of attenuation can be attributed to the dilution of incoming stormwater with water stored in the biofilter; removal above this threshold is presumably associated with non-conservative processes, such as physicochemical filtration, die-off, and predation. Our study documents high variability (>100-fold) in the removal of different microbial contaminants and ARGs by a field-scale stormwater biofilter operated under transient flow and raises further questions about the utility of human-associated fecal source markers as surrogates for pathogen removal.

  View details for DOI 10.1016/j.watres.2022.118525

  View details for PubMedID 35533621

• Wastewater-Based Estimation of the Effective Reproductive Number of SARS-CoV-2. Environmental health perspectives Huisman, J. S., Scire, J., Caduff, L., Fernandez-Cassi, X., Ganesanandamoorthy, P., Kull, A., Scheidegger, A., Stachler, E., Boehm, A. B., Hughes, B., Knudson, A., Topol, A., Wigginton, K. R., Wolfe, M. K., Kohn, T., Ort, C., Stadler, T., Julian, T. R. 2022; 130 (5): 57011

  Abstract

  BACKGROUND: The effective reproductive number, Re, is a critical indicator to monitor disease dynamics, inform regional and national policies, and estimate the effectiveness of interventions. It describes the average number of new infections caused by a single infectious person through time. To date, Re estimates are based on clinical data such as observed cases, hospitalizations, and/or deaths. These estimates are temporarily biased when clinical testing or reporting strategies change.OBJECTIVES: We show that the dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater can be used to estimate Re in near real time, independent of clinical data and without the associated biases.METHODS: We collected longitudinal measurements of SARS-CoV-2 RNA in wastewater in Zurich, Switzerland, and San Jose, California, USA. We combined this data with information on the temporal dynamics of shedding (the shedding load distribution) to estimate a time series proportional to the daily COVID-19 infection incidence. We estimated a wastewater-based Re from this incidence.RESULTS: The method to estimate Re from wastewater worked robustly on data from two different countries and two wastewater matrices. The resulting estimates were as similar to the Re estimates from case report data as Re estimates based on observed cases, hospitalizations, and deaths are among each other. We further provide details on the effect of sampling frequency and the shedding load distribution on the ability to infer Re.DISCUSSION: To our knowledge, this is the first time Re has been estimated from wastewater. This method provides a low-cost, rapid, and independent way to inform SARS-CoV-2 monitoring during the ongoing pandemic and is applicable to future wastewater-based epidemiology targeting other pathogens. https://doi.org/10.1289/EHP10050.

  View details for DOI 10.1289/EHP10050

  View details for PubMedID 35617001

• Estimating Relative Abundance of 2 SARS-CoV-2 Variants through Wastewater Surveillance at 2 Large Metropolitan Sites, United States EMERGING INFECTIOUS DISEASES Yu, A. T., Hughes, B., Wolfe, M. K., Leon, T., Duong, D., Rabe, A., Kennedy, L. C., Ravuri, S., White, B. J., Wigginton, K. R., Boehm, A. B., Vugia, D. J. 2022; 28 (5): 940-947

  Abstract

  Monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) is critical for public health management of coronavirus disease. Sequencing is resource-intensive and incompletely representative, and not all isolates can be sequenced. Because wastewater SARS-CoV-2 RNA concentrations correlate with coronavirus disease incidence in sewersheds, tracking VOCs through wastewater is appealing. We developed digital reverse transcription PCRs to monitor abundance of select mutations in Alpha and Delta VOCs in wastewater settled solids, applied these to July 2020-August 2021 samples from 2 large US metropolitan sewersheds, and compared results to estimates of VOC abundance from case isolate sequencing. Wastewater measurements tracked closely with case isolate estimates (Alpha, rp 0.82-0.88; Delta, rp 0.97). Mutations were detected in wastewater even at levels <5% of total SARS-CoV-2 RNA and in samples available 1-3 weeks before case isolate results. Wastewater variant monitoring should be strategically deployed to complement case isolate sequencing.

  View details for DOI 10.3201/eid2805.212488

  View details for Web of Science ID 000799694100004

  View details for PubMedID 35349402

  View details for PubMedCentralID PMC9045426

• Impact of Disaster Research on the Development of Early Career Researchers: Lessons Learned from the Wastewater Monitoring Pandemic Response Efforts. Environmental science & technology Delgado Vela, J., McClary-Gutierrez, J. S., Al-Faliti, M., Allan, V., Arts, P., Barbero, R., Bell, C., D'Souza, N., Bakker, K., Kaya, D., Gonzalez, R., Harrison, K., Kannoly, S., Keenum, I., Li, L., Pecson, B., Philo, S. E., Schneider, R., Schussman, M. K., Shrestha, A., Stadler, L. B., Wigginton, K. R., Boehm, A., Halden, R. U., Bibby, K. 2022

  View details for DOI 10.1021/acs.est.2c01583

  View details for PubMedID 35389620

• Detection of SARS-CoV-2 Variants Mu, Beta, Gamma, Lambda, Delta, Alpha, and Omicron in Wastewater Settled Solids Using Mutation-Specific Assays Is Associated with Regional Detection of Variants in Clinical Samples. Applied and environmental microbiology Wolfe, M., Hughes, B., Duong, D., Chan-Herur, V., Wigginton, K. R., White, B. J., Boehm, A. B. 2022: e0004522

  Abstract

  Changes in the circulation of SARS-CoV-2 variants of concern (VOCs) may require changes in the public health response to the COVID-19 pandemic, as they have the potential to evade vaccines and pharmaceutical interventions and may be more transmissive than other SARS-CoV-2 variants. As such, it is essential to track and prevent their spread in susceptible communities. We developed digital reverse transcription (RT)-PCR assays for mutations characteristic of VOCs and used them to quantify those mutations in samples of wastewater settled solids collected from a publicly owned treatment works (POTW) during different phases of the COVID-19 pandemic. Wastewater concentrations of single mutations characteristic of each VOC, normalized by the concentration of a conserved SARS-CoV-2 N gene, correlate with regional estimates of the proportion of clinical infections caused by each VOC. These results suggest that targeted RT-PCR assays can be used to detect variants circulating in communities and inform the public health response to the pandemic. IMPORTANCE Wastewater represents a pooled biological sample of the contributing community and thus a resource for assessing community health. Here, we show that emergence, spread, and disappearance of SARS-CoV-2 infections caused by variants of concern are reflected in the presence of variant genomic RNA in wastewater settled solids. This work highlights an important public health use case for wastewater.

  View details for DOI 10.1128/aem.00045-22

  View details for PubMedID 35380449

• SARS-CoV-2 RNA is enriched by orders of magnitude in primary settled solids relative to liquid wastewater at publicly owned treatment works. Environmental science : water research & technology Kim, S., Kennedy, L. C., Wolfe, M. K., Criddle, C. S., Duong, D. H., Topol, A., White, B. J., Kantor, R. S., Nelson, K. L., Steele, J. A., Langlois, K., Griffith, J. F., Zimmer-Faust, A. G., McLellan, S. L., Schussman, M. K., Ammerman, M., Wigginton, K. R., Bakker, K. M., Boehm, A. B. 2022; 8 (4): 757-770

  Abstract

  Wastewater-based epidemiology has gained attention throughout the world for detection of SARS-CoV-2 RNA in wastewater to supplement clinical testing. Raw wastewater consists of small particles, or solids, suspended in liquid. Methods have been developed to measure SARS-CoV-2 RNA in the liquid and the solid fraction of wastewater, with some studies reporting higher concentrations in the solid fraction. To investigate this relationship further, six laboratories collaborated to conduct a study across five publicly owned treatment works (POTWs) where both primary settled solids obtained from primary clarifiers and raw wastewater influent samples were collected and quantified for SARS-CoV-2 RNA. Settled solids and influent samples were processed by participating laboratories using their respective methods and retrospectively paired based on date of collection. SARS-CoV-2 RNA concentrations, on a mass equivalent basis, were higher in settled solids than in influent by approximately three orders of magnitude. Concentrations in matched settled solids and influent were positively and significantly correlated at all five POTWs. RNA concentrations in both settled solids and influent were correlated to COVID-19 incidence rates in the sewersheds and thus representative of disease occurrence; the settled solids methods appeared to produce a comparable relationship between SARS-CoV-2 RNA concentration measurements and incidence rates across all POTWs. Settled solids and influent methods showed comparable sensitivity, N gene detection frequency, and calculated empirical incidence rate lower limits. Analysis of settled solids for SARS-CoV-2 RNA has the advantage of using less sample volume to achieve similar sensitivity to influent methods.

  View details for DOI 10.1039/d1ew00826a

  View details for PubMedID 35433013

  View details for PubMedCentralID PMC8969789

• SARS-CoV-2 RNA is enriched by orders of magnitude in primary settled solids relative to liquid wastewater at publicly owned treatment works ENVIRONMENTAL SCIENCE-WATER RESEARCH & TECHNOLOGY Kim, S., Kennedy, L. C., Wolfe, M. K., Criddle, C. S., Duong, D. H., Topol, A., White, B. J., Kantor, R. S., Nelson, K. L., Steele, J. A., Langlois, K., Griffith, J. F., Zimmer-Faust, A. G., McLellan, S. L., Schussman, M. K., Ammerman, M., Wigginton, K. R., Bakker, K. M., Boehm, A. B. 2022

  View details for DOI 10.1039/d1ew00826a

  View details for Web of Science ID 000755179100001

• p Early Evidence of the SARS-CoV-2 B.1.1.529 (Omicron) Variant in CommunityWastewater - United States, November-December 2021 MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT Kirby, A. E., Welsh, R. M., Marsh, Z. A., Yu, A. T., Vugia, D. J., Boehm, A. B., Wolfe, M. K., White, B. J., Matzinger, S. R., Wheeler, A., Bankers, L., Andresen, K., Salatas, C., Gregory, D. A., Johnson, M. C., Trujillo, M., Kannoly, S., Smyth, D. S., Dennehy, J. J., Sapoval, N., Ensor, K., Treangen, T., Stadler, L. B., Hopkins, L., New York City Dept Environm Protec 2022; 71 (3): 103-105

  View details for DOI 10.1101/2021.07.26.21261142v1

  View details for Web of Science ID 000746445400001

  View details for PubMedID 35051130

  View details for PubMedCentralID PMC8774157

• Respiratory Syncytial Virus (RSV) RNA in Wastewater Settled Solids Reflects RSV Clinical Positivity Rates ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS Hughes, B., Duong, D., White, B. J., Wigginton, K. R., Chan, E. G., Wolfe, M. K., Boehm, A. B. 2022

  View details for DOI 10.1021/acs.estlett.1c00963

  View details for Web of Science ID 000743691100001

• James J. Morgan: Special Tribute Issue ENVIRONMENTAL SCIENCE & TECHNOLOGY Hering, J. G., Hoffmann, M. R., Boehm, A. B., Gardea-Torresdey, J. L. 2021; 55 (21): 14331-14332

  View details for DOI 10.1021/acs.est.1c06418

  View details for Web of Science ID 000714110200001

  View details for PubMedID 34724790

• Viral pathogens in urban stormwater runoff: Occurrence and removal via vegetated biochar-amended biofilters. Water research Graham, K. E., Anderson, C. E., Boehm, A. B. 2021; 207: 117829

  Abstract

  Urban runoff is one of the greatest sources of microbial pollution to surface waters. Biofilters can limit the impact of stormwater runoff on surface water quality by diverting runoff from receiving waters. However, our understanding of how biofilter design choices, including the addition of vegetation and geomedia, may impact the removal of pathogens is lacking. In this study, we characterized viruses (adenovirus, enterovirus, norovirus GII, crAssphage) in San Francisco Bay area urban runoff and assessed the removal of lab-cultured viruses (MS2, adenovirus 2, coxsackievirus B5) from biochar-amended biofilter mesocosms during challenge testing. We quantified viruses using (RT-)qPCR and F+ coliphage plaque assays. We found that all the pathogenic viruses targeted were found at low concentrations (adenovirus: all positive samples were

  View details for DOI 10.1016/j.watres.2021.117829

  View details for PubMedID 34763278

• Modeling Untreated Wastewater Evolution and Swimmer Illness for Four Wastewater Infrastructure Scenarios in the San Diego-Tijuana (US/MX) Border Region. GeoHealth Feddersen, F., Boehm, A. B., Giddings, S. N., Wu, X., Liden, D. 2021; 5 (11): e2021GH000490

  Abstract

  The popular beaches of the San Diego-Tijuana (US/MX) border region are often impacted by untreated wastewater sourced from Mexico-via the Tijuana River Estuary (TJRE) and San Antonio de los Buenos outfall at the Pt. Bandera (SAB/PTB) shoreline, leading to impacted beaches and human illness. The US-Mexico-Canada trade agreement will fund border infrastructure projects reducing untreated wastewater discharges. However, estimating project benefits such as reduced human illness and beach impacts is challenging. We develop a coupled hydrodynamic, norovirus (NoV) pathogen, and swimmer illness risk model with the wastewater sources for the year 2017. The model is used to evaluate the reduction in human illness and beach impacts under baseline conditions and three infrastructure diversion scenarios which (Scenario A) reduce SAB/PTB discharges and moderately reduce TJRE inflows or (Scenarios B, C) strongly reduce TJRE in inflows only. The model estimates shoreline untreated wastewater and NoV concentrations, and the number of NoV ill swimmers at Imperial Beach CA. In the Baseline, the percentage of swimmers becoming ill is 3.8% over 2017, increasing to 4.5% during the tourist season (Memorial to Labor Day) due to south-swell driven SAB/PTB plumes. Overall, Scenario A provides the largest reduction in ill swimmers and beach impacts for the tourist season and full year. The 2017 tourist season TJRE inflows were not representative of those in 2020, yet, Scenario A likely still provides the greatest benefit in other years. This methodology can be applied to other coastal regions with wastewater inputs.

  View details for DOI 10.1029/2021GH000490

  View details for PubMedID 34796313

• The impact of on-premises piped water supply on fecal contamination pathways in rural Zambia NPJ CLEAN WATER Winter, J. C., Darmstadt, G. L., Boehm, A. B., Davis, J. 2021; 4 (1)

  View details for DOI 10.1038/s41545-021-00138-x

  View details for Web of Science ID 000710124200001

• Systematic Review and Meta-Analysis of the Persistence of Enveloped Viruses in Environmental Waters and Wastewater in the Absence of Disinfectants. Environmental science & technology Silverman, A. I., Boehm, A. B. 2021

  Abstract

  Enveloped viruses are characterized by a lipid-containing envelope that encapsulates the virion, and they have been the cause of major outbreaks and pandemics. Some enveloped viruses are excreted in feces and other bodily fluids of infected people and animals, raising the question of their fate in the aquatic environment. Consequently, we conducted a systematic review and meta-analysis of the decay rate constants (k) of enveloped viruses from 12 families (i.e., Coronaviridae, Cystoviridae (specifically Phi6), Filoviridae, Hepadnaviridae, Herpesviridae, Orthomyxoviridae, Paramyxoviridae, Pneumoviridae, Poxviridae, Retroviridae, Rhabdoviridae, Togaviridae) in environmental waters and wastewater to evaluate their decay kinetics and identify the environmental and virus characteristics that influence k. A total of 812 k that met inclusion criteria were identified in the literature, with the number of k for each family ranging from 0 to 560, and the virus family averaged values of k ranging from 0.11 d-1 and 1.85 d-1. Virus type (i.e., genus, species, subspecies, or subtype), method of virus enumeration (i.e., culture-based or (RT-)QPCR), and experimental water matrix type, temperature and sterility were found to have significant effects on k. Additionally, enveloped viruses were found to have statistically significantly greater k than nonenveloped viruses. Multiple linear regression models that allow prediction of log10k as a function of virus type, enumeration method, water temperature, and water type are provided for six virus families that had sufficient data available for model fitting (i.e., Coronaviridae, Phi6, Herpesviridae, Orthomyxoviridae, Rhabdoviridae, Togaviridae). Compiled log10k and multiple regression models can be used to inform management of human and animal waste, operation of water and wastewater facilities, and exposure risks to treatment plant workers and communities living in regions that lack treatment facilities. Given limited data available for some enveloped virus families with a potential water-related transmission route, there is need for additional data collection to aid academic researchers, public health agencies, and water and wastewater professionals involved in outbreak response.

  View details for DOI 10.1021/acs.est.1c03977

  View details for PubMedID 34665598

• Standardizing data reporting in the research community to enhance the utility of open data for SARS-CoV-2 wastewater surveillance. Environmental science : water research & technology McClary-Gutierrez, J. S., Aanderud, Z. T., Al-Faliti, M., Duvallet, C., Gonzalez, R., Guzman, J., Holm, R. H., Jahne, M. A., Kantor, R. S., Katsivelis, P., Kuhn, K. G., Langan, L. M., Mansfeldt, C., McLellan, S. L., Grijalva, L. M., Murnane, K. S., Naughton, C. C., Packman, A. I., Paraskevopoulos, S., Radniecki, T. S., Roman, F. A., Shrestha, A., Stadler, L. B., Steele, J. A., Swalla, B. M., Vikesland, P., Wartell, B., Wilusz, C. J., Wong, J. C., Boehm, A. B., Halden, R. U., Bibby, K., Vela, J. D. 2021; 9

  Abstract

  SARS-CoV-2 RNA detection in wastewater is being rapidly developed and adopted as a public health monitoring tool worldwide. With wastewater surveillance programs being implemented across many different scales and by many different stakeholders, it is critical that data collected and shared are accompanied by an appropriate minimal amount of metainformation to enable meaningful interpretation and use of this new information source and intercomparison across datasets. While some databases are being developed for specific surveillance programs locally, regionally, nationally, and internationally, common globally-adopted data standards have not yet been established within the research community. Establishing such standards will require national and international consensus on what metainformation should accompany SARS-CoV-2 wastewater measurements. To establish a recommendation on minimum information to accompany reporting of SARS-CoV-2 occurrence in wastewater for the research community, the United States National Science Foundation (NSF) Research Coordination Network on Wastewater Surveillance for SARS-CoV-2 hosted a workshop in February 2021 with participants from academia, government agencies, private companies, wastewater utilities, public health laboratories, and research institutes. This report presents the primary two outcomes of the workshop: (i) a recommendation on the set of minimum meta-information that is needed to confidently interpret wastewater SARS-CoV-2 data, and (ii) insights from workshop discussions on how to improve standardization of data reporting.

  View details for DOI 10.1039/d1ew00235j

  View details for PubMedID 34567579

  View details for PubMedCentralID PMC8459677

• High-Frequency, High-Throughput Quantification of SARS-CoV-2 RNA in Wastewater Settled Solids at Eight Publicly Owned Treatment Works in Northern California Shows Strong Association with COVID-19 Incidence. mSystems Wolfe, M. K., Topol, A., Knudson, A., Simpson, A., White, B., Vugia, D. J., Yu, A. T., Li, L., Balliet, M., Stoddard, P., Han, G. S., Wigginton, K. R., Boehm, A. B. 2021: e0082921

  Abstract

  A number of recent retrospective studies have demonstrated that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concentrations in wastewater are associated with coronavirus disease 2019 (COVID-19) cases in the corresponding sewersheds. Implementing high-resolution, prospective efforts across multiple plants depends on sensitive measurements that are representative of COVID-19 cases, scalable for high-throughput analysis, and comparable across laboratories. We conducted a prospective study across eight publicly owned treatment works (POTWs). A focus on SARS-CoV-2 RNA in solids enabled us to scale up our measurements with a commercial lab partner. Samples were collected daily, and results were posted to a website within 24 h. SARS-CoV-2 RNA in daily samples correlated with the incidence of COVID-19 cases in the sewersheds; a 1 log10 increase in SARS-CoV-2 RNA in settled solids corresponds to a 0.58 log10 (4*) increase in sewershed incidence rate. SARS-CoV-2 RNA signals measured with the commercial laboratory partner were comparable across plants and comparable to measurements conducted in a university laboratory when normalized by pepper mild mottle virus (PMMoV) RNA. Results suggest that SARS-CoV-2 RNA should be detectable in settled solids for COVID-19 incidence rates of>1/100,000 (range, 0.8 to 2.3 cases per 100,000). These sensitive, representative, scalable, and comparable methods will be valuable for future efforts to scale up wastewater-based epidemiology. IMPORTANCE Access to reliable, rapid monitoring data is critical to guide response to an infectious disease outbreak. For pathogens that are shed in feces or urine, monitoring wastewater can provide a cost-effective snapshot of transmission in an entire community via a single sample. In order for a method to be useful for ongoing COVID-19 monitoring, it should be sensitive for detection of low concentrations of SARS-CoV-2, representative of incidence rates in the community, scalable to generate data quickly, and comparable across laboratories. This paper presents a method utilizing wastewater solids to meet these goals, producing measurements of SARS-CoV-2 RNA strongly associated with COVID-19 cases in the sewershed of a publicly owned treatment work. Results, provided within 24h, can be used to detect incidence rates as low as approximately 1/100,000 cases and can be normalized for comparison across locations generating data using different methods.

  View details for DOI 10.1128/mSystems.00829-21

  View details for PubMedID 34519528

• Transfer rate of enveloped and non-enveloped viruses between fingerpads and surfaces. Applied and environmental microbiology Anderson, C. E., Boehm, A. B. 2021: AEM0121521

  Abstract

  Fomites can represent a reservoir for pathogens, which may be subsequently transferred from surfaces to skin. In this study we aim to understand how different factors (including virus type, surface type, time since last handwash, and direction of transfer) affect virus transfer rates, defined as the fraction of virus transferred, between fingerpads and fomites. To determine this, 360 transfer events were performed with 20 volunteers using Phi6 (a surrogate for enveloped viruses) and MS2 (a surrogate for non-enveloped viruses), and three clean surfaces (stainless steel, painted wood, and plastic). Considering all transfer events (all surfaces and both transfer directions combined), the mean transfer rates of Phi6 and MS2 were 0.17 and 0.26, respectively. Transfer of MS2 was significantly higher than Phi6 (P<0.05). Surface type was a significant factor that affected the transfer rate of Phi6: Phi6 is more easily transferred to and from stainless steel and plastic than to and from painted wood. Direction of transfer was a significant factor affecting MS2 transfer rates: MS2 is more easily transferred from surfaces to fingerpads than from fingerpads to surfaces. Data from these virus transfer events, and subsequent transfer rate distributions, provide information which can be used to refine quantitative microbial risk assessments. This study provides a large-scale data set of transfer events with a surrogate for enveloped viruses, which extends the reach of the study to the role of fomites in the transmission of human enveloped viruses like influenza and SARS-CoV-2. Importance This study created a large-scale data set for the transfer of enveloped viruses between skin and surfaces. The data set produced by this study provides information on modelling the distribution of enveloped and non-enveloped virus transfer rates, which can aid in the implementation of risk assessment models in the future. Additionally, enveloped and non-enveloped viruses were applied to experimental surfaces in an equivalent matrix to avoid matrix effects, so results between different viral species can be directly compared without confounding effects of different matrices. Our results indicating how virus type, surface type, time since last handwash, and direction of transfer affect virus transfer rates can be used in decision-making processes to lower the risk of viral infection from transmission through fomites.

  View details for DOI 10.1128/AEM.01215-21

  View details for PubMedID 34469200

• SARS-CoV-2 Wastewater Surveillance for Public Health Action EMERGING INFECTIOUS DISEASES McClary-Gutierrez, J. S., Mattioli, M. C., Marcenac, P., Silverman, A., Boehm, A. B., Bibby, K., Balliet, M., de los Reyes, F. L., Gerrity, D., Griffith, J. F., Holden, P. A., Katehis, D., Kester, G., LaCross, N., Lipp, E. K., Meiman, J., Noble, R. T., Brossard, D., McLellan, S. L. 2021; 27 (9): 1-8

  Abstract

  Wastewater surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has garnered extensive public attention during the coronavirus disease pandemic as a proposed complement to existing disease surveillance systems. Over the past year, methods for detection and quantification of SARS-CoV-2 viral RNA in untreated sewage have advanced, and concentrations in wastewater have been shown to correlate with trends in reported cases. Despite the promise of wastewater surveillance, for these measurements to translate into useful public health tools, bridging the communication and knowledge gaps between researchers and public health responders is needed. We describe the key uses, barriers, and applicability of SARS-CoV-2 wastewater surveillance for supporting public health decisions and actions, including establishing ethics consideration for monitoring. Although wastewater surveillance to assess community infections is not a new idea, the coronavirus disease pandemic might be the initiating event to make this emerging public health tool a sustainable nationwide surveillance system, provided that these barriers are addressed.

  View details for DOI 10.3201/eid2709.210753

  View details for Web of Science ID 000757947200001

  View details for PubMedID 34424162

  View details for PubMedCentralID PMC8386792

• Preventing Scientific and Ethical Misuse of Wastewater Surveillance Data. Environmental science & technology Coffman, M. M., Guest, J. S., Wolfe, M. K., Naughton, C. C., Boehm, A. B., Vela, J. D., Carrera, J. S. 2021

  View details for DOI 10.1021/acs.est.1c04325

  View details for PubMedID 34431294

• Effect of storage conditions on SARS-CoV-2 RNA quantificaion in wastewater solids PEERJ Simpson, A., Topol, A., White, B., Wolfe, M. K., Wigginton, K., Boehm, A. B. 2021; 9

  View details for DOI 10.7717/peerj.11933

  View details for Web of Science ID 000683846800007

• The Environmental Microbiology Minimum Information (EMMI) Guidelines: qPCR and dPCR Quality and Reporting for Environmental Microbiology. Environmental science & technology Borchardt, M. A., Boehm, A. B., Salit, M., Spencer, S. K., Wigginton, K. R., Noble, R. T. 2021

  Abstract

  Real-time quantitative polymerase chain reaction (qPCR) and digital PCR (dPCR) methods have revolutionized environmental microbiology, yielding quantitative organism-specific data of nucleic acid targets in the environment. Such data are essential for characterizing interactions and processes of microbial communities, assessing microbial contaminants in the environment (water, air, fomites), and developing interventions (water treatment, surface disinfection, air purification) to curb infectious disease transmission. However, our review of recent qPCR and dPCR literature in our field of health-related environmental microbiology showed that many researchers are not reporting necessary and sufficient controls and methods, which would serve to strengthen their study results and conclusions. Here, we describe the application, utility, and interpretation of the suite of controls needed to make high quality qPCR and dPCR measurements of microorganisms in the environment. Our presentation is organized by the discrete steps and operations typical of this measurement process. We propose systematic terminology to minimize ambiguity and aid comparisons among studies. Example schemes for batching and combining controls for efficient work flow are demonstrated. We describe critical reporting elements for enhancing data credibility, and we provide an element checklist in the Supporting Information. Additionally, we present several key principles in metrology as context for laboratories to devise their own quality assurance and quality control reporting framework. Following the EMMI guidelines will improve comparability and reproducibility among qPCR and dPCR studies in environmental microbiology, better inform engineering and public health actions for preventing disease transmission through environmental pathways, and for the most pressing issues in the discipline, focus the weight of evidence in the direction toward solutions.

  View details for DOI 10.1021/acs.est.1c01767

  View details for PubMedID 34286966

• Standardizing data reporting in the research community to enhance the utility of open data for SARS-CoV-2 wastewater surveillance ENVIRONMENTAL SCIENCE-WATER RESEARCH & TECHNOLOGY McClary-Gutierrez, J. S., Aanderud, Z. T., Al-faliti, M., Duvallet, C., Gonzalez, R., Guzman, J., Holm, R. H., Jahne, M. A., Kantor, R. S., Katsivelis, P., Kuhn, K., Langan, L. M., Mansfeldt, C., McLellan, S. L., Grijalva, L., Murnane, K. S., Naughton, C. C., Packman, A., Paraskevopoulos, S., Radniecki, T. S., Roman, F., Shrestha, A., Stadler, L. B., Steele, J. A., Swalla, B. M., Vikesland, P., Wartell, B., Wilusz, C. J., Wong, J., Boehm, A. B., Halden, R. U., Bibby, K., Vela, J. 2021

  View details for DOI 10.1039/d1ew00235j

  View details for Web of Science ID 000672875100001

• Scaling of SARS-CoV-2 RNA in Settled Solids from Multiple Wastewater Treatment Plants to Compare Incidence Rates of Laboratory-Confirmed COVID-19 in Their Sewersheds ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS Wolfe, M. K., Archana, A., Catoe, D., Coffman, M. M., Dorevich, S., Graham, K. E., Kim, S., Grijalva, L., Roldan-Hernandez, L., Silverman, A., Sinnott-Armstrong, N., Vugia, D. J., Yu, A. T., Zambrana, W., Wigginton, K. R., Boehm, A. B. 2021; 8 (5): 398-404

  View details for DOI 10.1021/acs.estlett.1c00184

  View details for Web of Science ID 000651526300006

• Scaling of SARS-CoV-2 RNA in Settled Solids from Multiple Wastewater Treatment Plants to Compare Incidence Rates of Laboratory-Confirmed COVID-19 in Their Sewersheds. Environmental science & technology letters Wolfe, M. K., Archana, A., Catoe, D., Coffman, M. M., Dorevich, S., Graham, K. E., Kim, S., Grijalva, L. M., Roldan-Hernandez, L., Silverman, A. I., Sinnott-Armstrong, N., Vugia, D. J., Yu, A. T., Zambrana, W., Wigginton, K. R., Boehm, A. B. 2021; 8 (5): 398-404

  Abstract

  Published and unpublished reports show that SARS-CoV-2 RNA in publicly owned treatment work (POTW) wastewater influent and solids is associated with new COVID-19 cases or incidence in associated sewersheds, but methods for comparing data collected from diverse POTWs to infer information about the relative incidence of laboratory-confirmed COVID-19 cases, and scaling to allow such comparisons, have not been previously established. Here, we show that SARS-CoV-2 N1 and N2 concentrations in solids normalized by concentrations of PMMoV RNA in solids can be used to compare incidence of laboratory confirmed new COVID-19 cases across POTWs. Using data collected at seven POTWs along the United States West Coast, Midwest, and East Coast serving ∼3% of the U.S. population (9 million people), we show that a 1 log change in N gene/PMMoV is associated with a 0.24 (range 0.19 to 0.29) log10 change in incidence of laboratory confirmed COVID-19. Scaling of N1 and N2 by PMMoV is consistent, conceptually, with a mass balance model relating SARS-CoV-2 RNA to the number of infected individuals shedding virus in their stool. This information should support the application of wastewater-based epidemiology to inform the response to the COVID-19 pandemic and potentially future viral pandemics.

  View details for DOI 10.1021/acs.estlett.1c00184

  View details for PubMedID 37566351

  View details for PubMedCentralID PMC8056949

• Standardized and optimized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA. medRxiv : the preprint server for health sciences Natarajan, A., Han, A., Zlitni, S., Brooks, E. F., Vance, S. E., Wolfe, M., Singh, U., Jagannathan, P., Pinsky, B. A., Boehm, A., Bhatt, A. S. 2021

  Abstract

  COVID-19 patients shed SARS-CoV-2 viral RNA in their stool, sometimes well after they have cleared their respiratory infection. This feature of the disease may be significant for patient health, epidemiology, and diagnosis. However, to date, methods to preserve stool samples from COVID patients, and to extract and quantify viral RNA concentration have yet to be optimized. We sought to meet this urgent need by developing and benchmarking a standardized protocol for the fecal detection of SARS-CoV-2 RNA. We test three preservative conditions for their ability to yield detectable SARS-CoV-2 RNA: OMNIgene-GUT, Zymo DNA/RNA shield kit, and the most common condition, storage without any preservative. We test these in combination with three extraction kits: the QIAamp Viral RNA Mini Kit, Zymo Quick-RNA Viral Kit, and MagMAX Viral/Pathogen Kit. Finally, we also test the utility of two detection methods, ddPCR and RT-qPCR, for the robust quantification of SARS-CoV-2 viral RNA from stool. We identify that the Zymo DNA/RNA shield collection kit and the QiaAMP viral RNA mini kit yield more detectable RNA than the others, using both ddPCR and RT-qPCR assays. We also demonstrate key features of experimental design including the incorporation of appropriate controls and data analysis, and apply these techniques to effectively extract viral RNA from fecal samples acquired from COVID-19 outpatients enrolled in a clinical trial. Finally, we recommend a comprehensive methodology for future preservation, extraction and detection of RNA from SARS-CoV-2 and other coronaviruses in stool.

  View details for DOI 10.1101/2021.04.10.21255250

  View details for PubMedID 33880485

• Guest Comment: Environmental Transmission and Control of COVID-19 Special Issue ENVIRONMENTAL SCIENCE & TECHNOLOGY Jiang, G., Boehm, A. B., Li, X., Yao, M., Hu, L. 2021; 55 (7): 4081–83

  View details for DOI 10.1021/acs.est.1c01700

  View details for Web of Science ID 000638991400001

  View details for PubMedID 33820416

• A Day at the Beach: Enabling Coastal Water Quality Prediction with High-Frequency Sampling and Data-Driven Models. Environmental science & technology Searcy, R. T., Boehm, A. B. 2021

  Abstract

  To reduce the incidence of recreational waterborne illness, fecal indicator bacteria (FIB) are measured to assess water quality and inform beach management. Recently, predictive FIB models have been used to aid managers in making beach posting and closure decisions. However, those predictive models must be trained using rich historical data sets consisting of FIB and environmental data that span years, and many beaches lack such data sets. Here, we investigate whether water quality data collected during discrete short duration, high-frequency beach sampling events (e.g., samples collected at sub-hourly intervals for 24-48 h) are sufficient to train predictive models that can be used for beach management. We use data collected during six high-frequency sampling events at three California marine beaches and train a total of 126 models using common data-driven techniques. Tide, solar irradiation, water temperature, significant wave height, and offshore wind speed were found to be the most important environmental variables in the models. We validate the predictive performance of models using withheld data. Random forests are consistently the top performing model type. Overall, we find that data-driven models trained using high-frequency FIB and environmental data perform well at predicting water quality and can be used to inform public health decisions at beaches.

  View details for DOI 10.1021/acs.est.0c06742

  View details for PubMedID 33471505

• A Day at the Beach: Enabling Coastal Water Quality Prediction with High-Frequency Sampling and Data-Driven Models Environmental Science & Technology Searcy, R. T., Boehm, A. B. 2021

  View details for DOI 10.1021/acs.est.0c06742

• Effect of storage conditions on SARS-CoV-2 RNA quantification in wastewater solids. PeerJ Simpson, A., Topol, A., White, B. J., Wolfe, M. K., Wigginton, K. R., Boehm, A. B. 2021; 9: e11933

  Abstract

  SARS-CoV-2 RNA in wastewater settled solids is associated with COVID-19 incidence in sewersheds and therefore, there is a strong interest in using these measurements to augment traditional disease surveillance methods. A wastewater surveillance program should provide rapid turn around for sample measurements (ideally within 24 hours), but storage of samples is necessary for a variety of reasons including biobanking. Here we investigate how storage of wastewater solids at 4 °C, -20 °C, and -80 °C affects measured concentrations of SARS-CoV-2 RNA. We find that short term (7 or 8 d) storage of raw solids at 4 °C has little effect on measured concentrations of SARS-CoV-2 RNA, whereas longer term storage at 4 °C (35-122 d) or freezing reduces measurements by 60%, on average. We show that normalizing SARS-CoV-2 RNA concentrations by concentrations of pepper mild mottle virus (PMMoV) RNA, an endogenous wastewater virus, can correct for changes during storage as storage can have a similar effect on PMMoV RNA as on SARS-CoV-2 RNA. The reductions in SARS-CoV-2 RNA in solids during freeze thaws is less than those reported for the same target in liquid influent by several authors.

  View details for DOI 10.7717/peerj.11933

  View details for PubMedID 34447628

  View details for PubMedCentralID PMC8364322

• Standardized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA. Nature communications Natarajan, A., Han, A., Zlitni, S., Brooks, E. F., Vance, S. E., Wolfe, M., Singh, U., Jagannathan, P., Pinsky, B. A., Boehm, A., Bhatt, A. S. 2021; 12 (1): 5753

  Abstract

  Patients with COVID-19 shed SARS-CoV-2 RNA in stool, sometimes well after their respiratory infection has cleared. This may be significant for patient health, epidemiology, and diagnosis. However, methods to preserve stool, and to extract and quantify viral RNA are not standardized. We test the performance of three preservative approaches at yielding detectable SARS-CoV-2 RNA: the OMNIgene-GUT kit, Zymo DNA/RNA shield kit, and the most commonly applied, storage without preservative. We test these in combination with three extraction kits: QIAamp Viral RNA Mini Kit, Zymo Quick-RNA Viral Kit, and MagMAX Viral/Pathogen Kit. We also test the utility of ddPCR and RT-qPCR for the reliable quantification of SARS-CoV-2 RNA from stool. We identify that the Zymo DNA/RNA preservative and the QiaAMP extraction kit yield more detectable RNA than the others, using both ddPCR and RT-qPCR. Taken together, we recommend a comprehensive methodology for preservation, extraction and detection of RNA from SARS-CoV-2 and other coronaviruses in stool.

  View details for DOI 10.1038/s41467-021-25576-6

  View details for PubMedID 34599164

• Sunlight Inactivation of Human Norovirus and Bacteriophage MS2 Using a Genome-Wide PCR-Based Approach and Enzyme Pretreatment. Environmental science & technology Loeb, S. K., Jennings, W. C., Wigginton, K. R., Boehm, A. B. 2021

  Abstract

  Human norovirus (hNoV) is an important etiology of gastrointestinal illness and can be transmitted via ingestion of contaminated water. Currently impractical to culture, hNoV detection is reliant on real-time polymerase chain reaction (RT-PCR)-based methods. This approach cannot distinguish between infective and inactivated viruses because intact regions of the RNA genome can amplify even if the damage is present in other regions of the genome or because intact genetic material is not contained within an infectious virion. Herein, we employ a multiple long-amplicon RT-qPCR extrapolation approach to assay genome-wide damage and an enzymatic pretreatment to study the impact of simulated sunlight on the infectivity of hNoV in clear, sensitizer-free water. Using MS2 coliphage as an internal control, the genome-wide damage extrapolation approach, previously successfully applied for UV-254 inactivation, vastly overestimated sunlight inactivation, suggesting key differences in photoinactivation under different spectral conditions. hNoV genomic RNA was more susceptible to simulated sunlight degradation per base compared to MS2 genomic RNA, while enzymatic pretreatment indicated that hNoV experienced more capsid damage than MS2. This work provides practical and mechanistic insight into the endogenous sunlight inactivation of single-stranded RNA bacteriophage MS2, a widely used surrogate, and hNoV GII.4 Sydney, an important health-relevant virus, in clear sensitizer-free water.

  View details for DOI 10.1021/acs.est.1c01575

  View details for PubMedID 34101449

• Publisher Correction: Standardized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA. Nature communications Natarajan, A., Han, A., Zlitni, S., Brooks, E. F., Vance, S. E., Wolfe, M., Singh, U., Jagannathan, P., Pinsky, B. A., Boehm, A., Bhatt, A. S. 2021; 12 (1): 7100

  View details for DOI 10.1038/s41467-021-27392-4

  View details for PubMedID 34853336

• The Beach Aquifer Microbiome: Research Gaps and Data Needs Frontiers in Environmental Science Archana, A., Francis, C. A., Boehm, A. B. 2021

  View details for DOI 10.3389/fenvs.2021.653568

• SARS-CoV-2 RNA in Wastewater Settled Solids Is Associated with COVID-19 Cases in a Large Urban Sewershed. Environmental science & technology Graham, K. E., Loeb, S. K., Wolfe, M. K., Catoe, D., Sinnott-Armstrong, N., Kim, S., Yamahara, K. M., Sassoubre, L. M., Mendoza Grijalva, L. M., Roldan-Hernandez, L., Langenfeld, K., Wigginton, K. R., Boehm, A. B. 2020

  Abstract

  Wastewater-based epidemiology may be useful for informing public health response to viral diseases like COVID-19 caused by SARS-CoV-2. We quantified SARS-CoV-2 RNA in wastewater influent and primary settled solids in two wastewater treatment plants to inform the preanalytical and analytical approaches and to assess whether influent or solids harbored more viral targets. The primary settled solids samples resulted in higher SARS-CoV-2 detection frequencies than the corresponding influent samples. Likewise, SARS-CoV-2 RNA was more readily detected in solids using one-step digital droplet (dd)RT-PCR than with two-step RT-QPCR and two-step ddRT-PCR, likely owing to reduced inhibition with the one-step ddRT-PCR assay. We subsequently analyzed a longitudinal time series of 89 settled solids samples from a single plant for SARS-CoV-2 RNA as well as coronavirus recovery (bovine coronavirus) and fecal strength (pepper mild mottle virus) controls. SARS-CoV-2 RNA targets N1 and N2 concentrations correlated positively and significantly with COVID-19 clinically confirmed case counts in the sewershed. Together, the results demonstrate that measuring SARS-CoV-2 RNA concentrations in settled solids may be a more sensitive approach than measuring SARS-CoV-2 in influent.

  View details for DOI 10.1021/acs.est.0c06191

  View details for PubMedID 33283515

• Parachute Environmental Science and Engineering. Environmental science & technology Roldan-Hernandez, L., Boehm, A. B., Mihelcic, J. R. 2020; 54 (23): 14773–74

  View details for DOI 10.1021/acs.est.0c07462

  View details for PubMedID 33256416

• CrAssphage for fecal source tracking in Chile: Covariation with norovirus, HF183, and bacterial indicators. Water research X Jennings, W. C., Galvez-Arango, E., Prieto, A. L., Boehm, A. B. 2020; 9: 100071

  Abstract

  Anthropogenic fecal pollution in urban waterbodies can promote the spread of waterborne disease. The objective of this study was to test crAssphage, a novel viral human fecal marker not previously applied for fecal source tracking in Latin America, as a fecal pollution marker in an urban river in Chile. Human fecal markers crAssphage CPQ_064 and Bacteroides HF183, the human pathogen norovirus GII, and culturable fecal indicator bacteria (FIB) were quantified at six locations spanning reaches of the Mapocho River from upstream to downstream of Santiago, as well as in repeated sub-daily frequency samples at two urban locations. Norovirus showed positive correlation trends with crAssphage (tau=0.57, p=0.06) and HF183 (tau=0.64, p=0.03) in river water, but not with E.coli or enterococci. CrAssphage and HF183 concentrations were strongly linearly related (slope=0.97, p<0.001). Chlorinated wastewater effluent was an important source of norovirus GII genes to the Mapocho. Precipitation showed non-significant positive relationships with human and general fecal indicators. Concentrations of crAssphage and HF183 in untreated sewage were 8.35 and 8.07 log10 copy/100ml, respectively. Preliminary specificity testing did not detect crAssphage or HF183 in bird or dog feces, which are predominant non-human fecal sources in the urban Mapocho watershed. This study is the first to test crAssphage for microbial source tracking in Latin America, provides insight into fecal pollution dynamics in a highly engineered natural system, and indicates river reaches where exposure to human fecal pollution may pose a public health risk.

  View details for DOI 10.1016/j.wroa.2020.100071

  View details for PubMedID 33083778

• Systematic Review and Meta-Analysis of the Persistence and Disinfection of Human Coronaviruses and Their Viral Surrogates in Water and Wastewater ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS Silverman, A., Boehm, A. B. 2020; 7 (8): 544–53

  View details for DOI 10.1021/acs.estlett.0c00313

  View details for Web of Science ID 000562137900002

• Biochar-augmented biofilters to improve pollutant removal from stormwater - can they improve receiving water quality? ENVIRONMENTAL SCIENCE-WATER RESEARCH & TECHNOLOGY Boehm, A. B., Bell, C. D., Fitzgerald, N. M., Gallo, E., Higgins, C. P., Hogue, T. S., Luthy, R. G., Portmann, A. C., Ulrich, B. A., Wolfand, J. M. 2020; 6 (6): 1520–37

  View details for DOI 10.1039/d0ew00027b

  View details for Web of Science ID 000540808000001

• Environmental Engineers and Scientists Have Important Roles to Play in Stemming Outbreaks and Pandemics Caused by Enveloped Viruses. Environmental science & technology Wigginton, K. R., Boehm, A. B. 2020

  View details for DOI 10.1021/acs.est.0c01476

  View details for PubMedID 32207922

• Ruminant Fecal Contamination of Drinking Water Introduced Post-Collection in Rural Kenyan Households. International journal of environmental research and public health Hamzah, L., Boehm, A. B., Davis, J., Pickering, A. J., Wolfe, M., Mureithi, M., Harris, A. 2020; 17 (2)

  Abstract

  In sub-Saharan Africa, many families travel to collect water and store it in their homes for daily use, presenting an opportunity for the introduction of fecal contamination. One stored and one source water sample were each collected from 45 households in rural Kenya. All 90 samples were analyzed for fecal indicator bacteria (E. coli and enterococci) and species-specific contamination using molecular microbial source tracking assays. Human (HF183), avian (GFD), and ruminant (BacR) contamination were detected in 52, two, and four samples, respectively. Stored water samples had elevated enterococci concentrations (p < 0.01, Wilcoxon matched pairs test) and more frequent BacR detection (89% versus 27%, p < 0.01, McNemar's exact test) relative to source water samples. fsQCA (fuzzy set qualitative comparative analysis) was conducted on the subset of households with no source water BacR contamination to highlight combinations of factors associated with the introduction of BacR contamination to stored water supplies. Three combinations were identified: (i) ruminants in the compound, safe water extraction methods, and long storage time, (ii) ruminants, unsafe water extraction methods, and no soap at the household handwashing station, and (iii) long storage time and no soap. This suggests that multiple pathways contribute to the transmission of ruminant fecal contamination in this context, which would have been missed if data were analyzed using standard regression techniques.

  View details for DOI 10.3390/ijerph17020608

  View details for PubMedID 31963600

• Environmental DNA reveals seasonal shifts and potential interactions in a marine community. Nature communications Djurhuus, A., Closek, C. J., Kelly, R. P., Pitz, K. J., Michisaki, R. P., Starks, H. A., Walz, K. R., Andruszkiewicz, E. A., Olesin, E., Hubbard, K., Montes, E., Otis, D., Muller-Karger, F. E., Chavez, F. P., Boehm, A. B., Breitbart, M. 2020; 11 (1): 254

  Abstract

  Environmental DNA (eDNA) analysis allowsthe simultaneous examination of organisms across multiple trophic levels and domains of life, providing critical information about the complex biotic interactions related to ecosystem change. Here we used multilocus amplicon sequencing of eDNA to survey biodiversity from an eighteen-month (2015-2016) time-series of seawater samples from Monterey Bay, California. The resulting dataset encompasses 663 taxonomic groups (at Family or higher taxonomic rank) ranging from microorganisms to mammals. We inferred changes in the composition of communities, revealing putative interactions among taxa and identifying correlations between these communities and environmental properties over time. Community network analysis provided evidence of expected predator-prey relationships, trophic linkages, and seasonal shifts across all domains of life. We conclude that eDNA-based analyses can provide detailed information about marine ecosystem dynamics and identify sensitive biological indicators that can suggest ecosystem changes and inform conservation strategies.

  View details for DOI 10.1038/s41467-019-14105-1

  View details for PubMedID 31937756

• Systematic Review and Meta-Analysis of the Persistence and Disinfection of Human Coronaviruses and Their Viral Surrogates in Water and Wastewater. Environmental science & technology letters Silverman, A. I., Boehm, A. B. 2020; 7 (8): 544-553

  Abstract

  A systematic review and meta-analysis was conducted to identify decay rate constants (k) of human coronaviruses and their viral surrogates (i.e., animal coronaviruses and the enveloped bacteriophage Phi6) in water and wastewater and disinfection rates with exposure to free chlorine and germicidal ultraviolet light (UV254). Here, 73 k were identified, with only 12 for human coronaviruses, as opposed to animal coronaviruses or Phi6. In the absence of disinfectants, k increased with temperature. Between 22 and 25 °C, mean k for coronaviruses ranged from 0.19 ± 0.06 d-1 in laboratory buffer (n = 4) to 2.9 ± 0.03 d-1 in sterilized wastewater (n = 3), which are within the ranges observed for Phi6 and nonenveloped viruses. No free chlorine or UV254 disinfection studies for coronaviruses were identified that met the systematic review inclusion criteria, although evidence from the literature suggests that coronaviruses would be inactivated if disinfectant doses recommended for nonenveloped viruses were applied. Three disinfection experiments were identified for Phi6. However, given different genome compositions and virion structures between coronaviruses and Phi6, it is not clear whether Phi6 should be used as a surrogate for evaluating free chlorine or UV254k. Therefore, there is a critical need for additional studies that specifically evaluate disinfection kinetics of coronaviruses in the aqueous environment.

  View details for DOI 10.1021/acs.estlett.0c00313

  View details for PubMedID 37566367

  View details for PubMedCentralID PMC7294895

• Quantitative PCR assays to detect whales, rockfish, and common murre environmental DNA in marine water samples of the Northeastern Pacific. PloS one Andruszkiewicz, E. A., Yamahara, K. M., Closek, C. J., Boehm, A. B. 2020; 15 (12): e0242689

  Abstract

  Monitoring aquatic species by identification of environmental DNA (eDNA) is becoming more common. To obtain quantitative eDNA datasets for individual species, organism-specific quantitative PCR (qPCR) assays are required. Here, we present detailed methodology of qPCR assay design and testing, including in silico, in vitro, and in vivo testing, and comment on the challenges associated with assay design and performance. We use the presented methodology to design assays for three important marine organisms common in the California Current Ecosystem (CCE): humpback whale (Megaptera novaeangliae), shortbelly rockfish (Sebastes jordani), and common murre (Uria aalge). All three assays have excellent sensitivity and high efficiencies ranging from 92% to 99%. However, specificities of the assays varied from species-specific in the case of common murre, genus-specific for the shortbelly rockfish assay, and broadly whale-specific for the humpback whale assay, which cross-amplified with other two other whale species, including one in a different family. All assays detected their associated targets in complex environmental water samples.

  View details for DOI 10.1371/journal.pone.0242689

  View details for PubMedID 33264323

• Application of molecular source tracking and mass balance approach to identify potential sources of fecal indicator bacteria in a tropical river. PloS one Yamahara, K. M., Keymer, D. P., Layton, B. A., Walters, S. P., Thompson, R. S., Rosener, M. n., Boehm, A. B. 2020; 15 (4): e0232054

  Abstract

  Microbial source tracking and a mass balance approach were used to identify sources of fecal indicator bacteria (FIB) in the Hanalei River, Kaua'i, Hawai'i. Historically, concentrations enterococci and Clostridium perfringens were significantly higher during storm flows compared to non-storm flows in the Hanalei River, and correlated to total suspended solids in the river. During targeted dry weather studies, the Hanalei River bed sediments and streambank soils were documented to harbor E. coli, enterococci, and the human- and pig-specific fecal markers in Bacteroidales, suggesting that sediments and soils may be potential sources of these microorganisms to the Hanalei river. The human-specific marker in Bacteroidales was four times as likely to be detected in sediment and soil samples as in water samples. Furthermore, the occurrence of host-specific source tracking markers is indicative that a portion of FIB present in the Hanalei River are of fecal origin. A mass balance approach was used to explore causes of observed FIB loadings and losses along different reaches of the river. Resuspension or deposition of FIB-laden river sediments cannot account for changes in E. coli and enterococci concentrations along the river during dry weather. Additionally, losses due to bacterial inactivation were insignificant. Groundwater and ditches draining agricultural and urban lands were shown to provide sufficient FIB fluxes to account for the observed loads along some river reaches. The presence of the human-specific Bacteroidales marker in the river water, sediments and adjacent soils, as well as the presence of the human enterovirus marker in the water, suggests that there is widespread human fecal contamination in the Hanalei River that is likely a result of nearby wastewater disposal systems.

  View details for DOI 10.1371/journal.pone.0232054

  View details for PubMedID 32352994

• What Environmental Factors Influence the Concentration of Fecal Indicator Bacteria in Groundwater? Insights from Explanatory Modeling in Uganda and Bangladesh. Environmental science & technology Poulin, C. n., Peletz, R. n., Ercumen, A. n., Pickering, A. J., Marshall, K. n., Boehm, A. B., Khush, R. n., Delaire, C. n. 2020

  Abstract

  Information about microbial water quality is critical for managing water safety and protecting public health. In low-income countries, monitoring all drinking water supplies is impractical because financial resources and capacity are insufficient. Data sets derived from satellite imagery, census, and hydrological models provide an opportunity to examine relationships between a suite of environmental risk factors and microbial water quality over large geographical scales. We investigated the relationships between groundwater fecal contamination and different environmental parameters in Uganda and Bangladesh. In Uganda, groundwater contamination was associated with high population density (p < 0.001; OR = 1.27), high cropland coverage (p < 0.001; OR = 1.47), high average monthly precipitation (p < 0.001; OR = 1.14), and high surface runoff (p < 0.001; OR = 1.37), while low groundwater contamination was more likely in areas further from cities (p < 0.001; OR = 0.66) and with higher forest coverage (p < 0.001; OR = 0.70). In Bangladesh, contamination was associated with higher weekly precipitation (p < 0.001; OR = 1.44) and higher livestock density (p = 0.05; OR = 1.11), while low contamination was associated with low forest coverage (p < 0.001; OR = 1.23) and high cropland coverage (p < 0.001; OR = 0.80). We developed a groundwater contamination index for each country to help decision-makers identify areas where groundwater is most prone to fecal contamination and prioritize monitoring activities. Our approach demonstrates how to harness satellite-derived data to guide water safety management.

  View details for DOI 10.1021/acs.est.0c02567

  View details for PubMedID 32975935

• Participatory science for coastal water quality: Freshwater plume mapping and volunteer retention in a randomized informational intervention Environmental Science: Processes & Impacts Jennings, W. C., et al 2020

  View details for DOI 10.1039/C9EM00571D

• Wastewater-Based Epidemiology: Global Collaborative to Maximize Contributions in the Fight Against COVID-19. Environmental science & technology Bivins, A. n., North, D. n., Ahmad, A. n., Ahmed, W. n., Alm, E. n., Been, F. n., Bhattacharya, P. n., Bijlsma, L. n., Boehm, A. B., Brown, J. n., Buttiglieri, G. n., Calabro, V. n., Carducci, A. n., Castiglioni, S. n., Cetecioglu Gurol, Z. n., Chakraborty, S. n., Costa, F. n., Curcio, S. n., de Los Reyes, F. L., Delgado Vela, J. n., Farkas, K. n., Fernandez-Casi, X. n., Gerba, C. n., Gerrity, D. n., Girones, R. n., Gonzalez, R. n., Haramoto, E. n., Harris, A. n., Holden, P. A., Islam, M. T., Jones, D. L., Kasprzyk-Hordern, B. n., Kitajima, M. n., Kotlarz, N. n., Kumar, M. n., Kuroda, K. n., La Rosa, G. n., Malpei, F. n., Mautus, M. n., McLellan, S. L., Medema, G. n., Meschke, J. S., Mueller, J. n., Newton, R. J., Nilsson, D. n., Noble, R. T., van Nuijs, A. n., Peccia, J. n., Perkins, T. A., Pickering, A. J., Rose, J. n., Sanchez, G. n., Smith, A. n., Stadler, L. n., Stauber, C. n., Thomas, K. n., van der Voorn, T. n., Wigginton, K. n., Zhu, K. n., Bibby, K. n. 2020

  View details for DOI 10.1021/acs.est.0c02388

  View details for PubMedID 32530639

• Contamination Scenario Matters when Using Viral and Bacterial Human-Associated Genetic Markers as Indicators of a Health Risk in Untreated Sewage-Impacted Recreational Waters. Environmental science & technology Schoen, M. E., Boehm, A. B., Soller, J. n., Shanks, O. C. 2020

  Abstract

  Fecal pollution at beaches can pose a health risk to recreators. Quantitative microbial risk assessment (QMRA) is a tool to evaluate the use of candidate fecal indicators to signify a health risk from enteric pathogens in sewage-impacted waters. We extend the QMRA approach to model mixtures of sewage at different ages using genetic marker concentrations for human-associated crAssphage, Bacteroides spp., and polyomavirus in sewage samples from 49 wastewater facilities across the contiguous United States. Risk-based threshold (RBT) estimates varied across different mixture and sewage age scenarios. Fresh sewage RBT estimates were not always protective when aged sewage was present, and aged sewage RBT estimates often fell below the marker lower limit of quantification. Conservative RBT estimates of 9.3 × 102 and 9.1 × 103 (copies/100 mL) for HF183/BacR287 and CPQ_056, respectively, were predicted when fresh sewage was greater (by volume) than aged at the time of measurement. Conversely, genetic markers may not be effective indicators when aged sewage contributes the majority of pathogens, relative to fresh contamination, but minimal marker levels. Results highlight the utility of QMRA that incorporates pollutant age and mixture scenarios, the potential advantages of a crAssphage fecal indicator, and the potential influence of site-specific factors on estimating RBT values.

  View details for DOI 10.1021/acs.est.0c02189

  View details for PubMedID 32969642

• Marine Vertebrate Biodiversity and Distribution Within the Central California Current Using Environmental DNA (eDNA) Metabarcoding and Ecosystem Surveys FRONTIERS IN MARINE SCIENCE Closek, C. J., Santora, J. A., Starks, H. A., Schroeder, I. D., Andruszkiewicz, E. A., Sakuma, K. M., Bograd, S. J., Hazenv, E. L., Field, J. C., Boehm, A. B. 2019; 6

  View details for DOI 10.3389/fmars.2019.00732

  View details for Web of Science ID 000502974200001

• Systematic review and meta-analysis of decay rates of waterborne mammalian viruses and coliphages in surface waters WATER RESEARCH Boehm, A. B., Silverman, A. I., Schriewer, A., Goodwin, K. 2019; 164

  View details for DOI 10.1016/j.watres.2019.144898

  View details for Web of Science ID 000484645800029

• Risk-based water quality thresholds for coliphages in surface waters: effect of temperature and contamination aging. Environmental science. Processes & impacts Boehm, A. B. 2019

  Abstract

  Coliphages, viruses that infect Escherichia coli, have been used for decades to assess surface water quality yet there is no guideline for interpreting their concentrations. The present study uses a quantitative microbial risk assessment (QMRA) framework to derive risk-based surface water quality thresholds for somatic and F+ or male-specific coliphages. The risk-based threshold is the concentration at which the risk of gastro-intestinal illness is simulated to be 32/1000. The framework specifically investigates a simplified hazard scenario where recreational swimmers come into contact with water contaminated with untreated sewage containing coliphages and enteric pathogens. The framework considers exposure to sewage of diverse ages and thus accounts for the decay of coliphages and pathogens over time. As decay rate constants depend on temperature, the model considers the effect of temperature on the risk-based threshold. When exposure to fresh, unaged sewage contamination occurs, the risk-based water quality threshold for somatic and F+ coliphages is 60 PFU per 100 mL and 30 PFU per 100 mL, respectively, and temperature independent. The risk-based threshold decreases as the contamination ages because, on average, coliphages decay more quickly than norovirus, the pathogen that contributes the most to risk. The decrease in the risk-based threshold with contaminant age is equal to the difference in the first order decay rate constants of coliphages and norovirus. Since coliphage decay rate constants are larger at 25 °C than at 15 °C, and norovirus decay rate constants are a weak function of temperature, risk-based thresholds decrease more quickly with age at 25 °C than at 15 °C. For the common case where the age of contamination is unknown, the risk-based threshold for both coliphages is between 1 PFU per 100 mL and 10 PFU per 100 mL, depending on model assumptions. Future work can apply this QMRA framework for identifying risk-based thresholds for coliphages from different hazards (treated wastewater or animal feces) or from mixtures of contamination of different ages and sources.

  View details for DOI 10.1039/c9em00376b

  View details for PubMedID 31612888

• Biochar-augmented biofilters (BIOCHARge) to improve pollutant removal from stormwater: Can they improve receiving water quality? Boehm, A., Luthy, R., Wolfand, J., Higgins, C., Hogue, T., Fitzgerald, N., Kranner, B., Eisenstein, W., Ulrich, B. AMER CHEMICAL SOC. 2019

  View details for Web of Science ID 000525061500790

• Modeling Environmental DNA Transport in the Coastal Ocean Using Lagrangian Particle Tracking FRONTIERS IN MARINE SCIENCE Andruszkiewicz, E. A., Koseff, J. R., Fringer, O. B., Ouellette, N. T., Lowe, A. B., Edwards, C. A., Boehm, A. B. 2019; 6

  View details for DOI 10.3389/fmars.2019.00477

  View details for Web of Science ID 000479073400001

• Systematic review and meta-analysis of decay rates of waterborne mammalian viruses and coliphages in surface waters. Water research Boehm, A. B., Silverman, A. I., Schriewer, A., Goodwin, K. 2019; 164: 114898

  Abstract

  Surface waters are essential natural resources. They are also receiving waters for a variety of anthropogenic waste streams that carry a myriad of pollutants including pathogens. Watershed and fate and transport models can help inform the spatial and temporal extent of microbial pollution from point and non-point sources and thus provide useful information for managing surface waters. Viruses are particularly important water-related pathogens because they often have a low infectious dose, which means that ingestion of even a small volume of water containing a low concentration of virions has the potential to cause disease. We conducted a systematic review of the literature, following best practices, to gather decay rate constants (k) of mammalian waterborne viruses (enteroviruses, adenoviruses, noroviruses, astroviruses, rotaviruses, and hepatitis A viruses) and coliphages in raw surface waters to aid in the parameterization of virus fate and transport models. We identified 562 k values from the literature, with the largest number identified for enteroviruses and coliphages and the smallest for astrovirus, hepatitis A virus, and norovirus. Average k values for each virus varied from 0.07 to 0.9 per day, in order from smallest to largest: Norwalk virus (i.e., noroviruses) < Human astrovirus < Mastadenovirus (i.e., adenoviruses) < Hepatovirus A (i.e., hepatitis A viruses) < Rotavirus A < coliphages < Enterovirus. A meta-analysis investigated how k varied among viruses for experiments conducted with different virus serotypes or species at different temperatures, salinities, and sunlight exposures, and for experiments that enumerated viruses using different methodologies. Virus species or serotype did not affect k among decay experiments. k values were generally larger for experiments conducted at higher temperatures, in sunlight, and in estuarine waters, and enumerated using culture methods. k values were statistically different between virus types with Norwalk virus, Hepatovirus A, and Mastadenovirus having smaller k values than other viruses, controlling for experimental condition and enumeration method. While F+ coliphage k values were similar to those of Enterovirus, Human astrovirus, and Rotavirus A, they were different from those of the other mammalian viruses. This compilation of coliphage and mammalian virus k values provides essential information for researchers and risk assessors who model virus fate and transport in surface waters and identifies avenues for future research to fill knowledge gaps.

  View details for DOI 10.1016/j.watres.2019.114898

  View details for PubMedID 31404902

• Impacts of a changing earth on microbial dynamics and human health risks in the continuum between beach water and sand. Water research Weiskerger, C. J., Brandao, J., Ahmed, W., Aslan, A., Avolio, L., Badgley, B. D., Boehm, A. B., Edge, T. A., Fleisher, J. M., Heaney, C. D., Jordao, L., Kinzelman, J. L., Klaus, J. S., Kleinheinz, G. T., Merilainen, P., Nshimyimana, J. P., Phanikumar, M. S., Piggot, A. M., Pitkanen, T., Robinson, C., Sadowsky, M. J., Staley, C., Staley, Z. R., Symonds, E. M., Vogel, L. J., Yamahara, K. M., Whitman, R. L., Solo-Gabriele, H. M., Harwood, V. J. 2019; 162: 456–70

  Abstract

  Although infectious disease risk from recreational exposure to waterborne pathogens has been an active area of research for decades, beach sand is a relatively unexplored habitat for the persistence of pathogens and fecal indicator bacteria (FIB). Beach sand, biofilms, and water all present unique advantages and challenges to pathogen introduction, growth, and persistence. These dynamics are further complicated by continuous exchange between sand and water habitats. Models of FIB and pathogen fate and transport at beaches can help predict the risk of infectious disease from beach use, but knowledge gaps with respect to decay and growth rates of pathogens in beach habitats impede robust modeling. Climatic variability adds further complexity to predictive modeling because extreme weather events, warming water, and sea level change may increase human exposure to waterborne pathogens and alter relationships between FIB and pathogens. In addition, population growth and urbanization will exacerbate contamination events and increase the potential for human exposure. The cumulative effects of anthropogenic changes will alter microbial population dynamics in beach habitats and the assumptions and relationships used in quantitative microbial risk assessment (QMRA) and process-based models. Here, we review our current understanding of microbial populations and transport dynamics across the sand-water continuum at beaches, how these dynamics can be modeled, and how global change factors (e.g., climate and land use) should be integrated into more accurate beachscape-based models.

  View details for DOI 10.1016/j.watres.2019.07.006

  View details for PubMedID 31301475

• Correction for Pitol et al., "Transfer of Enteric Viruses Adenovirus and Coxsackievirus and Bacteriophage MS2 from Liquid to Human Skin". Applied and environmental microbiology Pitol, A. K., Bischel, H. N., Boehm, A. B., Kohn, T., Julian, T. R. 2019; 85 (11)

  View details for DOI 10.1128/AEM.00721-19

  View details for PubMedID 31097422

• Comparison of analytical techniques to explain variability in stored drinking water quality and microbial hand contamination of female caregivers in Tanzania ENVIRONMENTAL SCIENCE-PROCESSES & IMPACTS Harris, A. R., Pickering, A. J., Boehm, A. B., Mrisho, M., Davis, J. 2019; 21 (5): 893–903

  View details for DOI 10.1039/c8em00460a

  View details for Web of Science ID 000468787800010

• CHARACTERIZING ANTIBIOTIC RESISTOMES IN HUMANS AND DOMESTIC ANIMALS FROM RURAL AND URBAN BANGLADESH Swarthout, J., Fuhrmeister, E. R., Harris, A. R., Gurley, E. S., Satter, S. M., Boehm, A. B., Pickering, A. J. AMER SOC TROP MED & HYGIENE. 2019: 574

  View details for Web of Science ID 000507364504575

• Predictors of Enteric Pathogens in the Domestic Environment from Human and Animal Sources in Rural Bangladesh. Environmental science & technology Fuhrmeister, E. R., Ercumen, A. n., Pickering, A. J., Jeanis, K. M., Ahmed, M. n., Brown, S. n., Arnold, B. F., Hubbard, A. E., Alam, M. n., Sen, D. n., Islam, S. n., Kabir, M. H., Kwong, L. H., Islam, M. n., Unicomb, L. n., Rahman, M. n., Boehm, A. B., Luby, S. P., Colford, J. M., Nelson, K. L. 2019

  Abstract

  Fecal indicator organisms are measured to indicate the presence of fecal pollution, yet the association between indicators and pathogens varies by context. The goal of this study was to empirically evaluate the relationships between indicator Escherichia coli, microbial source tracking markers, select enteric pathogen genes, and potential sources of enteric pathogens in 600 rural Bangladeshi households. We measured indicators and pathogen genes in stored drinking water, soil, and on mother and child hands. Additionally, survey and observational data on sanitation and domestic hygiene practices were collected. Log10 concentrations of indicator E. coli were positively associated with the prevalence of pathogenic E. coli genes in all sample types. Given the current need to rely on indicators to assess fecal contamination in the field, it is significant that in this study context indicator E. coli concentrations, measured by IDEXX Colilert-18, provided quantitative information on the presence of pathogenic E. coli in different sample types. There were no significant associations between the human fecal marker (HumM2) and human-specific pathogens in any environmental sample type. There was an increase in the prevalence of Giardia lamblia genes, any E. coli virulence gene, and the specific E. coli virulence genes stx1/2 with every log10 increase in the concentration of the animal fecal marker (BacCow) on mothers' hands. Thus, domestic animals were important contributors to enteric pathogens in these households.

  View details for DOI 10.1021/acs.est.8b07192

  View details for PubMedID 31356066

• Fecal indicator bacteria and virus removal in stormwater biofilters: Effects of biochar, media saturation, and field conditioning. PloS one Kranner, B. P., Afrooz, A. R., Fitzgerald, N. J., Boehm, A. B. 2019; 14 (9): e0222719

  Abstract

  Stormwater biofilters are used to attenuate the flow and volume of runoff and reduce pollutant loading to aquatic systems. However, the capacity of biofilters to remove microbial contaminants remains inadequate. While biochar has demonstrated promise as an amendment to improve microbial removal in laboratory-scale biofilters, it is uncertain if the results are generalizable to the field. To assess biochar performance in a simulated field setting, sand and biochar-amended sand biofilters were periodically dosed with natural stormwater over a 61-week conditioning phase. Impact of media saturation was assessed by maintaining biofilters with and without a saturated zone. Biochar-amended biofilters demonstrated improved Escherichia coli removal over sand biofilters during the first 31 weeks of conditioning though media type did not impact E. coli removal during the last 30 weeks of conditioning. Presence of a saturated zone was not a significant factor influencing E. coli removal across the entire conditioning phase. Following conditioning, biofilters underwent challenge tests using stormwater spiked with wastewater to assess their capacity to remove wastewater-derived E. coli, enterococci, and male-specific (F+) coliphage. In challenge tests, biochar-amended biofilters demonstrated enhanced removal of all fecal indicators relative to sand biofilters. Additionally, saturated biofilters demonstrated greater removal of fecal indicators than unsaturated biofilters for both media types. Discrepant conclusions from the conditioning phase and challenge tests may be due to variable influent chemistry, dissimilar transport of E. coli indigenous to stormwater and those indigenous to wastewater, and differences in E. coli removal mechanisms between tests. Mobilization tests conducted following challenge tests showed minimal (<2.5%) observable mobilization of fecal indicators, regardless of media type and presence of a saturated zone. While our results emphasize the challenge of translating biochar's performance from the laboratory to the field, findings of this study inform biofilter design to remove microbial contaminants from urban stormwater.

  View details for DOI 10.1371/journal.pone.0222719

  View details for PubMedID 31553761

• Photoinactivation of uncultured, indigenous enterococci ENVIRONMENTAL SCIENCE-PROCESSES & IMPACTS McClary, J. S., Ramos, N. A., Boehm, A. B. 2019; 21 (1): 104–12

  View details for DOI 10.1039/c8em00443a

  View details for Web of Science ID 000457371100008

• Comparison of analytical techniques to explain variability in stored drinking water quality and microbial hand contamination of female caregivers in Tanzania. Environmental science. Processes & impacts Harris, A. R., Pickering, A. J., Boehm, A. B., Mrisho, M. n., Davis, J. n. 2019

  Abstract

  Exposure to fecal contamination continues to be a major public health concern for low-income households in sub-Saharan Africa. Drinking water and hands are known transmission routes for pathogens in household environments. In an effort to identify explanatory variables of water and hand contamination, a variety of analytical approaches have been employed that model variation in E. coli contamination as a function of behaviors and household characteristics. Using data collected from 1217 households in Bagamoyo, Tanzania, this investigation compares the explanatory variables identified in the three different modeling methods to explain hand and water contamination: ordinary least squares regression, logistic regression, and classification tree. Although the modeling approaches varied, there were some similarities in the results, with certain explanatory variables being consistently identified as being related to hand and water contamination (e.g., water source type for the water models and activity prior to sampling for the hand models). At the same time, there were also marked differences across the models. In sum, these results suggest there are benefits to using multiple analysis methods to assess relationships in complex systems. The models were also characterized by low explanatory power, suggesting that variation in hand and water contamination is difficult to capture when analyzing one-time water and hand rinse samples. For improved model performance, future studies could explore modeling of repeat measures of water quality and hand contamination.

  View details for PubMedID 31017132

• Photoinactivation of uncultured, indigenous enterococci. Environmental science. Processes & impacts McClary, J. S., Ramos, N. A., Boehm, A. B. 2018

  Abstract

  Enterococci are used to monitor recreational water quality worldwide, so understanding their fate and transport in the environment is essential to the protection of human health. As such, researchers have documented enterococci inactivation under various exposure conditions and in diverse water matrices. However, the majority of studies have been performed using lab-cultured bacteria, which are distinct from indigenous, uncultured bacteria found in the environment. Here we investigate the photoinactivation of indigenous, uncultured enterococci from a range of sources, including wastewater treatment plants (WWTPs), marine beaches, urban streams, and a wastewater-influenced pond. We concentrated indigenous enterococci from their sources using filtration and centrifugation, placed them in a clear buffer solution, and then exposed them to simulated sunlight to measure their photoinactivation rates. First order decay rate constants (k) of indigenous, uncultured enterococci spanned an order of magnitude, from 0.3 to 2.3 m2 kJUVB-1. k values of indigenous enterococci from WWTPs tended to be larger than those from surface waters. The k value of lab-cultured Enterococcus faecalis was larger than those of indigenous, uncultured enterococci from most sources. Negative associations between the fraction of pigmented enterococci and sunlight susceptibility were observed. This work suggests that caution should be taken when extending results on bacterial photoinactivation obtained using lab-cultured bacteria to environmental bacteria, and that enterococci pigmentation may be a useful metric for estimating photoinactivation rate constants.

  View details for PubMedID 30525134

• Role of microbial cell properties on bacterial pathogen and coliphage removal in biochar-modified stormwater biofilters ENVIRONMENTAL SCIENCE-WATER RESEARCH & TECHNOLOGY Afrooz, A., Pitol, A. K., Kitt, D., Boehm, A. B. 2018; 4 (12): 2160–69

  View details for DOI 10.1039/c8ew00297e

  View details for Web of Science ID 000451072500025

• Transfer of Enteric Viruses Adenovirus and Coxsackievirus and Bacteriophage MS2 from Liquid to Human Skin APPLIED AND ENVIRONMENTAL MICROBIOLOGY Pitol, A. K., Bischel, H. N., Boehm, A. B., Kohn, T., Julian, T. R. 2018; 84 (22)

  Abstract

  Indirect exposure to waterborne viruses increases the risk of infection, especially among children with frequent hand-to-mouth contacts. Here, we quantified the transfer of one bacteriophage (MS2) and two enteric viruses (adenovirus and coxsackievirus) from liquid to skin. MS2, a commonly used enteric virus surrogate, was used to compare virus transfer rates in a volunteer trial to those obtained using human cadaver skin and synthetic skin. MS2 transfer to volunteer skin was similar to transfer to cadaver skin but significantly different from transfer to synthetic skin. The transfer of MS2, adenovirus, and coxsackievirus to cadaver skin was modeled using measurements for viruses attaching to the skin (adsorbed) and viruses in liquid residual on skin (unadsorbed). We find virus transfer per surface area is a function of the concentration of virus in the liquid and the film thickness of liquid retained on the skin and is estimable using a linear model. Notably, the amount of MS2 adsorbed on the skin was on average 5 times higher than the amount of adenovirus and 4 times higher than the amount of coxsackievirus. Quantification of pathogenic virus retention to skin would thus be overestimated using MS2 adsorption data. This study provides models of virus transfer useful for risk assessments of water-related activities, demonstrates significant differences in the transfer of pathogenic virus and MS2, and suggests cadaver skin as an alternative testing system for studying interactions between viruses and skin.IMPORTANCE Enteric viruses (viruses that infect the gastrointestinal tract) are responsible for most water-transmitted diseases. They are shed in high concentrations in the feces of infected individuals, persist for an extended period of time in water, and are highly infective. Exposure to contaminated water directly (through ingestion) or indirectly (for example, through hand-water contacts followed by hand-to-mouth contacts) increases the risk of virus transmission. The work described herein provides a quantitative model for estimating human-pathogenic virus retention on skin following contact with contaminated water. The work will be important in refining the contribution of indirect transmission of virus to risks associated with water-related activities.

  View details for PubMedID 30217840

• Implementation of an automated beach water quality nowcast system at ten California oceanic beaches JOURNAL OF ENVIRONMENTAL MANAGEMENT Searcy, R. T., Taggart, M., Gold, M., Boehm, A. B. 2018; 223: 633–43

  Abstract

  Fecal indicator bacteria like Escherichia coli and entercococci are monitored at beaches around the world to reduce incidence of recreational waterborne illness. Measurements are usually made weekly, but FIB concentrations can exhibit extreme variability, fluctuating at shorter periods. The result is that water quality has likely changed by the time data are provided to beachgoers. Here, we present an automated water quality prediction system (called the nowcast system) that is capable of providing daily predictions of water quality for numerous beaches. We created nowcast models for 10 California beaches using weather, oceanographic, and other environmental variables as input to tuned regression models to predict if FIB concentrations were above single sample water quality standards. Rainfall was used as a variable in nearly every model. The models were calibrated and validated using historical data. Subsequently, models were implemented during the 2017 swim season in collaboration with local beach managers. During the 2017 swim season, the median sensitivity of the nowcast models was 0.5 compared to 0 for the current method of using day-to-week old measurements to make beach posting decisions. Model specificity was also high (median of 0.87). During the implementation phase, nowcast models provided an average of 140 additional days per beach of updated water quality information to managers when water quality measurements were not made. The work presented herein emphasizes that a one-size-fits all approach to nowcast modeling, even when beaches are in close proximity, is infeasible. Flexibility in modeling approaches and adaptive responses to modeling and data challenges are required when implementing nowcast models for beach management.

  View details for PubMedID 29975890

• Can We Swim Yet? Systematic Review, Meta-Analysis, and Risk Assessment of Aging Sewage in Surface Waters ENVIRONMENTAL SCIENCE & TECHNOLOGY Boehm, A. B., Graham, K. E., Jennings, W. C. 2018; 52 (17): 9634–45

  View details for DOI 10.1021/acs.est.8b01948

  View details for Web of Science ID 000444061100010

• Can We Swim Yet? Systematic Review, Meta-Analysis, and Risk Assessment of Aging Sewage in Surface Waters. Environmental science & technology Boehm, A. B., Graham, K. E., Jennings, W. C. 2018

  Abstract

  This study investigated the risk of gastrointestinal illness associated with swimming in surface waters with aged sewage contamination. First, a systematic review compiled 333 first order decay rate constants ( k) for human norovirus and its surrogates feline calicivirus and murine norovirus, Salmonella, Campylobacter, Escherichia coli O157:H7, Giardia, and Cryptosporidium, and human-associated indicators in surface water. A meta-analysis investigated effects of sunlight, temperature, and water matrix on k. There was a relatively large number of k for bacterial pathogens and some human-associated indicators ( n > 40), fewer for protozoans ( n = 14-22), and few for human norovirus and its Caliciviridae surrogates ( n = 2-4). Average k ranked: Campylobacter > human-associated markers > Salmonella> E. coli O157:H7 > norovirus and its surrogates > Giardia > Cryptosporidium. Compiled k values were used in a quantitative microbial risk assessment (QMRA) to simulate gastrointestinal illness risk associated with swimming in water with aged sewage contamination. The QMRA used human-associated fecal indicator HF183 as an index for the amount of sewage present and thereby provided insight into how risk relates to HF183 concentrations in surface water. Because exposure to norovirus contributed the majority of risk, and HF183 k is greater than norovirus k, the risk associated with exposure to a fixed HF183 concentration increases with the age of contamination. Swimmer exposure to sewage after it has aged 3 days results in median risks less than 30/1000. A risk-based water quality threshold for HF183 in surface waters that takes into account uncertainty in contamination age is derived to be 4100 copies/100 mL.

  View details for PubMedID 30080397

• Sunlight-mediated inactivation of health-relevant microorganisms in water: a review of mechanisms and modeling approaches ENVIRONMENTAL SCIENCE-PROCESSES & IMPACTS Nelson, K. L., Boehm, A. B., Davies-Colley, R. J., Dodd, M. C., Kohn, T., Linden, K. G., Liu, Y., Maraccini, P. A., McNeill, K., Mitch, W. A., Nguyen, T. H., Parker, K. M., Rodriguez, R. A., Sassoubre, L. M., Silverman, A. I., Wigginton, K. R., Zepp, R. G. 2018; 20 (8): 1089–1122

  Abstract

  Health-relevant microorganisms present in natural surface waters and engineered treatment systems that are exposed to sunlight can be inactivated by a complex set of interacting mechanisms. The net impact of sunlight depends on the solar spectral irradiance, the susceptibility of the specific microorganism to each mechanism, and the water quality; inactivation rates can vary by orders of magnitude depending on the organism and environmental conditions. Natural organic matter (NOM) has a large influence, as it can attenuate radiation and thus decrease inactivation by endogenous mechanisms. Simultaneously NOM sensitizes the formation of reactive intermediates that can damage microorganisms via exogenous mechanisms. To accurately predict inactivation and design engineered systems that enhance solar inactivation, it is necessary to model these processes, although some details are not yet sufficiently well understood. In this critical review, we summarize the photo-physics, -chemistry, and -biology that underpin sunlight-mediated inactivation, as well as the targets of damage and cellular responses to sunlight exposure. Viruses that are not susceptible to exogenous inactivation are only inactivated if UVB wavelengths (280-320 nm) are present, such as in very clear, open waters or in containers that are transparent to UVB. Bacteria are susceptible to slightly longer wavelengths. Some viruses and bacteria (especially Gram-positive) are susceptible to exogenous inactivation, which can be initiated by visible as well as UV wavelengths. We review approaches to model sunlight-mediated inactivation and illustrate how the environmental conditions can dramatically shift the inactivation rate of organisms. The implications of this mechanistic understanding of solar inactivation are discussed for a range of applications, including recreational water quality, natural treatment systems, solar disinfection of drinking water (SODIS), and enhanced inactivation via the use of sensitizers and photocatalysts. Finally, priorities for future research are identified that will further our understanding of the key role that sunlight disinfection plays in natural systems and the potential to enhance this process in engineered systems.

  View details for DOI 10.1039/c8em00047f

  View details for Web of Science ID 000441765000001

  View details for PubMedID 30047962

• Sewage loading and microbial risk in urban waters of the Great Lakes ELEMENTA-SCIENCE OF THE ANTHROPOCENE McLellan, S. L., Sauer, E. P., Corsi, S. R., Bootsma, M. J., Boehm, A. B., Spencer, S. K., Borchardt, M. A. 2018; 6

  View details for DOI 10.1525/elementa.301

  View details for Web of Science ID 000435687700001

• Sewage loading and microbial risk in urban waters of the Great Lakes. Elementa (Washington, D.C.) McLellan, S. L., Sauer, E. P., Corsi, S. R., Bootsma, M. J., Boehm, A. B., Spencer, S. K., Borchardt, M. A. 2018; 6

  Abstract

  Despite modern sewer system infrastructure, the release of sewage from deteriorating pipes and sewer overflows is a major water pollution problem in US cities, particularly in coastal watersheds that are highly developed with large human populations. We quantified fecal pollution sources and loads entering Lake Michigan from a large watershed of mixed land use using host-associated indicators. Wastewater treatment plant influent had stable concentrations of human Bacteroides and human Lachnospiraceae with geometric mean concentrations of 2.77 × 107 and 5.94 × 107 copy number (by quantitative PCR) per 100 ml, respectively. Human-associated indicator levels were four orders of magnitude higher than norovirus concentrations, suggesting that these human-associated bacteria could be sensitive indicators of pathogen risk. Norovirus concentrations in these same samples were used in calculations for quantitative microbial risk assessment. Assuming a typical recreational exposure to untreated sewage in water, concentrations of 7,800 copy number of human Bacteroides per 100 mL or 14,000 copy number of human Lachnospiraceae per 100 mL corresponded to an illness risk of 0.03. These levels were exceeded in estuarine waters during storm events with greater than 5 cm of rainfall. Following overflows from combined sewer systems (which must accommodate both sewage and stormwater), concentrations were 10-fold higher than under rainfall conditions. Automated high frequency sampling allowed for loads of human-associated markers to be determined, which could then be related back to equivalent volumes of untreated sewage that were released. Evidence of sewage contamination decreased as ruminant-associated indicators increased approximately one day post-storm, demonstrating the delayed impact of upstream agricultural sources on the estuary. These results demonstrate that urban areas are a diffuse source of sewage contamination to urban waters and that storm-driven release of sewage, particularly when sewage overflows occur, creates a serious though transient human health risk.

  View details for DOI 10.1525/elementa.301

  View details for PubMedID 30393748

  View details for PubMedCentralID PMC6211557

• Multiple Pathways to Bacterial Load Reduction by Stormwater Best Management Practices: Trade-Offs in Performance, Volume, and Treated Area ENVIRONMENTAL SCIENCE & TECHNOLOGY Wolfand, J. M., Bell, C. D., Boehm, A. B., Hogue, T. S., Luthy, R. G. 2018; 52 (11): 6370–79

  Abstract

  Stormwater best management practices (BMPs) are implemented to reduce microbial pollution in runoff, but their removal efficiencies differ. Enhanced BMPs, such as those with media amendments, can increase removal of fecal indicator bacteria (FIB) in runoff from 0.25-log10 to above 3-log10; however, their implications for watershed-scale management are poorly understood. In this work, a computational model was developed to simulate watershed-scale bacteria loading and BMP performance using the Ballona Creek Watershed (Los Angeles County, CA) as a case study. Over 1400 scenarios with varying BMP performance, percent watershed area treated, BMP treatment volume, and infiltrative capabilities were simulated. Incremental improvement of BMP performance by 0.25-log10, while keeping other scenario variables constant, reduces annual bacterial load at the outlet by a range of 0-29%. In addition, various simulated scenarios provide the same FIB load reduction; for example, 75% load reduction is achieved by diverting runoff from either 95% of the watershed area to 25 000 infiltrating BMPs with 0.5-log10 removal or 75% of the watershed area to 75 000 infiltrating BMPs with 1.5-log10 removal. Lastly, simulated infiltrating BMPs provide greater FIB reduction than noninfiltrating BMPs at the watershed scale. Results provide new insight on the trade-offs between BMP treatment volume, performance, and distribution.

  View details for DOI 10.1021/acs.est.8600408

  View details for Web of Science ID 000434892900032

  View details for PubMedID 29676892

• Microbial community structure of sea spray aerosols at three California beaches. FEMS microbiology ecology Graham, K. E., Prussin, A. J., Marr, L. C., Sassoubre, L. M., Boehm, A. B. 2018; 94 (3)

  Abstract

  We characterized the microbial communities in sea spray aerosols (SSA), water and sand of three beaches in central California (Cowell Beach, Baker Beach and Lovers Point) by sequencing the V4 region of the 16S rRNA gene. Average concentrations of 16S rRNA genes in SSA ranged from 2.4 * 104 to 1.4 * 105 gene copies per m3 of air. A total of 9781 distinct OTUs were identified in SSA and of these, 1042 OTUs were found in SSA of all beaches. SSA microbial communities included marine taxa, as well as some associated with the terrestrial environment. SSA taxa included organisms that play important roles in biogeochemical cycling of elements such as Planctomyces and Synechococcus, as well as those representing potential pathogens and fecal indicator bacteria including Staphylococcus epidermidis and Enterococcus spp. There were a large number of shared OTUs among SSA and water, and there was relatively high similarity between SSA and water communities. Results are consistent with a conceptual model where SSA is generated by breaking waves and bubble bursting in marine waters and that enables the transport of microorganisms from the sea to sand or other environments.

  View details for PubMedID 29346534

• Microbial community structure of sea spray aerosols at three California beaches FEMS MICROBIOLOGY ECOLOGY Graham, K. E., Prussin, A. J., Marr, L. C., Sassoubre, L. M., Boehm, A. B. 2018; 94 (3)

  View details for DOI 10.1093/femsec/fiy005

  View details for Web of Science ID 000429480200007

• Frequent detection of a human fecal indicator in the urban ocean: environmental drivers and covariation with enterococci ENVIRONMENTAL SCIENCE-PROCESSES & IMPACTS Jennings, W. C., Chern, E. C., O'Donohue, D., Kellogg, M. G., Boehm, A. B. 2018; 20 (3): 480–92

  Abstract

  Fecal pollution of surface waters presents a global human health threat. New molecular indicators of fecal pollution have been developed to address shortcomings of traditional culturable fecal indicators. However, there is still little information on their fate and transport in the environment. The present study uses spatially and temporally extensive data on traditional (culturable enterococci, cENT) and molecular (qPCR-enterococci, qENT and human-associated marker, HF183/BacR287) indicator concentrations in marine water surrounding highly-urbanized San Francisco, California, USA to investigate environmental and anthropogenic processes that impact fecal pollution. We constructed multivariable regression models for fecal indicator bacteria at 14 sampling stations. The human marker was detected more frequently in our study than in many other published studies, with detection frequency at some stations as high as 97%. The odds of cENT, qENT, and HF183/BacR287 exceeding health-relevant thresholds were statistically elevated immediately following discharges of partially treated combined sewage, and cENT levels dissipated after approximately 1 day. However, combined sewer discharges were not important predictors of indicator levels typically measured in weekly monitoring samples. Instead, precipitation and solar insolation were important predictors of cENT in weekly samples, while precipitation and water temperature were important predictors of HF183/BacR287 and qENT. The importance of precipitation highlights the significance of untreated storm water as a source of fecal pollution to the urban ocean, even for a city served by a combined sewage system. Sunlight and water temperature likely control persistence of the indicators via photoinactivation and dark decay processes, respectively.

  View details for PubMedID 29404550

• Transcriptional Response of Staphylococcus aureus to Sunlight in Oxic and Anoxic Conditions FRONTIERS IN MICROBIOLOGY McClary, J. S., Boehm, A. B. 2018; 9: 249

  Abstract

  The transcriptional response of Staphylococcus aureus strain Newman to sunlight exposure was investigated under both oxic and anoxic conditions using RNA sequencing to gain insight into potential mechanisms of inactivation. S. aureus is a pathogenic bacterium detected at recreational beaches which can cause gastrointestinal illness and skin infections, and is of increasing public health concern. To investigate the S. aureus photostress response in oligotrophic seawater, S. aureus cultures were suspended in seawater and exposed to full spectrum simulated sunlight. Experiments were performed under oxic or anoxic conditions to gain insight into the effects of oxygen-mediated and non-oxygen-mediated inactivation mechanisms. Transcript abundance was measured after 6 h of sunlight exposure using RNA sequencing and was compared to transcript abundance in paired dark control experiments. Culturable S. aureus decayed following biphasic inactivation kinetics with initial decay rate constants of 0.1 and 0.03 m2 kJ-1 in oxic and anoxic conditions, respectively. RNA sequencing revealed that 71 genes had different transcript abundance in the oxic sunlit experiments compared to dark controls, and 18 genes had different transcript abundance in the anoxic sunlit experiments compared to dark controls. The majority of genes showed reduced transcript abundance in the sunlit experiments under both conditions. Three genes (ebpS, NWMN_0867, and NWMN_1608) were found to have the same transcriptional response to sunlight between both oxic and anoxic conditions. In the oxic condition, transcripts associated with porphyrin metabolism, nitrate metabolism, and membrane transport functions were increased in abundance during sunlight exposure. Results suggest that S. aureus responds differently to oxygen-dependent and oxygen-independent photostress, and that endogenous photosensitizers play an important role during oxygen-dependent indirect photoinactivation.

  View details for PubMedID 29599752

• A human fecal contamination score for ranking recreational sites using the HF183/BacR287 quantitative real-time PCR method WATER RESEARCH Cao, Y., Sivaganesan, M., Kelty, C. A., Wang, D., Boehm, A. B., Griffith, J. F., Weisberg, S. B., Shanks, O. C. 2018; 128: 148–56

  Abstract

  Human fecal pollution of recreational waters remains a public health concern worldwide. As a result, there is a growing interest in the application of human-associated fecal source identification quantitative real-time PCR (qPCR) technologies for water quality research and management. However, there are currently no standardized approaches for field implementation and interpretation of qPCR data. In this study, a standardized HF183/BacR287 qPCR method was combined with a water sampling strategy and a novel Bayesian weighted average approach to establish a human fecal contamination score (HFS) that can be used to prioritize sampling sites for remediation based on measured human waste levels. The HFS was then used to investigate 975 study design scenarios utilizing different combinations of sites with varying sampling intensities (daily to once per week) and number of qPCR replicates per sample (2-14 replicates). Findings demonstrate that site prioritization with HFS is feasible and that both sampling intensity and number of qPCR replicates influence reliability of HFS estimates. The novel data analysis strategy presented here provides a prescribed approach for the implementation and interpretation of human-associated HF183/BacR287 qPCR data with the goal of site prioritization based on human fecal pollution levels. In addition, information is provided for future users to customize study designs for optimal HFS performance.

  View details for PubMedID 29101858

• Fecal Contamination on Produce from Wholesale and Retail Food Markets in Dhaka, Bangladesh AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE Harris, A. R., Islam, M., Unicomb, L., Boehm, A. B., Luby, S., Davis, J., Pickering, A. J. 2018; 98 (1): 287–94

  Abstract

  Fresh produce items can become contaminated with enteric pathogens along the supply chain at the preharvest (e.g., irrigation water, soil, fertilizer) or postharvest (e.g., vendor handling or consumer handling) stages. This study assesses the concentrations of fecal indicator bacteria Escherichia coli, enterococci (ENT), and Bacteriodales on surfaces of carrots, eggplants, red amaranth leaves, and tomatoes obtained from both a wholesale market (recently harvested) and neighborhood retail markets in Dhaka, Bangladesh. We detected E. coli in 100% of carrot and red amaranth rinses, 92% of eggplant rinses, and 46% of tomato rinses. Using a molecular microbial source tracking assay, we found that 32% of produce samples were positive for ruminant fecal contamination. Fecal indicator bacteria were more likely to be detected on produce collected in retail markets compared with that in the wholesale market; retail market produce were 1.25 times more likely to have E. coli detected (P = 0.03) and 1.24 times more likely to have ENT detected (P = 0.03) as compared with wholesale market produce. Bacteriodales was detected in higher concentrations in retail market produce samples compared with wholesale market produce samples (0.40 log10 gene copies per 100 cm2 higher, P = 0.03). Our results suggest that ruminant and general fecal contamination of produce in markets in Dhaka is common, and suggest that unsanitary conditions in markets are an important source of produce fecal contamination postharvest.

  View details for PubMedID 29165214

  View details for PubMedCentralID PMC5928698

• Estimating the probability of illness due to swimming in recreational water with a mixture of human- and gull-associated microbial source tracking markers ENVIRONMENTAL SCIENCE-PROCESSES & IMPACTS Brown, K. I., Graham, K. E., Soller, J. A., Boehm, A. B. 2017; 19 (12): 1528–41

  Abstract

  Beaches often receive fecal contamination from more than one source. Human sources include untreated sewage as well as treated wastewater effluent, and animal sources include wildlife such as gulls. Different contamination sources are expected to pose different health risks to swimmers. Genetic microbial source tracking (MST) markers can be used to detect bacteria that are associated with different animal sources, but the health risks associated with a mixture of MST markers are unknown. This study presents a method for predicting these health risks, using human- and gull-associated markers as an example. Quantitative Microbial Risk Assessment (QMRA) is conducted with MST markers as indicators. We find that risks associated with exposure to a specific concentration of a human-associated MST marker (HF) are greater if the HF source is untreated sewage rather than treated wastewater effluent. We also provide a risk-based threshold of HF from untreated sewage at a beach, to stay below a predicted illness risk of 3 per 100 swimmers, that is a function of gull-associated MST marker (CAT) concentration.

  View details for PubMedID 29114693

• DETECTING AND ENUMERATING SOIL-TRANSMITTED HELMINTH EGGS IN SOIL: NEW METHOD DEVELOPMENT AND RESULTS FROM FIELD TESTING IN BANGLADESH AND KENYA Steinbaum, L., Kwong, L., Ercumen, A., Negash, M. S., Lovely, A. J., Njenga, S. M., Boehm, A. B., Pickering, A. J., Nelson, K. L. AMER SOC TROP MED & HYGIENE. 2017: 185

  View details for Web of Science ID 000412851502115

• Persistence of marine fish environmental DNA and the influence of sunlight PLOS ONE Andruszkiewicz, E. A., Sassoubre, L. M., Boehm, A. B. 2017; 12 (9): e0185043

  Abstract

  Harnessing information encoded in environmental DNA (eDNA) in marine waters has the potential to revolutionize marine biomonitoring. Whether using organism-specific quantitative PCR assays or metabarcoding in conjunction with amplicon sequencing, scientists have illustrated that realistic organism censuses can be inferred from eDNA. The next step is establishing ways to link information obtained from eDNA analyses to actual organism abundance. This is only possible by understanding the processes that control eDNA concentrations. The present study uses mesocosm experiments to study the persistence of eDNA in marine waters and explore the role of sunlight in modulating eDNA persistence. We seeded solute-permeable dialysis bags with water containing indigenous eDNA and suspended them in a large tank containing seawater. Bags were subjected to two treatments: half the bags were suspended near the water surface where they received high doses of sunlight, and half at depth where they received lower doses of sunlight. Bags were destructively sampled over the course of 87 hours. eDNA was extracted from water samples and used as template for a Scomber japonicus qPCR assay and a marine fish-specific 12S rRNA PCR assay. The latter was subsequently sequenced using a metabarcoding approach. S. japonicus eDNA, as measured by qPCR, exhibited first order decay with a rate constant ~0.01 hr -1 with no difference in decay rate constants between the two experimental treatments. eDNA metabarcoding identified 190 organizational taxonomic units (OTUs) assigned to varying taxonomic ranks. There was no difference in marine fish communities as measured by eDNA metabarcoding between the two experimental treatments, but there was an effect of time. Given the differences in UVA and UVB fluence received by the two experimental treatments, we conclude that sunlight is not the main driver of fish eDNA decay in the experiments. However, there are clearly temporal effects that need to be considered when interpreting information obtained using eDNA approaches.

  View details for PubMedID 28915253

• Staphylococcus aureus Strain Newman Photoinactivation and Cellular Response to Sunlight Exposure APPLIED AND ENVIRONMENTAL MICROBIOLOGY McClary, J. S., Sassoubre, L. M., Boehm, A. B. 2017; 83 (17)

  Abstract

  Sunlight influences microbial water quality of surface waters. Previous studies have investigated photoinactivation mechanisms and cellular photostress responses of fecal indicator bacteria (FIB), including Escherichia coli and enterococci, but further work is needed to characterize photostress responses of bacterial pathogens. Here we investigate the photoinactivation of Staphylococcus aureus (strain Newman), a pigmented, waterborne pathogen of emerging concern. We measured photodecay using standard culture-based assays and cellular membrane integrity and investigated photostress response by measuring the relative number of mRNA transcripts of select oxidative stress, DNA repair, and metabolism genes. Photoinactivation experiments were performed in both oxic and anoxic systems to further investigate the role of oxygen-mediated and non-oxygen-mediated photoinactivation mechanisms. S. aureus lost culturability much faster in oxic systems than in anoxic systems, indicating an important role for oxygen in photodecay mechanisms. S. aureus cell membranes were damaged by sunlight exposure in anoxic systems but not in oxic systems, as measured by cell membrane permeability to propidium iodide. After sunlight exposure, S. aureus increased expression of a gene coding for methionine sulfoxide reductase after 12 h of sunlight exposure in the oxic system and after 6 h of sunlight exposure in the anoxic system, suggesting that methionine sulfoxide reductase is an important enzyme for defense against both oxygen-dependent and oxygen-independent photostresses. This research highlights the importance of oxygen in bacterial photoinactivation in environmentally relevant systems and the complexity of the bacterial photostress response with respect to cell structure and transcriptional regulation.IMPORTANCEStaphylococcus aureus is a pathogenic bacterium that causes gastrointestinal, respiratory, and skin infections. In severe cases, S. aureus infection can lead to life-threatening diseases, including pneumonia and sepsis. Cases of community-acquired S. aureus infection have been increasing in recent years, pointing to the importance of considering S. aureus transmission pathways outside the hospital environment. Associations have been observed between recreational water contact and staphylococcal skin infections, suggesting that recreational waters may be an important environmental transmission pathway for S. aureus However, prediction of human health risk in recreational waters is hindered by incomplete knowledge of pathogen sources, fate, and transport in this environment. This study is an in-depth investigation of the inactivation of a representative strain of S. aureus by sunlight exposure, one of the most important factors controlling the fate of microbial contaminants in clear waters, which will improve our ability to predict water quality changes and human health risk in recreational waters.

  View details for PubMedID 28646114

  View details for PubMedCentralID PMC5561283

• Environmental spread of NDM-1-producing multi-drug resistant bacteria in Dhaka, Bangladesh. Applied and environmental microbiology Islam, M. A., Islam, M., Hasan, R., Hossain, M. I., Nabi, A., Rahman, M., Goessens, W. H., Endtz, H. P., Boehm, A. B., Faruque, S. M. 2017

  Abstract

  Resistance to carbapenem antibiotics through the production of New Delhi Metallo-β-lactamase-1 (NDM-1) constitutes an emerging challenge in the treatment of bacterial infections. To monitor possible source of spread of these organisms in Dhaka, Bangladesh, we conducted comparative analysis of waste water samples from hospital adjacent areas (HAR) and from community areas (COM) as well as public tap water samples for the occurrence and characteristics of NDM-1 producing bacteria. Of 72 HAR samples tested 51 (71%) were positive for NDM-1-producing bacteria as evidenced by phenotypic tests and the presence of blaNDM-1 gene, compared to 5 of 41 (12.1%) from COM samples (P<0⋅001). All tap water samples were negative for NDM-1-producing bacteria. Klebsiella pneumoniae (44%) was the predominant bacterial species among blaNDM-1 positive isolates followed by E. coli (29%), Acinetobacter sp., (15%) and Enterobacter spp. (9%). These bacteria were also positive for one or more other antibiotic resistance genes including blaCTX-M-1 (80%),blaCTX-M-15 (63%), blaTEM (76%), blaSHV (33%), blaCMY-2 (16%), blaOXA-48-like (2%), blaOXA-1 (53%) and blaOXA-47-like (60%). Around 40% of the isolates contained qnr gene while 50% had 16s-rRNA methylase genes. The majority of isolates hosted multiple plasmids, and plasmids of 30-50 MDa carrying blaNDM-1 were self-transmissible. Our results highlight a number of issues related to the characteristics and source of spread of multiple drug resistant bacteria as a potential public health threat. In view of existing practice of discharging untreated liquid wastes into the environment, hospitals in Dhaka city contribute to potential dissemination of NDM-1-producing bacteria into the community.IMPORTANCE. Infections caused by carbapenemase-producing Enterobacteriaceae are extremely difficult to manage due to their marked resistance to a wide range of antibiotics. NDM-1 is the most recently-described carbapenemase, and the blaNDM-1 gene encoding NDM-1 is located on self-transmissible plasmids that also carry a considerable number of other antibiotic resistance genes. The present study shows high prevalence of NDM-1-producing organisms in the wastewater samples from hospital adjacent areas as a potential source for spread of these organisms to community areas in Dhaka, Bangladesh. The study also examines characteristics of the isolates and their potential to horizontally transmit the resistance determinants. The significance of our research is in identifying the mode of spread of multiple antibiotic resistant organisms, which will allow the development of containment measures, leading to broader impacts in reducing their spread to the community.

  View details for DOI 10.1128/AEM.00793-17

  View details for PubMedID 28526792

• Effects of submerged zone, media aging, and antecedent dry period on the performance of biochar-amended biofilters in removing fecal indicators and nutrients from natural stormwater ECOLOGICAL ENGINEERING Afrooz, A. R., Boehm, A. B. 2017; 102: 320-330

  View details for DOI 10.1016/j.ecoleng.2017.02.053

  View details for Web of Science ID 000399623700033

• Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding PLOS ONE Andruszkiewicz, E. A., Starks, H. A., Chavez, F. P., Sassoubre, L. M., Block, B. A., Boehm, A. B. 2017; 12 (4)

  Abstract

  Molecular analysis of environmental DNA (eDNA) can be used to assess vertebrate biodiversity in aquatic systems, but limited work has applied eDNA technologies to marine waters. Further, there is limited understanding of the spatial distribution of vertebrate eDNA in marine waters. Here, we use an eDNA metabarcoding approach to target and amplify a hypervariable region of the mitochondrial 12S rRNA gene to characterize vertebrate communities at 10 oceanographic stations spanning 45 km within the Monterey Bay National Marine Sanctuary (MBNMS). In this study, we collected three biological replicates of small volume water samples (1 L) at 2 depths at each of the 10 stations. We amplified fish mitochondrial DNA using a universal primer set. We obtained 5,644,299 high quality Illumina sequence reads from the environmental samples. The sequence reads were annotated to the lowest taxonomic assignment using a bioinformatics pipeline. The eDNA survey identified, to the lowest taxonomic rank, 7 families, 3 subfamilies, 10 genera, and 72 species of vertebrates at the study sites. These 92 distinct taxa come from 33 unique marine vertebrate families. We observed significantly different vertebrate community composition between sampling depths (0 m and 20/40 m deep) across all stations and significantly different communities at stations located on the continental shelf (<200 m bottom depth) versus in the deeper waters of the canyons of Monterey Bay (>200 m bottom depth). All but 1 family identified using eDNA metabarcoding is known to occur in MBNMS. The study informs the implementation of eDNA metabarcoding for vertebrate biomonitoring.

  View details for DOI 10.1371/journal.pone.0176343

  View details for Web of Science ID 000400308800048

  View details for PubMedID 28441466

• Detecting and enumerating soil-transmitted helminth eggs in soil: New method development and results from field testing in Kenya and Bangladesh. PLoS neglected tropical diseases Steinbaum, L., Kwong, L. H., Ercumen, A., Negash, M. S., Lovely, A. J., Njenga, S. M., Boehm, A. B., Pickering, A. J., Nelson, K. L. 2017; 11 (4)

  Abstract

  Globally, about 1.5 billion people are infected with at least one species of soil-transmitted helminth (STH). Soil is a critical environmental reservoir of STH, yet there is no standard method for detecting STH eggs in soil. We developed a field method for enumerating STH eggs in soil and tested the method in Bangladesh and Kenya. The US Environmental Protection Agency (EPA) method for enumerating Ascaris eggs in biosolids was modified through a series of recovery efficiency experiments; we seeded soil samples with a known number of Ascaris suum eggs and assessed the effect of protocol modifications on egg recovery. We found the use of 1% 7X as a surfactant compared to 0.1% Tween 80 significantly improved recovery efficiency (two-sided t-test, t = 5.03, p = 0.007) while other protocol modifications-including different agitation and flotation methods-did not have a significant impact. Soil texture affected the egg recovery efficiency; sandy samples resulted in higher recovery compared to loamy samples processed using the same method (two-sided t-test, t = 2.56, p = 0.083). We documented a recovery efficiency of 73% for the final improved method using loamy soil in the lab. To field test the improved method, we processed soil samples from 100 households in Bangladesh and 100 households in Kenya from June to November 2015. The prevalence of any STH (Ascaris, Trichuris or hookworm) egg in soil was 78% in Bangladesh and 37% in Kenya. The median concentration of STH eggs in soil in positive samples was 0.59 eggs/g dry soil in Bangladesh and 0.15 eggs/g dry soil in Kenya. The prevalence of STH eggs in soil was significantly higher in Bangladesh than Kenya (chi-square, χ2 = 34.39, p < 0.001) as was the concentration (Mann-Whitney, z = 7.10, p < 0.001). This new method allows for detecting STH eggs in soil in low-resource settings and could be used for standardizing soil STH detection globally.

  View details for DOI 10.1371/journal.pntd.0005522

  View details for PubMedID 28379956

• Occurrence of norovirus in raw sewage - A systematic literature review and meta-analysis. Water research Eftim, S. E., Hong, T., Soller, J., Boehm, A., Warren, I., Ichida, A., Nappier, S. P. 2017; 111: 366-374

  Abstract

  Human noroviruses (NoV) are a leading cause of recreational waterborne illnesses and responsible for the majority of viral-associated gastrointestinal illnesses nationwide. We conducted a systematic literature review of published peer-reviewed publications to identify NoV density data in wastewater influent, and provided an approach for developing pathogen density distributions, using the NoV data. Literature review inclusion criteria included scope, study quality, and data availability. A non-parametric bootstrap statistical model was used to estimate the NoV distribution in wastewater influent. The approach used accounts for heterogeneity in study-specific distribution curves, sampling locations, and sampling season and provides a comprehensive representation of the data. Study results illustrate that pooling all of the available NoV data together in a meta-analysis provides a more comprehensive understanding of the technical literature than what could be appreciated from individual studies. The studies included in this analysis indicate a high density of NoV in wastewater influent (overall mean = 4.6 log10 genome copies (GC)/liter (L)), with a higher density of NoV genogroup (G) II (overall mean = 4.9 log10 GC/L) than for GI (overall mean = 4.4 log10 GC/L for GI). The bootstrapping approach was also used to account for differences in seasonal and geographical occurrences of NoV GI and GII. The methods presented are reproducible and can be used to develop QMRA-ready density distributions for other viral pathogens in wastewater influent, effluent, and ambient waters. To our knowledge, our results are the first to quantitatively characterize seasonal and geographic differences, which could be particularly useful for future risk assessments.

  View details for DOI 10.1016/j.watres.2017.01.017

  View details for PubMedID 28110140

• Risk-Based Threshold of Gull-Associated Fecal Marker Concentrations for Recreational Water ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS Brown, K. I., Graham, K. E., Boehm, A. B. 2017; 4 (2): 44-48

  View details for DOI 10.1021/acs.estlett.6b00473

  View details for Web of Science ID 000394412300003

• Oceans in Peril: Grand Challenges in Applied Water Quality Research for the 21st Century ENVIRONMENTAL ENGINEERING SCIENCE Boehm, A. B., Ismail, N. S., Sassoubre, L. M., Andruszkiewicz, E. A. 2017; 34 (1): 3-15

  View details for DOI 10.1089/ees.2015.0252

  View details for Web of Science ID 000391851300002

• Evaluation of filtration and DNA extraction methods for environmental DNA biodiversity assessments across multiple trophic levels FRONTIERS IN MARINE SCIENCE Djurhuus, A., Port, J., Closek, C. J., Yamahara, K. M., Romero-Maraccini, O., Walz, K. R., Goldsmith, D. B., Michisaki, R., Boehm, A. B., Breitbart, M., Chavez, F. P. 2017: 314

  View details for DOI 10.3389/fmars.2017.00314

• Decay of sewage-sourced microbial source tracking markers and fecal indicator bacteria in marine waters WATER RESEARCH Mattioli, M. C., Sassoubre, L. M., Russell, T. L., Boehm, A. B. 2017; 108: 106-114

  Abstract

  The decay of sewage-sourced enterococci, Escherichia coli, three human-associated microbial source tracking (MST) markers, Salmonella, Campylobacter, and norovirus GII was measured in situ in coastal, marine waters. Experiments examined the effects of sunlight intensity and season on decay. Seawater was seeded with untreated sewage, placed into permeable dialysis bags, and deployed in the coastal ocean near the water surface, and at 18 cm, and 99 cm depths, to vary solar intensity, during winter and summer seasons. Microbial decay was modeled using a log-linear or shoulder log-linear decay model. Pathogen levels were too low in sewage to obtain kinetic parameters. Human-associated MST markers all decayed with approximately the same rate constant (k ∼ 1.5 d(-1)) in all experimental treatments, suggesting markers could be detectable up to ∼6 days after a raw sewage spill. E. coli and enterococci (culturable and molecular marker) k significantly varied with season and depth; enterococci decayed faster at shallow depths and during the summer, while E. coli decayed faster at shallow depths and during the winter. Rate constants for MST markers and culturable FIB diverged except at the deepest depth in the water column potentially complicating the use of MST marker concentrations to allocate sources of FIB contamination.

  View details for DOI 10.1016/j.watres.2016.10.066

  View details for Web of Science ID 000390181600011

  View details for PubMedID 27855952

• Transport of Fecal Indicators from Beach Sand to the Surf Zone by Recirculating Seawater: Laboratory Experiments and Numerical Modeling ENVIRONMENTAL SCIENCE & TECHNOLOGY Brown, K. I., Boehm, A. B. 2016; 50 (23): 12840-12847

  Abstract

  Recirculating seawater is an important component of submarine groundwater discharge, yet its role in transporting microbial contaminants from beach sand to coastal water is unknown. This study investigated the extent to which recirculating seawater carries fecal indicators, Enterococcus and bird-associated Catellicoccus, through the beach subsurface. Laboratory experiments and numerical modeling were performed to characterize the transport of fecal indicators suspended in seawater through medium-grained beach sand under transient and saturated flow conditions. Enterococcus was measured both by culture (cENT) and DNA assay (tENT), and Catellicoccus (CAT) by DNA assay. There were differences between transport of tENT and CAT compared to cENT through laboratory columns containing beach sands. Under transient flow conditions, first-order attachment rate coefficients (katt) of DNA markers were greater (∼10 h(-1)) than katt of cENT (∼1 h(-1)), although under saturated conditions katt values were similar (∼1 h(-1)). First-order detachment rate coefficients, kdet, of DNA markers were greater (∼1 h(-1)) than kdet of cENT (∼0.1h(-1)) under both types of flow conditions. Incorporating the rate coefficients into field-scale subsurface transport simulations showed that, in this sand type, the contribution of recirculating seawater to surf zone contamination is likely to be minimal unless bird feces are deposited close to the land-sea interface.

  View details for DOI 10.1021/acs.est.6b02534

  View details for Web of Science ID 000389557100036

  View details for PubMedID 27783485

• Rapid water disinfection using vertically aligned MoS2 nanofilms and visible light NATURE NANOTECHNOLOGY Liu, C., Kong, D., Hsu, P., Yuan, H., Lee, H., Liu, Y., Wang, H., Wang, S., Yan, K., Lin, D., Maraccini, P. A., Parker, K. M., Boehm, A. B., Cui, Y. 2016; 11 (12): 1098-1104

  Abstract

  Solar energy is readily available in most climates and can be used for water purification. However, solar disinfection of drinking water mostly relies on ultraviolet light, which represents only 4% of the total solar energy, and this leads to a slow treatment speed. Therefore, the development of new materials that can harvest visible light for water disinfection, and so speed up solar water purification, is highly desirable. Here we show that few-layered vertically aligned MoS2 (FLV-MoS2) films can be used to harvest the whole spectrum of visible light (∼50% of solar energy) and achieve highly efficient water disinfection. The bandgap of MoS2 was increased from 1.3 to 1.55 eV by decreasing the domain size, which allowed the FLV-MoS2 to generate reactive oxygen species (ROS) for bacterial inactivation in the water. The FLV-MoS2 showed a ∼15 times better log inactivation efficiency of the indicator bacteria compared with that of bulk MoS2, and a much faster inactivation of bacteria under both visible light and sunlight illumination compared with the widely used TiO2. Moreover, by using a 5 nm copper film on top of the FLV-MoS2 as a catalyst to facilitate electron-hole pair separation and promote the generation of ROS, the disinfection rate was increased a further sixfold. With our approach, we achieved water disinfection of >99.999% inactivation of bacteria in 20 min with a small amount of material (1.6 mg l(-1)) under simulated visible light.

  View details for DOI 10.1038/NNANO.2016.138

  View details for Web of Science ID 000389962500021

• Escherichia coli Removal in Biochar-Modified Biofilters: Effects of Biofilm PLOS ONE Afrooz, A. R., Boehm, A. B. 2016; 11 (12)

  Abstract

  The presence of microbial contaminants in urban stormwater is a significant concern for public health; however, their removal by traditional stormwater biofilters has been reported as inconsistent and inadequate. Recent work has explored the use of biochar to improve performance of stormwater biofilters under simplified conditions that do not consider potential effects of biofilm development on filter media. The present study investigates the role of biofilm on microbial contaminant removal performance of stormwater biofilters. Pseudomonas aeruginosa biofilms were formed in laboratory-scale sand and biochar-modified sand packed columns, which were then challenged with Escherichia coli laden synthetic stormwater containing natural organic matter. Results suggests that the presence of biofilm influences the removal of E. coli. However, the nature of the influence depends on the specific surface area and the relative hydrophobicity of filter media. The distribution of attached bacteria within the columns indicates that removal by filter media varies along the length of the column: the inlet was the primary removal zone regardless of experimental conditions. Findings from this research inform the design of field-scale biofilters for better and consistent performance in removing microbial contaminants from urban stormwater.

  View details for DOI 10.1371/journal.pone.0167489

  View details for Web of Science ID 000389482700168

  View details for PubMedID 27907127

  View details for PubMedCentralID PMC5132165

• Occurrence of Host-Associated Fecal Markers on Child Hands, Household Soil, and Drinking Water in Rural Bangladeshi Households. Environmental science & technology letters Boehm, A. B., Wang, D., Ercumen, A., Shea, M., Harris, A. R., Shanks, O. C., Kelty, C., Ahmed, A., Mahmud, Z. H., Arnold, B. F., Chase, C., Kullmann, C., Colford, J. M., Luby, S. P., Pickering, A. J. 2016; 3 (11): 393-398

  Abstract

  We evaluated whether provision and promotion of improved sanitation hardware (toilets and child feces management tools) reduced rotavirus and human fecal contamination of drinking water, child hands, and soil among rural Bangladeshi compounds enrolled in a cluster-randomized trial. We also measured host-associated genetic markers of ruminant and avian feces. We found evidence of widespread ruminant and avian fecal contamination in the compound environment; non-human fecal marker occurrence scaled with animal ownership. Strategies for controlling non- human fecal waste should be considered when designing interventions to reduce exposure to fecal contamination in low-income settings. Detection of a human- associated fecal marker and rotavirus was rare and unchanged by provision and promotion of improved sanitation to intervention compounds. The sanitation intervention reduced ruminant fecal contamination in drinking water and general (non-host specific) fecal contamination in soil but overall had limited effects on reducing fecal contamination in the household environment.

  View details for PubMedID 32607385

  View details for PubMedCentralID PMC7326215

• Occurrence of Host-Associated Fecal Markers on Child Hands, Household Soil, and Drinking Water in Rural Bangladeshi Households ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS Boehm, A. B., Wang, D., Ercumen, A., Shea, M., Harris, A. R., Shanks, O. C., Kelty, C., Ahmed, A., Mahmud, Z. H., Arnold, B. F., Chase, C., Kullmann, C., Colford, J. M., Luby, S. P., Pickering, A. J. 2016; 3 (11): 393-398

  View details for DOI 10.1021/acs.estlett.6b00382

  View details for Web of Science ID 000387528200003

• Escherichia coli Reduction by Bivalves in an Impaired River Impacted by Agricultural Land Use. Environmental science & technology Ismail, N. S., Tommerdahl, J. P., Boehm, A. B., Luthy, R. G. 2016; 50 (20): 11025-11033

  Abstract

  Fecal indicator bacteria (FIB) are leading causes of impaired surface waters. Innovative and environmentally appropriate best management practices are needed to reduce FIB concentrations and associated risk. This study examines the ability of the native freshwater mussel Anodonta californiensis and an invasive freshwater clam Corbicula fluminea to reduce concentrations of the FIB Escherichia coli in natural waters. Laboratory batch experiments were used to show bivalve species-specific E. coli removal capabilities and to develop a relationship between bivalve size and clearance rates. A field survey within an impaired coastal river containing both species of bivalves in an agricultural- and grazing-dominated area of the central coast of California showed a significant inverse correlation between E. coli concentration and bivalve density. An in situ field spiking and sampling study showed filtration by freshwater bivalves resulting in 1-1.5 log10 reduction of E. coli over 24 h, and calculated clearance rates ranged from 1.2 to 7.4 L hr(-1) bivalve(-1). Results of this study show the importance of freshwater bivalves for improving water quality through the removal of E. coli. While both native and invasive bivalves can reduce E. coli levels, the use of native bivalves through integration into best management practices is recommended as a way to improve water quality and protect and encourage re-establishment of native bivalve species that are in decline.

  View details for PubMedID 27616202

• Quantification of Environmental DNA (eDNA) Shedding and Decay Rates for Three Marine Fish ENVIRONMENTAL SCIENCE & TECHNOLOGY Sassoubre, L. M., Yamahara, K. M., Gardner, L. D., Block, B. A., Boehm, A. B. 2016; 50 (19): 10456-10464

  Abstract

  Analysis of environmental DNA (eDNA) to identify macroorganisms and biodiversity has the potential to significantly augment spatial and temporal biological monitoring in aquatic ecosystems. Current monitoring methods relying on the physical identification of organisms can be time consuming, expensive, and invasive. Measuring eDNA shed from organisms provides detailed information on the presence and abundance of communities of organisms. However, little is known about eDNA shedding and decay in aquatic environments. In the present study, we designed novel Taqman qPCR assays for three ecologically and economically important marine fish-Engraulis mordax (Northern Anchovy), Sardinops sagax (Pacific Sardine), and Scomber japonicas (Pacific Chub Mackerel). We subsequently measured fish eDNA shedding and decay rates in seawater mesocosms. eDNA shedding rates ranged from 165 to 3368 pg of DNA per hour per gram of biomass. First-order decay rate constants ranged from 0.055 to 0.101 per hour. We also examined the size fractionation of eDNA and concluded eDNA is both intra- and extracellular. Finally, we derived a simple mass-balance model to estimate fish abundance from eDNA concentration. The mesocosm-derived shedding and decay rates inform the interpretation of eDNA concentrations measured in environmental samples and future use of eDNA as a monitoring tool.

  View details for DOI 10.1021/acs.est.6b03114

  View details for Web of Science ID 000384841900019

  View details for PubMedID 27580258

• Rapid water disinfection using vertically aligned MoS2 nanofilms and visible light. Nature nanotechnology Liu, C., Kong, D., Hsu, P., Yuan, H., Lee, H., Liu, Y., Wang, H., Wang, S., Yan, K., Lin, D., Maraccini, P. A., Parker, K. M., Boehm, A. B., Cui, Y. 2016

  Abstract

  Solar energy is readily available in most climates and can be used for water purification. However, solar disinfection of drinking water mostly relies on ultraviolet light, which represents only 4% of the total solar energy, and this leads to a slow treatment speed. Therefore, the development of new materials that can harvest visible light for water disinfection, and so speed up solar water purification, is highly desirable. Here we show that few-layered vertically aligned MoS2 (FLV-MoS2) films can be used to harvest the whole spectrum of visible light (∼50% of solar energy) and achieve highly efficient water disinfection. The bandgap of MoS2 was increased from 1.3 to 1.55 eV by decreasing the domain size, which allowed the FLV-MoS2 to generate reactive oxygen species (ROS) for bacterial inactivation in the water. The FLV-MoS2 showed a ∼15 times better log inactivation efficiency of the indicator bacteria compared with that of bulk MoS2, and a much faster inactivation of bacteria under both visible light and sunlight illumination compared with the widely used TiO2. Moreover, by using a 5 nm copper film on top of the FLV-MoS2 as a catalyst to facilitate electron-hole pair separation and promote the generation of ROS, the disinfection rate was increased a further sixfold. With our approach, we achieved water disinfection of >99.999% inactivation of bacteria in 20 min with a small amount of material (1.6 mg l(-1)) under simulated visible light.

  View details for DOI 10.1038/nnano.2016.138

  View details for PubMedID 27525474

• Exogenous indirect photoinactivation of bacterial pathogens and indicators in water with natural and synthetic photosensitizers in simulated sunlight with reduced UVB. Journal of applied microbiology Maraccini, P. A., Wenk, J., Boehm, A. B. 2016; 121 (2): 587-597

  Abstract

  To investigate the UVB-independent and exogenous indirect photoinactivation of eight human health-relevant bacterial species in the presence of photosensitizers.Eight bacterial species were exposed to simulated sunlight with greatly reduced UVB light intensity in the presence of three synthetic photosensitizers and two natural photosensitizers. Inactivation curves were fit with shoulder log-linear or first-order kinetic models, from which the presence of a shoulder and magnitude of inactivation rate constants were compared. Eighty-four percent reduction in the UVB light intensity roughly matched a 72-95% reduction in the overall bacterial photoinactivation rate constants in sensitizer-free water. With the UVB light mostly reduced, the exogenous indirect mechanism contribution was evident for most bacteria and photosensitizers tested, although most prominently with the Gram-positive bacteria.Results confirm the importance of UVB light in bacterial photoinactivation and, with the reduction of the UVB light intensity, that the Gram-positive bacteria are more vulnerable to the exogenous indirect mechanism than Gram-negative bacteria.UVB is the most important range of the sunlight spectrum for bacterial photoinactivation. In aquatic environments where photosensitizers are present and there is high UVB light attenuation, UVA and visible wavelengths can contribute to exogenous indirect photoinactivation.

  View details for DOI 10.1111/jam.13183

  View details for PubMedID 27207818

• Soil-Transmitted Helminth Eggs Are Present in Soil at Multiple Locations within Households in Rural Kenya PLOS ONE Steinbaum, L., Njenga, S. M., Kihara, J., Boehm, A. B., Davis, J., Null, C., Pickering, A. J. 2016; 11 (6)

  Abstract

  Almost one-quarter of the world's population is infected with soil-transmitted helminths (STH). We conducted a study to determine the prevalence and location of STH-Ascaris, Trichuris, and hookworm spp.-egg contamination in soil within rural household plots in Kenya. Field staff collected soil samples from July to September 2014 from the house entrance and the latrine entrance of households in Kakamega County; additional spatial sampling was conducted at a subset of households (N = 22 samples from 3 households). We analyzed soil samples using a modified version of the US Environmental Protection Agency (EPA) method for enumerating Ascaris in biosolids. We found 26.8% of households had one or more species of STH eggs present in the soil in at least one household location (n = 18 out of 67 households), and Ascaris was the most commonly detected STH (19.4%, n = 13 out of 67 households). Prevalence of STH eggs in soil was equally likely at the house entrance (19.4%, N = 67) as at the latrine entrance (11.3%, N = 62) (p = 0.41). We also detected STH eggs at bathing and food preparation areas in the three houses revisited for additional spatial sampling, indicating STH exposure can occur at multiple sites within a household plot, not just near the latrine. The highest concentration of eggs in one house occurred in the child's play area. Our findings suggest interventions to limit child exposure to household soil could complement other STH control strategies.

  View details for DOI 10.1371/journal.pone.0157780

  View details for Web of Science ID 000378393600017

  View details for PubMedID 27341102

  View details for PubMedCentralID PMC4920396

• Water quality criteria for an acidifying ocean: Challenges and opportunities for improvement OCEAN & COASTAL MANAGEMENT Weisberg, S. B., Bednarsek, N., Feely, R. A., Chan, F., Boehm, A. B., Sutula, M., Ruesink, J. L., Hales, B., Largier, J. L., Newton, J. A. 2016; 126: 31-41

  View details for DOI 10.1016/j.ocecoaman.2016.03.010

  View details for Web of Science ID 000376840300004

• Photoinactivation of Eight Health-Relevant Bacterial Species: Determining the Importance of the Exogenous Indirect Mechanism ENVIRONMENTAL SCIENCE & TECHNOLOGY Maraccini, P. A., Wenk, J., Boehm, A. B. 2016; 50 (10): 5050-5059

  Abstract

  It is presently unknown to what extent the endogenous direct, endogenous indirect, and exogenous indirect mechanisms contribute to bacterial photoinactivation in natural surface waters. In this study, we investigated the importance of the exogenous indirect mechanism by conducting photoinactivation experiments with eight health-relevant bacterial species (Bacteroides thetaiotaomicron, Campylobacter jejuni, Enterococcus faecalis, Escherichia coli K12, E. coli O157:H7, Salmonella enterica serovar Typhimurium LT2, Staphylococcus aureus, and Streptococcus bovis). We used three synthetic photosensitizers (methylene blue, rose bengal, and nitrite) and two model natural photosensitizers (Suwannee River natural organic matter and dissolved organic matter isolated from a wastewater treatment wetland) that generated singlet oxygen and hydroxyl radical. B. thetaiotaomicron had larger first order rate constants than all other organisms under all conditions tested. The presence of the synthetic photosensitizers generally enhanced photoinactivation of Gram-positive facultative anaerobes (Ent. faecalis, Staph. aureus, and Strep. bovis). Among Gram-negative bacteria, only methylene blue with E. coli K12 and rose bengal with C. jejuni showed an enhancing effect. The presence of model natural photosensitizers either reduced or did not affect photoinactivation rate constants. Our findings highlight the importance of the cellular membrane and photosensitizer properties in modulating the contribution of the exogenous indirect mechanism to the overall bacterial photoinactivation.

  View details for DOI 10.1021/acs.est.6b00074

  View details for Web of Science ID 000376331500018

  View details for PubMedID 27121126

• Solar Inactivation of Enterococci and Escherichia coli in Natural Waters: Effects of Water Absorbance and Depth ENVIRONMENTAL SCIENCE & TECHNOLOGY Maraccini, P. A., Mattioli, M. C., Sassoubre, L. M., Cao, Y., Griffith, J. F., Ervin, J. S., Van De Werfhorst, L. C., Boehm, A. B. 2016; 50 (10): 5068-5076

  Abstract

  The decay of sewage-sourced Escherichia coli and enterococci was measured at multiple depths in a freshwater marsh, a brackish water lagoon, and a marine site, all located in California. The marine site had very clear water, while the waters from the marsh and lagoon contained colored dissolved organic matter that not only blocked light but also produced reactive oxygen species. First order decay rate constants of both enterococci and E. coli were between 1 and 2 d(-1) under low light conditions and as high as 6 d(-1) under high light conditions. First order decay rate constants were well correlated to the daily average UVB light intensity corrected for light screening incorporating water absorbance and depth, suggesting endogenous photoinactivation is a major pathway for bacterial decay. Additional laboratory experiments demonstrated the presence of colored dissolved organic matter in marsh water enhanced photoinactivation of a laboratory strain of Enterococcus faecalis, but depressed photoinactivation of sewage-sourced enterococci and E. coli after correcting for UVB light screening, suggesting that although the exogenous indirect photoinactivation mechanism may be active against Ent. faecalis, it is not for the sewage-source organisms. A simple linear regression model based on UVB light intensity appears to be a useful tool for predicting inactivation rate constants in natural waters of any depth and absorbance.

  View details for DOI 10.1021/acs.est.6b00505

  View details for Web of Science ID 000376331500020

  View details for PubMedID 27119980

• Ruminants Contribute Fecal Contamination to the Urban Household Environment in Dhaka, Bangladesh ENVIRONMENTAL SCIENCE & TECHNOLOGY Harris, A. R., Pickering, A. J., Harris, M., Doza, S., Islam, M. S., Unicomb, L., Luby, S., Davis, J., Boehm, A. B. 2016; 50 (9): 4642-4649

  Abstract

  In Dhaka, Bangladesh, the sensitivity and specificity of three human, three ruminant, and one avian source-associated QPCR microbial source tracking assays were evaluated using fecal samples collected on site. Ruminant-associated assays performed well, whereas the avian and human assays exhibited unacceptable cross-reactions with feces from other hosts. Subsequently, child hand rinses (n = 44) and floor sponge samples (n = 44) from low-income-households in Dhaka were assayed for fecal indicator bacteria (enterococci, Bacteroidales, and Escherichia coli) and a ruminant-associated bacterial target (BacR). Mean enterococci concentrations were of 100 most probable number (MPN)/2 hands and 1000 MPN/225 cm(2) floor. Mean concentrations of Bacteroidales were 10(6) copies/2 hands and 10(5) copies/225 cm(2) floor. E. coli were detected in a quarter of hand rinse and floor samples. BacR was detected in 18% of hand rinse and 27% of floor samples. Results suggest that effective household fecal management should account not only for human sources of contamination but also for animal sources. The poor performance of the human-associated assays in the study area calls into the question the feasibility of developing a human-associated marker in urban slum environments, where domestic animals are exposed to human feces that have been disposed in pits and open drains.

  View details for DOI 10.1021/acs.est.5b06282

  View details for Web of Science ID 000375521400007

  View details for PubMedID 27045990

• Absolute Quantification of Enterococcal 23S rRNA Gene Using Digital PCR ENVIRONMENTAL SCIENCE & TECHNOLOGY Wang, D., Yamahara, K. M., Cao, Y., Boehm, A. B. 2016; 50 (7): 3399-3408

  Abstract

  We evaluated the ability of chip-based digital PCR (dPCR) to quantify enterococci, the fecal indicator recommended by the United States Environmental Protection Agency (USEPA) for water-quality monitoring. dPCR uses Poisson statistics to estimate the number of DNA fragments in a sample with a specific sequence. Underestimation may occur when a gene is redundantly encoded in the genome and multiple copies of that gene are on one DNA fragment. When genomic DNA (gDNA) was extracted using two commercial DNA extraction kits, we confirmed that dPCR could discern individual copies of the redundant 23s rRNA gene in the enterococcal genome. dPCR quantification was accurate when compared to the nominal concentration inferred from fluorometer measurements (linear regression slope = 0.98, intercept = 0.03, R(2) = 0.99, and p value <0.0001). dPCR quantification was also consistent with quantitative PCR (qPCR) measurements as well as cell counts for BioBall reference standard and 24 environmental water samples. qPCR and dPCR quantification of enterococci in the 24 environmental samples were significantly correlated (linear regression slope =1.08, R(2) of 0.96, and p value <0.0001); the group mean of the qPCR measurements was 0.19 log units higher than that of the dPCR measurements. At environmentally relevant concentrations, dPCR quantification was more precise (i.e., had narrower 95% confidence intervals than qPCR quantification). We observed that humic acid caused a similar level of inhibition in both dPCR and qPCR, but calcium inhibited dPCR to a lesser degree than qPCR. Inhibition of dPCR was partially relieved when the number of thermal cycles was increased. Based on these results, we conclude that dPCR is a viable option for enumerating enterococci in ambient water.

  View details for DOI 10.1021/acs.est.5b05747

  View details for Web of Science ID 000373655800013

  View details for PubMedID 26903207

• Transport of enterococci and F+ coliphage through the saturated zone of the beach aquifer. Journal of water and health de Sieyes, N. R., Russell, T. L., Brown, K. I., Mohanty, S. K., Boehm, A. B. 2016; 14 (1): 26-38

  Abstract

  Coastal groundwater has been implicated as a source of microbial pollution to recreational beaches. However, there is little work investigating the transport of fecal microbes through beach aquifers where waters of variable salinity are present. In this study, the potential for fecal indicator organisms enterococci (ENT) and F+ coliphage to be transported through marine beach aquifers was investigated. Native sediment and groundwaters were collected from the fresh and saline sections of the subterranean estuary at three beaches along the California coast where coastal communities utilize septic systems for wastewater treatment. Groundwaters were seeded with sewage and removal of F+ coliphage and ENT by the sediments during saturated flow was tested in laboratory column experiments. Removal varied significantly between beach and organism. F+ coliphage was removed to a greater extent than ENT, and removal was greater in saline sediments and groundwater than fresh. At one of the three beaches, a field experiment was conducted to investigate the attenuation of F+ coliphage and ENT down gradient of a septic leach field. ENT were detected up to 24 m from the leach field. The column study and field observations together suggest ENT can be mobile within native aquifer sediments and groundwater under certain conditions.

  View details for DOI 10.2166/wh.2015.290

  View details for PubMedID 26837827

• Effect of weathering on mobilization of biochar particles and bacterial removal in a stormwater biofilter. Water research Mohanty, S. K., Boehm, A. B. 2015; 85: 208-215

  Abstract

  To improve bacterial removal, a traditional stormwater biofilter can be augmented with biochar, but it is unknown whether bacterial removal remains consistent as the biochar weathers during intermittent exposure to stormwater under dry-wet and freeze-thaw cycles. To examine the effect of weathering on bacterial removal capacity of biochar, we subjected biochar-augmented sand filters (or simplified biofilters) to multiple freeze-thaw or dry-wet cycles for a month and then compared their bacterial removal capacity with the removal capacity of unweathered biofilters. To isolate the effect of physical and chemical weathering processes from that of biological processes, the biofilters were operated without any developed biofilm. Biochar particles were mobilized during intermittent infiltration of stormwater, but the mobilization depended on temperature and antecedent conditions. During stormwater infiltration without intermediate drying, exposure to natural organic matter (NOM) in the stormwater decreased the bacterial removal capacity of biochar, partly due to exhaustion of attachment sites by NOM adsorption. In contrast, exposure to the same amount of NOM during stormwater infiltration with intermediate drying resulted in higher bacterial removal. This result suggests that dry-wet cycles may enhance recovery of the previously exhausted attachment sites, possibly due to diffusion of NOM from biochar surfaces into intraparticle pores during intermediate drying periods. Overall, these results indicate that physical weathering has net positive effect on bacterial removal by biochar-augmented biofilters.

  View details for DOI 10.1016/j.watres.2015.08.026

  View details for PubMedID 26320722

• Sunlight inactivation of fecal indicator bacteria in open-water unit process treatment wetlands: Modeling endogenous and exogenous inactivation rates WATER RESEARCH Nguyen, M. T., Jasper, J. T., Boehm, A. B., Nelson, K. L. 2015; 83: 282-292

  Abstract

  A pilot-scale open-water unit process wetland was monitored for one year and found to be effective in enhancing sunlight inactivation of fecal indicator bacteria (FIB). The removal of Escherichia coli and enterococci in the open-water wetland receiving non-disinfected secondary municipal wastewater reached 3 logs and 2 logs in summer time, respectively. Pigmented enterococci were shown to be significantly more resistant to sunlight inactivation than non-pigmented enterococci. A model was developed to predict the inactivation of E. coli, and pigmented and non-pigmented enterococci that accounts for endogenous and exogenous sunlight inactivation mechanisms and dark processes. Endogenous inactivation rates were modeled using the sum of UVA and UVB irradiance. Exogenous inactivation was only significant for enterococci, and was modeled as a function of steady-state singlet oxygen concentration. The rate constants were determined from lab experiments and an empirical correction factor was used to account for differences between lab and field conditions. The model was used to predict removal rate constants for FIB in the pilot-scale wetland; considering the variability of the monitoring data, there was general agreement between the modeled values and those determined from measurements. Using the model, we estimate that open-water wetlands at 40° latitude with practical sizes can achieve 3-log (99.9%) removal of E. coli and non-pigmented enterococci throughout the year [5.5 ha and 7.0 ha per million gallons of wastewater effluent per day (MGD), respectively]. Differences in sunlight inactivation rates observed between pigmented and non-pigmented enterococci, as well as between lab-cultured and indigenous wastewater bacteria highlight the challenges of using FIB as model organisms for actual pathogens in natural sunlit environments.

  View details for DOI 10.1016/j.watres.2015.06.043

  View details for Web of Science ID 000360418000028

• Comparative decay of Catellicoccus marimmalium and enterococci in beach sand and seawater. Water research Brown, K. I., Boehm, A. B. 2015; 83: 377-84

  Abstract

  Most studies characterize microbial source tracking (MST) target performance using sensitivity and specificity metrics. However, it is important to also consider the temporal stability of MST targets in relation to regulated microbial pollutants. Differences among bacterial target stabilities may lead to erroneous conclusions about sources of contamination. The present study evaluates the relative stability of MST targets and fecal indicator organisms using the gull/pigeon-associated Catellicoccus marimammalium (CAT) marker and enterococci (ENT). The decay rates of CAT and ENT measured by culture (cENT) and QPCR (tENT) were compared in sand and seawater laboratory microcosms under environmentally relevant conditions (subject to tidal wetting versus no wetting in sand, and sunlit versus dark conditions in seawater). Bacterial targets were more persistent in beach sand than in seawater with decay rates on the order of 0.01-0.1 per day and 1 to 10 per day, respectively. Targets were more persistent in unwetted compared to wetted sand, and dark compared to sunlit seawater. During the first 8 days of the sand experiment, the decay rate k of CAT was greater than that of cENT. The decay rates of CAT, tENT, and cENT were similar in sand after day 8 and in dark seawater. In sunlit seawater, the decay rates were different between targets with kcENT > kCAT > ktENT. The decay rates presented here are useful for fate and transport models and also inform the use of MST marker concentrations to infer ENT sources in the environment.

  View details for DOI 10.1016/j.watres.2015.06.055

  View details for PubMedID 26196307

• Comparative decay of Catellicoccus marimmalium and enterococci in beach sand and seawater WATER RESEARCH Brown, K. I., Boehm, A. B. 2015; 83: 377-384

  Abstract

  Most studies characterize microbial source tracking (MST) target performance using sensitivity and specificity metrics. However, it is important to also consider the temporal stability of MST targets in relation to regulated microbial pollutants. Differences among bacterial target stabilities may lead to erroneous conclusions about sources of contamination. The present study evaluates the relative stability of MST targets and fecal indicator organisms using the gull/pigeon-associated Catellicoccus marimammalium (CAT) marker and enterococci (ENT). The decay rates of CAT and ENT measured by culture (cENT) and QPCR (tENT) were compared in sand and seawater laboratory microcosms under environmentally relevant conditions (subject to tidal wetting versus no wetting in sand, and sunlit versus dark conditions in seawater). Bacterial targets were more persistent in beach sand than in seawater with decay rates on the order of 0.01-0.1 per day and 1 to 10 per day, respectively. Targets were more persistent in unwetted compared to wetted sand, and dark compared to sunlit seawater. During the first 8 days of the sand experiment, the decay rate k of CAT was greater than that of cENT. The decay rates of CAT, tENT, and cENT were similar in sand after day 8 and in dark seawater. In sunlit seawater, the decay rates were different between targets with kcENT > kCAT > ktENT. The decay rates presented here are useful for fate and transport models and also inform the use of MST marker concentrations to infer ENT sources in the environment.

  View details for DOI 10.1016/j.watres.2015.06.055

  View details for Web of Science ID 000360418000038

• Sunlight inactivation of fecal indicator bacteria in open-water unit process treatment wetlands: Modeling endogenous and exogenous inactivation rates. Water research Nguyen, M. T., Jasper, J. T., Boehm, A. B., Nelson, K. L. 2015; 83: 282-292

  Abstract

  A pilot-scale open-water unit process wetland was monitored for one year and found to be effective in enhancing sunlight inactivation of fecal indicator bacteria (FIB). The removal of Escherichia coli and enterococci in the open-water wetland receiving non-disinfected secondary municipal wastewater reached 3 logs and 2 logs in summer time, respectively. Pigmented enterococci were shown to be significantly more resistant to sunlight inactivation than non-pigmented enterococci. A model was developed to predict the inactivation of E. coli, and pigmented and non-pigmented enterococci that accounts for endogenous and exogenous sunlight inactivation mechanisms and dark processes. Endogenous inactivation rates were modeled using the sum of UVA and UVB irradiance. Exogenous inactivation was only significant for enterococci, and was modeled as a function of steady-state singlet oxygen concentration. The rate constants were determined from lab experiments and an empirical correction factor was used to account for differences between lab and field conditions. The model was used to predict removal rate constants for FIB in the pilot-scale wetland; considering the variability of the monitoring data, there was general agreement between the modeled values and those determined from measurements. Using the model, we estimate that open-water wetlands at 40° latitude with practical sizes can achieve 3-log (99.9%) removal of E. coli and non-pigmented enterococci throughout the year [5.5 ha and 7.0 ha per million gallons of wastewater effluent per day (MGD), respectively]. Differences in sunlight inactivation rates observed between pigmented and non-pigmented enterococci, as well as between lab-cultured and indigenous wastewater bacteria highlight the challenges of using FIB as model organisms for actual pathogens in natural sunlit environments.

  View details for DOI 10.1016/j.watres.2015.06.043

  View details for PubMedID 26164800

• Human-Associated Fecal Quantitative Polymerase Chain Reaction Measurements and Simulated Risk of Gastrointestinal Illness in Recreational Waters Contaminated with Raw Sewage ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS Boehm, A. B., Soller, J. A., Shanks, O. C. 2015; 2 (10): 270-275

  View details for DOI 10.1021/acs.estlett.5b00219

  View details for Web of Science ID 000362930700003

• SOIL-TRANSMITTED HELMINTH CONTAMINATION OF SOIL IN RURAL KENYAN HOUSEHOLDS Steinbaum, L. E., Nelson, K., Ercumen, A., Kwong, L., Kihara, J., Njenga, S., Boehm, A., Davis, J., Null, C., Pickering, A. AMER SOC TROP MED & HYGIENE. 2015: 9

  View details for Web of Science ID 000412844101025

• Quantification of Human Norovirus GII on Hands of Mothers with Children Under the Age of Five Years in Bagamoyo, Tanzania. The American journal of tropical medicine and hygiene Mattioli, M. C., Davis, J., Mrisho, M., Boehm, A. B. 2015; 93 (3): 478-484

  Abstract

  Human noroviruses are the most common cause of viral gastroenteritis worldwide and one of the leading causes of viral diarrhea in children under the age of 5 years. Hands have been shown to play an important role in norovirus transmission. Norovirus outbreaks tend to exhibit strong seasonality, most often occurring during cold, dry months, but recently have also been documented during hot, dry winter months in the southern hemisphere. Other research suggests that rainfall is an important factor in norovirus outbreaks. This study examines the prevalence and concentration of human norovirus GII on the hands of mothers in Bagamoyo, Tanzania, during the rainy and dry seasons. Norovirus GII was detected in approximately 5% of hand rinse samples during both the rainy and dry seasons. Fecal indicator bacteria levels, Escherichia coli and enterococci, in hand rinse samples were not associated with norovirus hand contamination. Turbidity of the hand rinses was found to be associated with norovirus presence on mothers' hands; however, this relationship was only observed during the rainy season. The results suggest mothers' hands serve as a source of norovirus exposure for young children in Tanzanian households, and further work is needed to determine better indicators of norovirus contamination in these environments.

  View details for DOI 10.4269/ajtmh.14-0778

  View details for PubMedID 26149861

  View details for PubMedCentralID PMC4559683

• Simultaneous monitoring of faecal indicators and harmful algae using an in-situ autonomous sensor. Letters in applied microbiology Yamahara, K. M., Demir-Hilton, E., Preston, C. M., Marin, R., Pargett, D., Roman, B., JENSEN, S., Birch, J. M., Boehm, A. B., Scholin, C. A. 2015; 61 (2): 130-138

  Abstract

  Faecal indicator bacteria (FIB) and harmful algal blooms (HABs) threaten the health and the economy of coastal communities worldwide. Emerging automated sampling technologies combined with molecular analytical techniques could enable rapid detection of micro-organisms in-situ, thereby improving resource management and public health decision-making. We evaluated this concept using a robotic device, the Environmental Sample Processor (ESP). The ESP automates in-situ sample collection, nucleic acid extraction and molecular analyses. Here, the ESP measured and reported concentrations of FIB (Enterococcus spp.), a microbial source-tracking marker (human-specific Bacteriodales) and a HAB species (Psuedo-nitzschia spp.) over a 45-day deployment on the Santa Cruz Municipal Wharf (Santa Cruz, CA, USA). Both FIB and HABs were enumerated from single in-situ collected water samples. The in-situ qPCR efficiencies ranged from 86% to 105%, while the limit of quantifications during the deployment was 10 copies reaction(-1) . No differences were observed in the concentrations of enterococci, the human-specific marker in Bacteroidales spp., and P. australis between in-situ collected sample and traditional hand sampling methods (P > 0·05). Analytical results were Internet-accessible within hours of sample collection, demonstrating the feasibility of same-day public notification of current water quality conditions.This study presents the first report of in-situ qPCR enumeration of both faecal indicators and harmful algal species in coastal marine waters. We utilize a robotic device for in-situ quantification of enterococci, the human-specific marker in Bacteriodales and Pseudo-nitzschia spp. from the same water samples collected and processed in-situ. The results demonstrate that rapid, in-situ monitoring can be utilized to identify and quantify multiple health-relevant micro-organisms important in water quality monitoring and that this monitoring can be used to inform same-day notifications.

  View details for DOI 10.1111/lam.12432

  View details for PubMedID 25900660

• Ocean Acidification Science Needs for Natural Resource Managers of the North American West Coast OCEANOGRAPHY Boehm, A. B., Jacobson, M. Z., O'Donnell, M. J., Sutula, M., Wakefield, W. W., Weisberg, S. B., Whiteman, E. 2015; 28 (2): 170-181

  View details for DOI 10.5670/oceanog.2015.40

  View details for Web of Science ID 000357231700018

• Growth-dependent photoinactivation kinetics of Enterococcus faecalis JOURNAL OF APPLIED MICROBIOLOGY Maraccini, P. A., Wang, D., McClary, J. S., Boehm, A. B. 2015; 118 (5): 1226-1237

  Abstract

  To investigate how the growth stage of Enterococcus faecalis affects its photoinactivation in clear water.Enterococcus faecalis were grown in batch cultures to four different growth stages or grown in chemostats set at four different dilution rates, then harvested and exposed to full spectrum or UVB-blocked simulated sunlight. Experiments were conducted in triplicate in clear water with no added sensitizers. Decay curves were shoulder-log linear and were generally not statistically different in experiments conducted under full spectrum light. Shoulders were longer and first order inactivation rates smaller when experiments were seeded with cells grown to stationary as compared to exponential phase, and for slower growing cells when experiments were done under UVB-blocked light. Chemostat-sourced bacteria generally showed less variability among replicates than batch-sourced cells.The physiological state of cells and the method via which they are being generated may affect the photoinactivation experimental results.Photoinactivation experiments conducted with exponential phase cells may overestimate the photoinactivation kinetics in the environment, particular if UVB-independent mechanisms predominate. Chemostat-sourced cells are likely to provide more consistent experimental results than batch-sourced cells.

  View details for DOI 10.1111/jam.12773

  View details for Web of Science ID 000352577000015

  View details for PubMedID 25688992

• Temporal stability of the microbial community in sewage-polluted seawater exposed to natural sunlight cycles and marine microbiota. Applied and environmental microbiology Sassoubre, L. M., Yamahara, K. M., Boehm, A. B. 2015; 81 (6): 2107-2116

  Abstract

  Billions of gallons of untreated wastewater enter the coastal ocean each year. Once sewage microorganisms are in the marine environment, they are exposed to environmental stressors, such as sunlight and predation. Previous research has investigated the fate of individual sewage microorganisms in seawater but not the entire sewage microbial community. The present study used next-generation sequencing (NGS) to examine how the microbial community in sewage-impacted seawater changes over 48 h when exposed to natural sunlight cycles and marine microbiota. We compared the results from microcosms composed of unfiltered seawater (containing naturally occurring marine microbiota) and filtered seawater (containing no marine microbiota) to investigate the effect of marine microbiota. We also compared the results from microcosms that were exposed to natural sunlight cycles with those from microcosms kept in the dark to investigate the effect of sunlight. The microbial community composition and the relative abundance of operational taxonomic units (OTUs) changed over 48 h in all microcosms. Exposure to sunlight had a significant effect on both community composition and OTU abundance. The effect of marine microbiota, however, was minimal. The proportion of sewage-derived microorganisms present in the microcosms decreased rapidly within 48 h, and the decrease was the most pronounced in the presence of both sunlight and marine microbiota, where the proportion decreased from 85% to 3% of the total microbial community. The results from this study demonstrate the strong effect that sunlight has on microbial community composition, as measured by NGS, and the importance of considering temporal effects in future applications of NGS to identify microbial pollution sources.

  View details for DOI 10.1128/AEM.03950-14

  View details for PubMedID 25576619

  View details for PubMedCentralID PMC4345398

• Improvement of Urban Lake Water Quality by Removal of Escherichia coli through the Action of the Bivalve Anodonta californiensis. Environmental science & technology Ismail, N. S., Dodd, H., Sassoubre, L. M., Horne, A. J., Boehm, A. B., Luthy, R. G. 2015; 49 (3): 1664-1672

  Abstract

  High levels of fecal indicator bacteria, such as Escherichia coli, can be indicative of poor water quality. The use of shellfish to reduce eutrophication has been proposed, but application of bivalves to reduce bacterial levels has not been extensively reported. Removal of E. coli by the native freshwater mussel Anodonta californiensis was studied using laboratory batch systems and field-based flow-through systems. Batch systems were utilized to determine the fate and inactivation of E. coli after uptake by the mussel. Batch experiments demonstrated that uptake patterns followed first order kinetics and E. coli was inactivated with less than 5% of the initial colonies recoverable in fecal matter or tissue. Flow-through systems located at an urban impaired lake in San Francisco, CA were utilized to determine uptake kinetics under environmentally relevant conditions. The bivalves maintained a 1-log removal of E. coli for the duration of exposure. The calculated uptake rates can be used in conjunction with hydrologic models to determine the number of bivalves needed to maintain removal of E. coli in different freshwater systems. The outcomes of this study support the use of native freshwater bivalves to achieve the co-benefits of rehabilitating a freshwater ecosystem and improving water quality via reduction of E. coli in contaminated freshwater systems.

  View details for DOI 10.1021/es5033212

  View details for PubMedID 25587628

• Hand-to-Mouth Contacts Result in Greater Ingestion of Feces than Dietary Water Consumption in Tanzania: A Quantitative Fecal Exposure Assessment Model. Environmental science & technology Mattioli, M. C., Davis, J., Boehm, A. B. 2015; 49 (3): 1912-1920

  Abstract

  Diarrheal diseases kill 1800 children under the age of five die each day, and nearly half of these deaths occur in sub-Saharan Africa. Contaminated drinking water and hands are two important environmental transmission routes of diarrhea-causing pathogens to young children in low-income countries. The objective of this research is to evaluate the relative contribution of these two major exposure pathways in a low-income country setting. A Monte Carlo simulation was used to model the amount of human feces ingested by children under five years old from exposure via hand-to-mouth contacts and stored drinking water ingestion in Bagamoyo, Tanzania. Child specific exposure data were obtained from the USEPA 2011 Exposure Factors Handbook, and fecal contamination was estimated using hand rinse and stored water fecal indicator bacteria concentrations from over 1200 Tanzanian households. The model outcome is a distribution of a child's daily dose of feces via each exposure route. The model results show that Tanzanian children ingest a significantly greater amount of feces each day from hand-to-mouth contacts than from drinking water, which may help elucidate why interventions focused on water without also addressing hygiene often see little to no effect on reported incidence of diarrhea.

  View details for DOI 10.1021/es505555f

  View details for PubMedID 25559008

• Sunny with a chance of gastroenteritis: predicting swimmer risk at california beaches. Environmental science & technology Thoe, W., Gold, M., Griesbach, A., Grimmer, M., Taggart, M. L., Boehm, A. B. 2015; 49 (1): 423-431

  Abstract

  Traditional beach management that uses concentrations of cultivatable fecal indicator bacteria (FIB) may lead to delayed notification of unsafe swimming conditions. Predictive, nowcast models of beach water quality may help reduce beach management errors and enhance protection of public health. This study compares performances of five different types of statistical, data-driven predictive models: multiple linear regression model, binary logistic regression model, partial least-squares regression model, artificial neural network, and classification tree, in predicting advisories due to FIB contamination at 25 beaches along the California coastline. Classification tree and the binary logistic regression model with threshold tuning are consistently the best performing model types for California beaches. Beaches with good performing models usually have a rainfall/flow related dominating factor affecting beach water quality, while beaches having a deteriorating water quality trend or low FIB exceedance rates are less likely to have a good performing model. This study identifies circumstances when predictive models are the most effective, and suggests that using predictive models for public notification of unsafe swimming conditions may improve public health protection at California beaches relative to current practices.

  View details for DOI 10.1021/es504701j

  View details for PubMedID 25489920

• Mobilization of Microspheres from a Fractured Soil during Intermittent Infiltration Events VADOSE ZONE JOURNAL Mohanty, S. K., Bulicek, M. C., Metge, D. W., Harvey, R. W., Ryan, J. N., Boehm, A. B. 2015; 14 (1)

  View details for DOI 10.2136/vzj2014.05.0058

  View details for Web of Science ID 000349222300001

• Predicting water quality at Santa Monica Beach: Evaluation of five different models for public notification of unsafe swimming conditions WATER RESEARCH Thoe, W., Gold, M., Griesbach, A., Grimmer, M., Taggart, M. L., Boehm, A. B. 2014; 67: 105-117

  Abstract

  Bathing beaches are monitored for fecal indicator bacteria (FIB) to protect swimmers from unsafe conditions. However, FIB assays take ∼24 h and water quality conditions can change dramatically in that time, so unsafe conditions cannot presently be identified in a timely manner. Statistical, data-driven predictive models use information on environmental conditions (i.e., rainfall, turbidity) to provide nowcasts of FIB concentrations. Their ability to predict real time FIB concentrations can make them more accurate at identifying unsafe conditions than the current method of using day or older FIB measurements. Predictive models are used in the Great Lakes, Hong Kong, and Scotland for beach management, but they are presently not used in California - the location of some of the world's most popular beaches. California beaches are unique as point source pollution has generally been mitigated, the summer bathing season receives little to no rainfall, and in situ measurements of turbidity and salinity are not readily available. These characteristics may make modeling FIB difficult, as many current FIB models rely heavily on rainfall or salinity. The current study investigates the potential for FIB models to predict water quality at a quintessential California Beach: Santa Monica Beach. This study compares the performance of five predictive models, multiple linear regression model, binary logistic regression model, partial least square regression model, artificial neural network, and classification tree, to predict concentrations of summertime fecal coliform and enterococci concentrations. Past measurements of bacterial concentration, storm drain condition, and tide level are found to be critical factors in the predictive models. The models perform better than the current beach management method. The classification tree models perform the best; for example they correctly predict 42% of beach postings due to fecal coliform exceedances during model validation, as compared to 28% by the current method. Artificial neural network is the second best model which minimizes the number of incorrect beach postings. The binary logistic regression model also gives promising results, comparable to classification tree, by adjusting the posting decision thresholds to maximize correct beach postings. This study indicates that predictive models hold promise as a beach management tool at Santa Monica Beach. However, there are opportunities to further refine predictive models.

  View details for DOI 10.1016/j.watres.2014.09.001

  View details for Web of Science ID 000346394900011

  View details for PubMedID 25262555

• Human health risk implications of multiple sources of faecal indicator bacteria in a recreational waterbody WATER RESEARCH Soller, J. A., Schoen, M. E., Varghese, A., Ichida, A. M., Boehm, A. B., Eftim, S., Ashbolt, N. J., Ravenscroft, J. E. 2014; 66: 254-264

  Abstract

  We simulate the influence of multiple sources of enterococci (ENT) as faecal indicator bacteria (FIB) in recreational water bodies on potential human health risk by considering waters impacted by human and animal sources, human and non-pathogenic sources, and animal and non-pathogenic sources. We illustrate that risks vary with the proportion of culturable ENT in water bodies derived from these sources and estimate corresponding ENT densities that yield the same level of health protection that the recreational water quality criteria in the United States seeks (benchmark risk). The benchmark risk is based on epidemiological studies conducted in water bodies predominantly impacted by human faecal sources. The key result is that the risks from mixed sources are driven predominantly by the proportion of the contamination source with the greatest ability to cause human infection (potency), not necessarily the greatest source(s) of FIB. Predicted risks from exposures to mixtures comprised of approximately 30% ENT from human sources were up to 50% lower than the risks expected from purely human sources when contamination is recent and ENT levels are at the current water quality criteria levels (35 CFU 100 mL(-1)). For human/non-pathogenic, human/gull, human/pig, and human/chicken faecal mixtures with relatively low human contribution, the predicted culturable enterococci densities that correspond to the benchmark risk are substantially greater than the current water quality criteria values. These findings are important because they highlight the potential applicability of site specific water quality criteria for waters that are predominantly un-impacted by human sources.

  View details for DOI 10.1016/j.watres.2014.08.026

  View details for Web of Science ID 000344823500024

  View details for PubMedID 25222329

• Static electricity powered copper oxide nanowire microbicidal electroporation for water disinfection. Nano letters Liu, C., Xie, X., Zhao, W., Yao, J., Kong, D., Boehm, A. B., Cui, Y. 2014; 14 (10): 5603-5608

  Abstract

  Safe water scarcity occurs mostly in developing regions that also suffer from energy shortages and infrastructure deficiencies. Low-cost and energy-efficient water disinfection methods have the potential to make great impacts on people in these regions. At the present time, most water disinfection methods being promoted to households in developing countries are aqueous chemical-reaction-based or filtration-based. Incorporating nanomaterials into these existing disinfection methods could improve the performance; however, the high cost of material synthesis and recovery as well as fouling and slow treatment speed is still limiting their application. Here, we demonstrate a novel flow device that enables fast water disinfection using one-dimensional copper oxide nanowire (CuONW) assisted electroporation powered by static electricity. Electroporation relies on a strong electric field to break down microorganism membranes and only consumes a very small amount of energy. Static electricity as the power source can be generated by an individual person's motion in a facile and low-cost manner, which ensures its application anywhere in the world. The CuONWs used were synthesized through a scalable one-step air oxidation of low-cost copper mesh. With a single filtration, we achieved complete disinfection of bacteria and viruses in both raw tap and lake water with a high flow rate of 3000 L/(h·m(2)), equivalent to only 1 s of contact time. Copper leaching from the nanowire mesh was minimal.

  View details for DOI 10.1021/nl5020958

  View details for PubMedID 25247233

• Escherichia coli Removal in Biochar-Augmented Biofilter: Effect of Infiltration Rate, Initial Bacterial Concentration, Biochar Particle Size, and Presence of Compost ENVIRONMENTAL SCIENCE & TECHNOLOGY Mohanty, S. K., Boehm, A. B. 2014; 48 (19): 11535-11542

  Abstract

  Bioretention systems and biofilters are used in low impact development to passively treat urban stormwater. However, these engineered natural systems are not efficient at removing fecal indicator bacteria, the contaminants responsible for a majority of surface water impairments. The present study investigates the efficacy of biochar-augmented model sand biofilters for Escherichia coli removal under a variety of stormwater bacterial concentrations and infiltration rates. Additionally, we test the role of biochar particle size and "presence of compost on model" biofilter performance. Our results show that E. coli removal in a biochar-augmented sand biofilter is ∼ 96% and is not greatly affected by increases in stormwater infiltration rates and influent bacterial concentrations, particularly within the ranges expected in field. Removal of fine (<125 μm) biochar particles from the biochar-sand biofilter decreased the removal capacity from 95% to 62%, indicating biochar size is important. Addition of compost to biochar-sand biofilters not only lowered E. coli removal capacity but also increased the mobilization of deposited bacteria during intermittent infiltration. This result is attributed to exhaustion of attachment sites on biochar by the dissolved organic carbon leached from compost. Overall, our study indicates that biochar has potential to remove bacteria from stormwater under a wide range of field conditions, but for biochar to be effective, the size should be small and biochar should be applied without compost. Although the results aid in the optimization of biofilter design, further studies are needed to examine biochar potential in the field over an entire rainy season.

  View details for DOI 10.1021/es5033162

  View details for Web of Science ID 000343016600065

• Escherichia coli removal in biochar-augmented biofilter: effect of infiltration rate, initial bacterial concentration, biochar particle size, and presence of compost. Environmental science & technology Mohanty, S. K., Boehm, A. B. 2014; 48 (19): 11535-11542

  Abstract

  Bioretention systems and biofilters are used in low impact development to passively treat urban stormwater. However, these engineered natural systems are not efficient at removing fecal indicator bacteria, the contaminants responsible for a majority of surface water impairments. The present study investigates the efficacy of biochar-augmented model sand biofilters for Escherichia coli removal under a variety of stormwater bacterial concentrations and infiltration rates. Additionally, we test the role of biochar particle size and "presence of compost on model" biofilter performance. Our results show that E. coli removal in a biochar-augmented sand biofilter is ∼ 96% and is not greatly affected by increases in stormwater infiltration rates and influent bacterial concentrations, particularly within the ranges expected in field. Removal of fine (<125 μm) biochar particles from the biochar-sand biofilter decreased the removal capacity from 95% to 62%, indicating biochar size is important. Addition of compost to biochar-sand biofilters not only lowered E. coli removal capacity but also increased the mobilization of deposited bacteria during intermittent infiltration. This result is attributed to exhaustion of attachment sites on biochar by the dissolved organic carbon leached from compost. Overall, our study indicates that biochar has potential to remove bacteria from stormwater under a wide range of field conditions, but for biochar to be effective, the size should be small and biochar should be applied without compost. Although the results aid in the optimization of biofilter design, further studies are needed to examine biochar potential in the field over an entire rainy season.

  View details for DOI 10.1021/es5033162

  View details for PubMedID 25222640

• Static Electricity Powered Copper Oxide Nanowire Microbicidal Electroporation for Water Disinfection NANO LETTERS Liu, C., Xie, X., Zhao, W., Yao, J., Kong, D., Boehm, A. B., Cui, Y. 2014; 14 (10): 5603-5608

  Abstract

  Safe water scarcity occurs mostly in developing regions that also suffer from energy shortages and infrastructure deficiencies. Low-cost and energy-efficient water disinfection methods have the potential to make great impacts on people in these regions. At the present time, most water disinfection methods being promoted to households in developing countries are aqueous chemical-reaction-based or filtration-based. Incorporating nanomaterials into these existing disinfection methods could improve the performance; however, the high cost of material synthesis and recovery as well as fouling and slow treatment speed is still limiting their application. Here, we demonstrate a novel flow device that enables fast water disinfection using one-dimensional copper oxide nanowire (CuONW) assisted electroporation powered by static electricity. Electroporation relies on a strong electric field to break down microorganism membranes and only consumes a very small amount of energy. Static electricity as the power source can be generated by an individual person's motion in a facile and low-cost manner, which ensures its application anywhere in the world. The CuONWs used were synthesized through a scalable one-step air oxidation of low-cost copper mesh. With a single filtration, we achieved complete disinfection of bacteria and viruses in both raw tap and lake water with a high flow rate of 3000 L/(h·m(2)), equivalent to only 1 s of contact time. Copper leaching from the nanowire mesh was minimal.

  View details for DOI 10.1021/nl5020958

  View details for Web of Science ID 000343016400019

• Efficacy of biochar to remove Escherichia coli from stormwater under steady and intermittent flow. Water research Mohanty, S. K., Cantrell, K. B., Nelson, K. L., Boehm, A. B. 2014; 61: 288-296

  Abstract

  Biofilters, designed to facilitate the infiltration of stormwater into soil, are generally ineffective in removing bacteria from stormwater, thereby causing pollution of groundwater and receiving surface waters. The bacterial removal capacity of biofilters has been shown to be lower in the presence of natural organic matter (NOM) and during intermittent infiltration of stormwater. To improve the removal of fecal indicator bacteria (Escherichia coli) under these conditions, we amended sand with 5% (by weight) biochar, a carbonaceous geomedia produced by pyrolysis of biomass, and investigated the removal and remobilization of E. coli. Three types of biochar were used to evaluate the role of biochar properties on the removal. Compared to sand, biochar not only retained up to 3 orders of magnitude more E. coli, but also prevented their mobilization during successive intermittent flows. In the presence of NOM, the removal capacity of biochar was lower, but remained higher than sand alone. The improved retention with the biochar amendment is attributed to an increase in the attachment of E. coli at the primary minimum and to an increase in the water-holding capacity of biochar-amended sand, which renders driving forces such as moving air-water interfaces less effective in detaching bacteria from grain surfaces. Biochars with lower volatile matter and polarity appear to be more effective in removing bacteria from stormwater. Overall, our results suggest that a biochar amendment to biofilter media has the potential to effectively remove bacteria from stormwater.

  View details for DOI 10.1016/j.watres.2014.05.026

  View details for PubMedID 24952272

• Effect of submarine groundwater discharge on bacterial indicators and swimmer health at Avalon Beach, CA, USA. Water research Yau, V. M., Schiff, K. C., Arnold, B. F., Griffith, J. F., Gruber, J. S., Wright, C. C., Wade, T. J., Burns, S., Hayes, J. M., Mcgee, C., Gold, M., Cao, Y., Boehm, A. B., Weisberg, S. B., Colford, J. M. 2014; 59: 23-36

  Abstract

  Use of fecal indicator bacteria (FIB) for monitoring beach water quality is based on their co-occurrence with human pathogens, a relationship that can be dramatically altered by fate and transport processes after leaving the human intestine. We conducted a prospective cohort study at Avalon Beach, California (USA), where the indicator relationship is potentially affected by the discharge of sewage-contaminated groundwater and by solar radiation levels at this shallow, relatively quiescent beach. The goals of this study were to determine: 1) if swimmers exposed to marine water were at higher risk of illness than non-swimmers; 2) if FIB measured in marine water were associated with swimmer illness, and; 3) if the associations between FIB and swimmer health were modified by either submarine groundwater discharge or solar radiation levels. There were 7317 individuals recruited during the summers of 2007-08, 6165 (84%) of whom completed follow-up within two weeks of the beach visit. A total of 703 water quality samples were collected across multiple sites and time periods during recruitment days and analyzed for FIB using both culture-based and molecular methods. Adjusted odds ratios (AOR) indicated that swimmers who swallowed water were more likely to experience Gastrointestinal Illness (GI Illness) within three days of their beach visit than non-swimmers, and that this risk was significantly elevated when either submarine groundwater discharge was high (AOR [95% CI]:2.18 [1.22-3.89]) or solar radiation was low (2.45 [1.25-4.79]). The risk of GI Illness was not significantly elevated for swimmers who swallowed water when groundwater discharge was low or solar radiation was high. Associations between GI Illness incidence and FIB levels (Enterococcus EPA Method 1600) among swimmers who swallowed water were not significant when we did not account for groundwater discharge, but were strongly associated when groundwater discharge was high (1.85 [1.06, 3.23]) compared to when it was low (0.77 [0.42, 1.42]; test of interaction: P = 0.03). These results demonstrate the need to account for local environmental conditions when monitoring for, and making decisions about, public health at recreational beaches. The views expressed in this article are those of the authors and do not necessarily reflect the views or policies of the U.S. Environmental Protection Agency.

  View details for DOI 10.1016/j.watres.2014.03.050

  View details for PubMedID 24776951

• Diversity and Transport of Microorganisms in Intertidal Sands of the California Coast APPLIED AND ENVIRONMENTAL MICROBIOLOGY Boehm, A. B., Yamahara, K. M., Sassoubre, L. M. 2014; 80 (13): 3943-3951

  Abstract

  Forced by tides and waves, large volumes of seawater are flushed through the beach daily. Organic material and nutrients in seawater are remineralized and cycled as they pass through the beach. Microorganisms are responsible for most of the biogeochemical cycling in the beach; however, few studies have characterized their diversity in intertidal sands, and little work has characterized the extent to which microbes are transported between different compartments of the beach. The present study uses next-generation massively parallel sequencing to characterize the microbial community present at 49 beaches along the coast of California. In addition, we characterize the transport of microorganisms within intertidal sands using laboratory column experiments. We identified extensive diversity in the beach sands. Nearly 1,000 unique taxa were identified in sands from 10 or more unique beaches, suggesting the existence of a group of "cosmopolitan" sand microorganisms. A biogeographical analysis identified a taxon-distance relationship among the beaches. In addition, sands with similar grain size, organic carbon content, exposed to a similar wave climate, and having the same degree of anthropogenic influence tended to have similar microbial communities. Column experiments identified microbes readily mobilized by seawater infiltrating through unsaturated intertidal sands. The ease with which microbes were mobilized suggests that intertidal sands may represent a reservoir of bacteria that seed the beach aquifer where they may partake in biogeochemical cycling.

  View details for DOI 10.1128/AEM.00513-14

  View details for Web of Science ID 000337241400018

  View details for PubMedCentralID PMC4054206

• Diversity and transport of microorganisms in intertidal sands of the California coast. Applied and environmental microbiology Boehm, A. B., Yamahara, K. M., Sassoubre, L. M. 2014; 80 (13): 3943-3951

  Abstract

  Forced by tides and waves, large volumes of seawater are flushed through the beach daily. Organic material and nutrients in seawater are remineralized and cycled as they pass through the beach. Microorganisms are responsible for most of the biogeochemical cycling in the beach; however, few studies have characterized their diversity in intertidal sands, and little work has characterized the extent to which microbes are transported between different compartments of the beach. The present study uses next-generation massively parallel sequencing to characterize the microbial community present at 49 beaches along the coast of California. In addition, we characterize the transport of microorganisms within intertidal sands using laboratory column experiments. We identified extensive diversity in the beach sands. Nearly 1,000 unique taxa were identified in sands from 10 or more unique beaches, suggesting the existence of a group of "cosmopolitan" sand microorganisms. A biogeographical analysis identified a taxon-distance relationship among the beaches. In addition, sands with similar grain size, organic carbon content, exposed to a similar wave climate, and having the same degree of anthropogenic influence tended to have similar microbial communities. Column experiments identified microbes readily mobilized by seawater infiltrating through unsaturated intertidal sands. The ease with which microbes were mobilized suggests that intertidal sands may represent a reservoir of bacteria that seed the beach aquifer where they may partake in biogeochemical cycling.

  View details for DOI 10.1128/AEM.00513-14

  View details for PubMedID 24747906

• Hand bacterial communities vary across two different human populations. Microbiology (Reading, England) Hospodsky, D., Pickering, A. J., Julian, T. R., Miller, D., Gorthala, S., Boehm, A. B., Peccia, J. 2014; 160: 1144-1152

  Abstract

  This study utilized pyrosequencing-based phylogenetic library results to assess bacterial communities on the hands of women in Tanzania and compared these communities with bacteria assemblages on the hands of US women. Bacterial population profiles and phylogenetically based ordinate analysis demonstrated that the bacterial communities on hands were more similar for selected populations within a country than between the two countries considered. Organisms that have commonly been identified in prior human skin microbiome studies, including members of the Propionibacteriaceae, Staphylococcaceae and Streptococceacea families, were highly abundant on US hands and drove the clustering of US hand microbial communities into a distinct group. The most abundant bacterial taxa on Tanzanian hands were the soil-associated Rhodobacteraceae and Nocardioidaceae. These results help to expand human microbiome results beyond US and European populations, and the identification and abundance of soil-associated bacteria on Tanzanian hands demonstrated the important role of the environment in shaping the microbial communities on human hands.

  View details for DOI 10.1099/mic.0.075390-0

  View details for PubMedID 24817404

• Mechanisms for Photoinactivation of Enterococcus faecalis in Seawater. Applied and environmental microbiology Sassoubre, L. M., Nelson, K. L., Boehm, A. B. 2014; 80 (9): 2964-?

  View details for DOI 10.1128/AEM.00913-14

  View details for PubMedID 24732731

• Detection limits and cost comparisons of human- and gull-associated conventional and quantitative PCR assays in artificial and environmental waters. Journal of environmental management Riedel, T. E., Zimmer-Faust, A. G., Thulsiraj, V., Madi, T., Hanley, K. T., Ebentier, D. L., Byappanahalli, M., Layton, B., Raith, M., Boehm, A. B., Griffith, J. F., Holden, P. A., Shanks, O. C., Weisberg, S. B., Jay, J. A. 2014; 136: 112-120

  Abstract

  Some molecular methods for tracking fecal pollution in environmental waters have both PCR and quantitative PCR (qPCR) assays available for use. To assist managers in deciding whether to implement newer qPCR techniques in routine monitoring programs, we compared detection limits (LODs) and costs of PCR and qPCR assays with identical targets that are relevant to beach water quality assessment. For human-associated assays targeting Bacteroidales HF183 genetic marker, qPCR LODs were 70 times lower and there was no effect of target matrix (artificial freshwater, environmental creek water, and environmental marine water) on PCR or qPCR LODs. The PCR startup and annual costs were the lowest, while the per reaction cost was 62% lower than the Taqman based qPCR and 180% higher than the SYBR based qPCR. For gull-associated assays, there was no significant difference between PCR and qPCR LODs, target matrix did not effect PCR or qPCR LODs, and PCR startup, annual, and per reaction costs were lower. Upgrading to qPCR involves greater startup and annual costs, but this increase may be justified in the case of the human-associated assays with lower detection limits and reduced cost per sample.

  View details for DOI 10.1016/j.jenvman.2014.01.029

  View details for PubMedID 24583609

• Impacts of Beach Wrack Removal via Grooming on Surf Zone Water Quality. Environmental science & technology Russell, T. L., Sassoubre, L. M., Zhou, C., French-Owen, D., Hassaballah, A., Boehm, A. B. 2014; 48 (4): 2203-2211

  Abstract

  Fecal indicator bacteria (FIB) are used to assess the microbial water quality of recreational waters. Increasingly, nonfecal sources of FIB have been implicated as causes of poor microbial water quality in the coastal environment. These sources are challenging to quantify and difficult to remediate. The present study investigates one nonfecal FIB source, beach wrack (decaying aquatic plants), and its impacts on water quality along the Central California coast. The prevalence of FIB on wrack was studied using a multibeach survey, collecting wrack throughout Central California. The impacts of beach grooming, to remove wrack, were investigated at Cowell Beach in Santa Cruz, California using a long-term survey (two summers, one with and one without grooming) and a 48 h survey during the first ever intensive grooming event. FIB were prevalent on wrack but highly variable spatially and temporally along the nine beaches sampled in Central California. Beach grooming was generally associated with either no change or a slight increase in coastal FIB concentrations and increases in surf zone turbidity and silicate, phosphate, and dissolved inorganic nitrogen concentrations. The findings suggest that beach grooming for wrack removal is not justified as a microbial pollution remediation strategy.

  View details for DOI 10.1021/es405536q

  View details for PubMedID 24437501

• Transcriptional response of Enterococcus faecalis to sunlight. Journal of photochemistry and photobiology. B, Biology Sassoubre, L. M., Ramsey, M. M., Gilmore, M. S., Boehm, A. B. 2014; 130: 349-356

  Abstract

  Microarrays were used to investigate the transcriptional response of Enterococcus faecalis to photostress. E. faecalis are Gram-positive bacteria used as indicators of water quality and have been shown to vary diurnally in response to sunlight. E. faecalis in filtered seawater microcosms were exposed to artificial sunlight for 12h and then placed in the dark for 12h. Transcript abundance was measured at 0, 2, 6, 12, and 24h in the sunlit microcosm and a dark control using microarrays. Culturable E. faecalis concentrations decreased 6-7 orders of magnitude within the first 6h of light exposure. After 12h in the dark, no evidence of dark-repair was observed. Expression data collected after 12h of sunlight exposure revealed a difference in transcript abundance in the light relative to dark microcosms for 35 unique ORFs, 33 ORFs showed increased transcript abundance and 2 ORFs showed reduced transcript abundance. A majority (51%) of the ORFs with increased transcript abundance in the sunlit relative to dark microcosms encoded hypothetical proteins; others were associated with protein synthesis, oxidative stress and DNA repair. Results suggest that E. faecalis exposed to sunlight actively transcribe RNA in response to photostress.

  View details for DOI 10.1016/j.jphotobiol.2013.12.013

  View details for PubMedID 24434819

• Enteric Pathogens in Stored Drinking Water and on Caregiver's Hands in Tanzanian Households with and without Reported Cases of Child Diarrhea PLOS ONE Mattioli, M. C., Boehm, A. B., Davis, J., Harris, A. R., Mrisho, M., Pickering, A. J. 2014; 9 (1)

  Abstract

  Diarrhea is one of the leading causes of mortality in young children. Diarrheal pathogens are transmitted via the fecal-oral route, and for children the majority of this transmission is thought to occur within the home. However, very few studies have documented enteric pathogens within households of low-income countries.The presence of molecular markers for three enteric viruses (enterovirus, adenovirus, and rotavirus), seven Escherichia coli virulence genes (ECVG), and human-specific Bacteroidales was assessed in hand rinses and household stored drinking water in Bagamoyo, Tanzania. Using a matched case-control study design, we examined the relationship between contamination of hands and water with these markers and child diarrhea. We found that the presence of ECVG in household stored water was associated with a significant decrease in the odds of a child within the home having diarrhea (OR = 0.51; 95% confidence interval 0.27-0.93). We also evaluated water management and hygiene behaviors. Recent hand contact with water or food was positively associated with detection of enteric pathogen markers on hands, as was relatively lower volumes of water reportedly used for daily hand washing. Enteropathogen markers in stored drinking water were more likely found among households in which the markers were also detected on hands, as well as in households with unimproved water supply and sanitation infrastructure.The prevalence of enteric pathogen genes and the human-specific Bacteroidales fecal marker in stored water and on hands suggests extensive environmental contamination within homes both with and without reported child diarrhea. Better stored water quality among households with diarrhea indicates caregivers with sick children may be more likely to ensure safe drinking water in the home. Interventions to increase the quantity of water available for hand washing, and to improve food hygiene, may reduce exposure to enteric pathogens in the domestic environment.

  View details for DOI 10.1371/journal.pone.0084939

  View details for Web of Science ID 000329460100084

  View details for PubMedID 24392161

  View details for PubMedCentralID PMC3879350

• Enteric pathogens in stored drinking water and on caregiver's hands in Tanzanian households with and without reported cases of child diarrhea. PLoS One Mattioli, M., C., Boehm, A., B., Davis, J., Harris, A., R., Mrisho, M., Pickering., A., J. 2014; 9: e84939
• Enteric pathogens in stored drinking water and on caregiver's hands in Tanzanian households with and without reported cases of child diarrhea. PloS one Mattioli, M. C., Boehm, A. B., Davis, J., Harris, A. R., Mrisho, M., Pickering, A. J. 2014; 9 (1)

  Abstract

  Diarrhea is one of the leading causes of mortality in young children. Diarrheal pathogens are transmitted via the fecal-oral route, and for children the majority of this transmission is thought to occur within the home. However, very few studies have documented enteric pathogens within households of low-income countries.The presence of molecular markers for three enteric viruses (enterovirus, adenovirus, and rotavirus), seven Escherichia coli virulence genes (ECVG), and human-specific Bacteroidales was assessed in hand rinses and household stored drinking water in Bagamoyo, Tanzania. Using a matched case-control study design, we examined the relationship between contamination of hands and water with these markers and child diarrhea. We found that the presence of ECVG in household stored water was associated with a significant decrease in the odds of a child within the home having diarrhea (OR = 0.51; 95% confidence interval 0.27-0.93). We also evaluated water management and hygiene behaviors. Recent hand contact with water or food was positively associated with detection of enteric pathogen markers on hands, as was relatively lower volumes of water reportedly used for daily hand washing. Enteropathogen markers in stored drinking water were more likely found among households in which the markers were also detected on hands, as well as in households with unimproved water supply and sanitation infrastructure.The prevalence of enteric pathogen genes and the human-specific Bacteroidales fecal marker in stored water and on hands suggests extensive environmental contamination within homes both with and without reported child diarrhea. Better stored water quality among households with diarrhea indicates caregivers with sick children may be more likely to ensure safe drinking water in the home. Interventions to increase the quantity of water available for hand washing, and to improve food hygiene, may reduce exposure to enteric pathogens in the domestic environment.

  View details for DOI 10.1371/journal.pone.0084939

  View details for PubMedID 24392161

• New Performance Metrics for Quantitative Polymerase Chain Reaction-Based Microbial Source Tracking Methods ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS Wang, D., Green, H. C., Shanks, O. C., Boehm, A. B. 2014; 1 (1): 20-25

  View details for DOI 10.1021/ez400022t

  View details for Web of Science ID 000350830700005

• New performance metrics for quantitative PCR microbial source tracking methods. Environmental Science & Technology Letters Wang, D., Green, H., Shanks, O., Boehm., A., B. 2014; 1: 20-25
• Simple Estimate of Entrainment Rate of Pollutants from a Coastal Discharge into the Surf Zone (vol 47, pg 11554, 2013) ENVIRONMENTAL SCIENCE & TECHNOLOGY Wong, S. C., Monismith, S. G., Boehm, A. B. 2013; 47 (22): 13208

  View details for DOI 10.1021/es4048736

  View details for Web of Science ID 000327360600077

• Performance of forty-one microbial source tracking methods: A twenty-seven lab evaluation study. Water research Boehm, A. B., Van De Werfhorst, L. C., Griffith, J. F., Holden, P. A., Jay, J. A., Shanks, O. C., Wang, D., Weisberg, S. B. 2013; 47 (18): 6812-6828

  Abstract

  The last decade has seen development of numerous new microbial source tracking (MST) methodologies, but many of these have been tested in just a few laboratories with a limited number of fecal samples. This method evaluation study examined the specificity and sensitivity of 41 MST methodologies by analyzing data generated in 27 laboratories. MST methodologies that targeted human, cow, ruminant, dog, gull, pig, horse, and sheep were tested against sewage, septage, human, cow, dog, deer, pig, chicken, pigeon, gull, horse, and goose fecal samples. Each laboratory received 64 blind samples containing a single source (singletons) or two sources (doubletons), as well as diluted singleton samples to assess method sensitivity. Laboratories utilized their own protocols when performing the methods and data were deposited in a central database before samples were unblinded. Between one and seven laboratories tested each method. The most sensitive and specific assays, based on an analysis of presence/absence of each marker in target and non-target fecal samples, were HF183 endpoint and HF183SYBR (human), CF193 and Rum2Bac (ruminant), CowM2 and CowM3 (cow), BacCan (dog), Gull2SYBR and LeeSeaGull (gull), PF163 and pigmtDNA (pig), HoF597 (horse), PhyloChip (pig, horse, chicken, deer), Universal 16S TRFLP (deer), and Bacteroidales 16S TRFLP (pig, horse, chicken, deer); all had sensitivity and specificity higher than 80% in all or the majority of laboratories. When the abundance of MST markers in target and non-target fecal samples was examined, some assays that performed well in the binary analysis were found to not be sensitive enough as median concentrations fell below a minimum abundance criterion (set at 50 copies per colony forming units of enterococci) in target fecal samples. Similarly, some assays that cross-reacted with non-target fecal sources in the binary analysis were found to perform well in a quantitative analysis because the cross-reaction occurred at very low levels. Based on a quantitative analysis, the best performing methods were HF183Taqman and BacH (human), Rum2Bac and BacR (ruminant), LeeSeaGull (gull), and Pig2Bac (pig); no cow or dog-specific assay met the quantitative specificity and sensitivity criteria. Some of the best performing assays in the study were run by just one laboratory so further testing of assay portability is needed. While this study evaluated the marker performance in defined samples, further field testing as well as development of frameworks for fecal source allocation and risk assessment are needed.

  View details for DOI 10.1016/j.watres.2012.12.046

  View details for PubMedID 23880218

• Evaluation of the repeatability and reproducibility of a suite of qPCR-based microbial source tracking methods WATER RESEARCH Ebentier, D. L., Hanley, K. T., Cao, Y., Badgley, B. D., Boehm, A. B., Ervin, J. S., Goodwin, K. D., Gourmelon, M., Griffith, J. F., Holden, P. A., Kelty, C. A., Lozach, S., Mcgee, C., Peed, L. A., Raith, M., Ryu, H., Sadowsky, M. J., Scott, E. A., Domingo, J. S., Schriewer, A., Sinigalliano, C. D., Shanks, O. C., Van De Werfhorst, L. C., Wang, D., Wuertz, S., Jay, J. A. 2013; 47 (18): 6839-6848

  Abstract

  Many PCR-based methods for microbial source tracking (MST) have been developed and validated within individual research laboratories. Inter-laboratory validation of these methods, however, has been minimal, and the effects of protocol standardization regimes have not been thoroughly evaluated. Knowledge of factors influencing PCR in different laboratories is vital to future technology transfer for use of MST methods as a tool for water quality management. In this study, a blinded set of 64 filters (containing 32 duplicate samples generated from 12 composite fecal sources) were analyzed by three to five core laboratories with a suite of PCR-based methods utilizing standardized reagents and protocols. Repeatability (intra-laboratory variability) and reproducibility (inter-laboratory variability) of observed results were assessed. When standardized methodologies were used, intra- and inter-laboratory %CVs were generally low (median %CV 0.1-3.3% and 1.9-7.1%, respectively) and comparable to those observed in similar inter-laboratory validation studies performed on other methods of quantifying fecal indicator bacteria (FIB) in environmental samples. ANOVA of %CV values found three human-associated methods (BsteriF1, BacHum, and HF183Taqman) to be similarly reproducible (p > 0.05) and significantly more reproducible (p < 0.05) than HumM2. This was attributed to the increased variability associated with low target concentrations detected by HumM2 (approximately 1-2 log10copies/filter lower) compared to other human-associated methods. Cow-associated methods (BacCow and CowM2) were similarly reproducible (p > 0.05). When using standardized protocols, variance component analysis indicated sample type (fecal source and concentration) to be the major contributor to total variability with that from replicate filters and inter-laboratory analysis to be within the same order of magnitude but larger than inherent intra-laboratory variability. However, when reagents and protocols were not standardized, inter-laboratory %CV generally increased with a corresponding decline in reproducibility. Overall, these findings verify the repeatability and reproducibility of these MST methods and highlight the need for standardization of protocols and consumables prior to implementation of larger scale MST studies involving multiple laboratories.

  View details for DOI 10.1016/j.watres.2013.01.060

  View details for Web of Science ID 000328444000004

• Performance of viruses and bacteriophages for fecal source determination in a multi-laboratory, comparative study WATER RESEARCH Harwood, V. J., Boehm, A. B., Sassoubre, L. M., Vijayavel, K., Stewart, J. R., Fong, T., Caprais, M., Converse, R. R., Diston, D., Ebdon, J., Fuhrman, J. A., Gourmelon, M., Gentry-Shields, J., Griffith, J. F., Kashian, D. R., Noble, R. T., Taylor, H., Wicki, M. 2013; 47 (18): 6929-6943

  Abstract

  An inter-laboratory study of the accuracy of microbial source tracking (MST) methods was conducted using challenge fecal and sewage samples that were spiked into artificial freshwater and provided as unknowns (blind test samples) to the laboratories. The results of the Source Identification Protocol Project (SIPP) are presented in a series of papers that cover 41 MST methods. This contribution details the results of the virus and bacteriophage methods targeting human fecal or sewage contamination. Human viruses used as source identifiers included adenoviruses (HAdV), enteroviruses (EV), norovirus Groups I and II (NoVI and NoVII), and polyomaviruses (HPyVs). Bacteriophages were also employed, including somatic coliphages and F-specific RNA bacteriophages (FRNAPH) as general indicators of fecal contamination. Bacteriophage methods targeting human fecal sources included genotyping of FRNAPH isolates and plaque formation on bacterial hosts Enterococcus faecium MB-55, Bacteroides HB-73 and Bacteroides GB-124. The use of small sample volumes (≤50 ml) resulted in relatively insensitive theoretical limits of detection (10-50 gene copies or plaques × 50 ml(-1)) which, coupled with low virus concentrations in samples, resulted in high false-negative rates, low sensitivity, and low negative predictive values. On the other hand, the specificity of the human virus methods was generally close to 100% and positive predictive values were ∼40-70% with the exception of NoVs, which were not detected. The bacteriophage methods were generally much less specific toward human sewage than virus methods, although FRNAPH II genotyping was relatively successful, with 18% sensitivity and 85% specificity. While the specificity of the human virus methods engenders great confidence in a positive result, better concentration methods and larger sample volumes must be utilized for greater accuracy of negative results, i.e. the prediction that a human contamination source is absent.

  View details for DOI 10.1016/j.watres.2013.04.064

  View details for Web of Science ID 000328444000012

  View details for PubMedID 23886543

• Comparison of PCR and quantitative real-time PCR methods for the characterization of ruminant and cattle fecal pollution sources WATER RESEARCH Raith, M. R., Kelty, C. A., Griffith, J. F., Schriewer, A., Wuertz, S., Mieszkin, S., Gourmelon, M., Reischer, G. H., Farnleitner, A. H., Ervin, J. S., Holden, P. A., Ebentier, D. L., Jay, J. A., Wang, D., Boehm, A. B., Aw, T. G., Rose, J. B., Balleste, E., Meijer, W. G., Sivaganesan, M., Shanks, O. C. 2013; 47 (18): 6921-6928

  Abstract

  The State of California has mandated the preparation of a guidance document on the application of fecal source identification methods for recreational water quality management. California contains the fifth highest population of cattle in the United States, making the inclusion of cow-associated methods a logical choice. Because the performance of these methods has been shown to change based on geography and/or local animal feeding practices, laboratory comparisons are needed to determine which assays are best suited for implementation. We describe the performance characterization of two end-point PCR assays (CF128 and CF193) and five real-time quantitative PCR (qPCR) assays (Rum2Bac, BacR, BacCow, CowM2, and CowM3) reported to be associated with either ruminant or cattle feces. Each assay was tested against a blinded set of 38 reference challenge filters (19 duplicate samples) containing fecal pollution from 12 different sources suspected to impact water quality. The abundance of each host-associated genetic marker was measured for qPCR-based assays in both target and non-target animals and compared to quantities of total DNA mass, wet mass of fecal material, as well as Bacteroidales, and enterococci determined by 16S rRNA qPCR and culture-based approaches (enterococci only). Ruminant- and cow-associated genetic markers were detected in all filters containing a cattle fecal source. However, some assays cross-reacted with non-target pollution sources. A large amount of variability was evident across laboratories when protocols were not fixed suggesting that protocol standardization will be necessary for widespread implementation. Finally, performance metrics indicate that the cattle-associated CowM2 qPCR method combined with either the BacR or Rum2Bac ruminant-associated methods are most suitable for implementation.

  View details for DOI 10.1016/j.watres.2013.03.061

  View details for Web of Science ID 000328444000011

  View details for PubMedID 23871256

• Multi-laboratory evaluations of the performance of Catellicoccus marimammalium PCR assays developed to target gull fecal sources WATER RESEARCH Sinigalliano, C. D., Ervin, J. S., Van De Werfhorst, L. C., Badgley, B. D., Balleste, E., Bartkowiak, J., Boehm, A. B., Byappanahalli, M., Goodwin, K. D., Gourmelon, M., Griffith, J., Holden, P. A., Jay, J., Layton, B., Lee, C., Lee, J., Meijer, W. G., Noble, R., Raith, M., Ryu, H., Sadowsky, M. J., Schriewer, A., Wang, D., Wanless, D., Whitman, R., Wuertz, S., Domingo, J. W. 2013; 47 (18): 6883-6896

  Abstract

  Here we report results from a multi-laboratory (n = 11) evaluation of four different PCR methods targeting the 16S rRNA gene of Catellicoccus marimammalium originally developed to detect gull fecal contamination in coastal environments. The methods included a conventional end-point PCR method, a SYBR(®) Green qPCR method, and two TaqMan(®) qPCR methods. Different techniques for data normalization and analysis were tested. Data analysis methods had a pronounced impact on assay sensitivity and specificity calculations. Across-laboratory standardization of metrics including the lower limit of quantification (LLOQ), target detected but not quantifiable (DNQ), and target not detected (ND) significantly improved results compared to results submitted by individual laboratories prior to definition standardization. The unit of measure used for data normalization also had a pronounced effect on measured assay performance. Data normalization to DNA mass improved quantitative method performance as compared to enterococcus normalization. The MST methods tested here were originally designed for gulls but were found in this study to also detect feces from other birds, particularly feces composited from pigeons. Sequencing efforts showed that some pigeon feces from California contained sequences similar to C. marimammalium found in gull feces. These data suggest that the prevalence, geographic scope, and ecology of C. marimammalium in host birds other than gulls require further investigation. This study represents an important first step in the multi-laboratory assessment of these methods and highlights the need to broaden and standardize additional evaluations, including environmentally relevant target concentrations in ambient waters from diverse geographic regions.

  View details for DOI 10.1016/j.watres.2013.02.059

  View details for Web of Science ID 000328444000008

  View details for PubMedID 23916157

• Recommendations following a multi-laboratory comparison of microbial source tracking methods WATER RESEARCH Stewart, J. R., Boehm, A. B., Dubinsky, E. A., Fong, T., Goodwin, K. D., Griffith, J. F., Noble, R. T., Shanks, O. C., Vijayavel, K., Weisberg, S. B. 2013; 47 (18): 6829-6838

  Abstract

  Microbial source tracking (MST) methods were evaluated in the Source Identification Protocol Project (SIPP), in which 27 laboratories compared methods to identify host sources of fecal pollution from blinded water samples containing either one or two different fecal types collected from California. This paper details lessons learned from the SIPP study and makes recommendations to further advance the field of MST. Overall, results from the SIPP study demonstrated that methods are available that can correctly identify whether particular host sources including humans, cows and birds have contributed to contamination in a body of water. However, differences between laboratory protocols and data processing affected results and complicated interpretation of MST method performance in some cases. This was an issue particularly for samples that tested positive (non-zero Ct values) but below the limits of quantification or detection of a PCR assay. Although false positives were observed, such samples in the SIPP study often contained the fecal pollution source that was being targeted, i.e., the samples were true positives. Given these results, and the fact that MST often requires detection of targets present in low concentrations, we propose that such samples be reported and identified in a unique category to facilitate data analysis and method comparisons. Important data can be lost when such samples are simply reported as positive or negative. Actionable thresholds were not derived in the SIPP study due to limitations that included geographic scope, age of samples, and difficulties interpreting low concentrations of target in environmental samples. Nevertheless, the results of the study support the use of MST for water management, especially to prioritize impaired waters in need of remediation. Future integration of MST data into quantitative microbial risk assessments and other models could allow managers to more efficiently protect public health based on site conditions.

  View details for DOI 10.1016/j.watres.2013.04.063

  View details for Web of Science ID 000328444000003

  View details for PubMedID 23891204

• Enterococcus and Escherichia coli fecal source apportionment with microbial source tracking genetic markers - Is it feasible? Water research Wang, D., Farnleitner, A. H., Field, K. G., Green, H. C., Shanks, O. C., Boehm, A. B. 2013; 47 (18): 6849-6861

  Abstract

  Fecal pollution is measured in surface waters using culture-based measurements of enterococci and Escherichia coli bacteria. Source apportionment of these two fecal indicator bacteria is an urgent need for prioritizing remediation efforts and quantifying health risks associated with source-specific pathogens. There are a number of quantitative real-time PCR (QPCR) assays that estimate concentrations of source-associated genetic markers; however, their concentrations are not necessarily amenable to source apportionment because the markers may differ in prevalence across sources. Here we mathematically derive and test, under ideal conditions, a method that utilizes the ratios of fecal source-associated genetic markers and culture and molecular measurements of general fecal indicators to apportion enterococci and E. coli. The source contribution is approximately equal to the ratio of the source-associated and the general fecal indicator concentrations in a water sample divided by their ratio in the source material, so long as cross-reactivity is negligible. We illustrate the utility of the ratio method using samples consisting of mixtures of various fecal pollution sources. The results from the ratio method correlated well with the actual source apportionment in artificial samples. However, aging of contamination can confound source allocation predictions. In particular, culturable enterococci and E. coli, the organisms presently regulated in the United States and much of the world, decay at different rates compared to source-associated markers and as a result cannot be apportioned using this method. However, limited data suggest a similar decay rate between source-associated and QPCR-measured Enterococcus and E. coli genetic markers, indicating that apportionment may be possible for these organisms; however further work is needed to confirm.

  View details for DOI 10.1016/j.watres.2013.02.058

  View details for PubMedID 23890872

• Performance of human fecal anaerobe-associated PCR-based assays in a multi-laboratory method evaluation study WATER RESEARCH Layton, B. A., Cao, Y., Ebentier, D. L., Hanley, K., Balleste, E., Brandao, J., Byappanahalli, M., Converse, R., Farnleitner, A. H., Gentry-Shields, J., Gidley, M. L., Gourmelon, M., Lee, C. S., Lee, J., Lozach, S., Madi, T., Meijer, W. G., Noble, R., Peed, L., Reischer, G. H., Rodrigues, R., Rose, J. B., Schriewer, A., Sinigalliano, C., Srinivasan, S., Stewart, J., Van De Werfhorst, L. C., Wang, D., Whitman, R., Wuertz, S., Jay, J., Holden, P. A., Boehm, A. B., Shanks, O., Griffith, J. F. 2013; 47 (18): 6897-6908

  Abstract

  A number of PCR-based methods for detecting human fecal material in environmental waters have been developed over the past decade, but these methods have rarely received independent comparative testing in large multi-laboratory studies. Here, we evaluated ten of these methods (BacH, BacHum-UCD, Bacteroides thetaiotaomicron (BtH), BsteriF1, gyrB, HF183 endpoint, HF183 SYBR, HF183 Taqman(®), HumM2, and Methanobrevibacter smithii nifH (Mnif)) using 64 blind samples prepared in one laboratory. The blind samples contained either one or two fecal sources from human, wastewater or non-human sources. The assay results were assessed for presence/absence of the human markers and also quantitatively while varying the following: 1) classification of samples that were detected but not quantifiable (DNQ) as positive or negative; 2) reference fecal sample concentration unit of measure (such as culturable indicator bacteria, wet mass, total DNA, etc); and 3) human fecal source type (stool, sewage or septage). Assay performance using presence/absence metrics was found to depend on the classification of DNQ samples. The assays that performed best quantitatively varied based on the fecal concentration unit of measure and laboratory protocol. All methods were consistently more sensitive to human stools compared to sewage or septage in both the presence/absence and quantitative analysis. Overall, HF183 Taqman(®) was found to be the most effective marker of human fecal contamination in this California-based study.

  View details for DOI 10.1016/j.watres.2013.05.060

  View details for Web of Science ID 000328444000009

  View details for PubMedID 23992621

• Characterization of fecal concentrations in human and other animal sources by physical, culture-based, and quantitative real-time PCR methods WATER RESEARCH Ervin, J. S., Russell, T. L., Layton, B. A., Yamahara, K. M., Wang, D., Sassoubre, L. M., Cao, Y., Kelty, C. A., Sivaganesan, M., Boehm, A. B., Holden, P. A., Weisberg, S. B., Shanks, O. C. 2013; 47 (18): 6873-6882

  Abstract

  The characteristics of fecal sources, and the ways in which they are measured, can profoundly influence the interpretation of which sources are contaminating a body of water. Although feces from various hosts are known to differ in mass and composition, it is not well understood how those differences compare across fecal sources and how differences depend on characterization methods. This study investigated how nine different fecal characterization methods provide different measures of fecal concentration in water, and how results varied across twelve different fecal pollution sources. Sources investigated included chicken, cow, deer, dog, goose, gull, horse, human, pig, pigeon, septage and sewage. A composite fecal slurry was prepared for each source by mixing feces from 6 to 22 individual samples with artificial freshwater. Fecal concentrations were estimated by physical (wet fecal mass added and total DNA mass extracted), culture-based (Escherichia coli and enterococci by membrane filtration and defined substrate), and quantitative real-time PCR (Bacteroidales, E. coli, and enterococci) characterization methods. The characteristics of each composite fecal slurry and the relationships between physical, culture-based and qPCR-based characteristics varied within and among different fecal sources. An in silico exercise was performed to assess how different characterization methods can impact identification of the dominant fecal pollution source in a mixed source sample. A comparison of simulated 10:90 mixtures based on enterococci by defined substrate predicted a source reversal in 27% of all possible combinations, while mixtures based on E. coli membrane filtration resulted in a reversal 29% of the time. This potential for disagreement in minor or dominant source identification based on different methods of measurement represents an important challenge for water quality managers and researchers.

  View details for DOI 10.1016/j.watres.2013.02.060

  View details for Web of Science ID 000328444000007

  View details for PubMedID 23871252

• Simple estimate of entrainment rate of pollutants from a coastal discharge into the surf zone. Environmental science & technology Wong, S. H., Monismith, S. G., Boehm, A. B. 2013; 47 (20): 11554-11561

  Abstract

  Microbial pollutants from coastal discharges can increase illness risks for swimmers and cause beach advisories. There is presently no predictive model for estimating the entrainment of pollution from coastal discharges into the surf zone. We present a novel, quantitative framework for estimating surf zone entrainment of pollution at a wave-dominant open beach. Using physical arguments, we identify a dimensionless parameter equal to the quotient of the surf zone width l(sz) and the cross-flow length scale of the discharge la = M(j) (1/2)/U(sz), where M(j) is the discharge's momentum flux and U(sz) is a representative alongshore velocity in the surf zone. We conducted numerical modeling of a nonbuoyant discharge at an alongshore uniform beach with constant slope using a wave-resolving hydrodynamic model. Using results from 144 numerical experiments we develop an empirical relationship between the surf zone entrainment rate α and l(sz)/(la). The empirical relationship can reasonably explain seven measurements of surf zone entrainment at three diverse coastal discharges. This predictive relationship can be a useful tool in coastal water quality management and can be used to develop predictive beach water quality models.

  View details for DOI 10.1021/es402492f

  View details for PubMedID 24006887

• Engineering Solutions to Improve the Removal of Fecal Indicator Bacteria by Bioinfiltration Systems during Intermittent Flow of Stormwater. Environmental science & technology Mohanty, S. K., Torkelson, A. A., Dodd, H., Nelson, K. L., Boehm, A. B. 2013; 47 (19): 10791-10798

  Abstract

  Bioinfiltration systems facilitate the infiltration of urban stormwater into soil and reduce high flow events and flooding. Stormwater carries a myriad of pollutants including fecal indicator bacteria (FIB). Significant knowledge gaps exist about the ability of bioinfiltration systems to remove and retain FIB. The present study investigates the ability of model, simplified bioinfiltration systems containing quartz sand and iron oxide-coated quartz sand (IOCS) to remove two FIB (Enterococcus faecalis and Escherichia coli) suspended in synthetic stormwater with and without natural organic matter (NOM) as well as the potential for accumulated FIB to be remobilized during intermittent flow. The experiments were conducted in two phases: (1) the saturated columns packed with either sand or IOCS were contaminated by injecting stormwater with bacteria followed by injection of sterile stormwater and (2) the contaminated columns were subjected to intermittent infiltration of sterile stormwater preceded by a pause during which columns were either kept saturated or drained by gravity. During intermittent flow, fewer bacteria were released from the saturated column compared to the column drained by gravity: 12% of attached E. coli and 3% of attached Ent. faecalis were mobilized from the drained sand column compared to 3% of attached E. coli and 2% attached Ent. faecalis mobilized from the saturated sand column. Dry and wet cycles introduce moving air-water interfaces that can scour bacteria from grain surfaces. During intermittent flows, less than 0.2% of attached bacteria were mobilized from IOCS, which bound both bacteria irreversibly in the absence of NOM. Addition of NOM, however, increased bacterial mobilization from IOCS: 50% of attached E. coli and 8% of attached Ent. faecalis were released from IOCS columns during draining and rewetting. Results indicate that using geomedia such as IOCS that promote irreversible attachment of bacteria, and maintaining saturated condition, could minimize the mobilization of previous attached bacteria from bioinfiltration systems, although NOM may significantly decrease these benefits.

  View details for DOI 10.1021/es305136b

  View details for PubMedID 23721343

• A Coupled Modeling and Molecular Biology Approach to Microbial Source Tracking at Cowell Beach, Santa Cruz, CA, United States. Environmental science & technology Russell, T. L., Sassoubre, L. M., Wang, D., Masuda, S., Chen, H., Soetjipto, C., Hassaballah, A., Boehm, A. B. 2013; 47 (18): 10231-10239

  Abstract

  Consistently high levels of bacterial indicators of fecal pollution rank Cowell Beach as the most polluted beach in California. High levels of fecal indicator bacteria (FIB), E. coli and enterococci, are measured throughout the summer, resulting in beach advisories with social and economic consequences. The source of FIB, however, is unknown. Speculations have been made that the wrack accumulating on the beach is a major source of FIB to the surf zone. The present study uses spatial and temporal sampling coupled with process-modeling to investigate potential FIB sources and the relative contributions of those sources. Temporal sampling showed consistently high FIB concentrations in the surf zone, sand, and wrack at Cowell Beach, and ruled out the storm drain, the river, the harbor, and the adjacent wharf as the sources of the high concentrations observed in the surf zone. Spatial sampling confirmed that the source of FIB to the beach is terrestrial rather than marine. Modeling results showed two dominant FIB sources to the surf zone: sand for enterococci and groundwater for E. coli. FIB from wrack represented a minor contribution to bacterial levels in the water. Molecular source tracking methods indicate the FIB at the beach is of human and bird origin. The microbial source tracking (MST) approach presented here provides a framework for future efforts.

  View details for DOI 10.1021/es402303w

  View details for PubMedID 23924260

• A coupled modeling and molecular biology approach to microbial source tracking at Cowell Beach, Santa Cruz, CA, United States. Environmental science & technology Russell, T. L., Sassoubre, L. M., Wang, D., Masuda, S., Chen, H., Soetjipto, C., Hassaballah, A., Boehm, A. B. 2013; 47 (18): 10231-10239

  Abstract

  Consistently high levels of bacterial indicators of fecal pollution rank Cowell Beach as the most polluted beach in California. High levels of fecal indicator bacteria (FIB), E. coli and enterococci, are measured throughout the summer, resulting in beach advisories with social and economic consequences. The source of FIB, however, is unknown. Speculations have been made that the wrack accumulating on the beach is a major source of FIB to the surf zone. The present study uses spatial and temporal sampling coupled with process-modeling to investigate potential FIB sources and the relative contributions of those sources. Temporal sampling showed consistently high FIB concentrations in the surf zone, sand, and wrack at Cowell Beach, and ruled out the storm drain, the river, the harbor, and the adjacent wharf as the sources of the high concentrations observed in the surf zone. Spatial sampling confirmed that the source of FIB to the beach is terrestrial rather than marine. Modeling results showed two dominant FIB sources to the surf zone: sand for enterococci and groundwater for E. coli. FIB from wrack represented a minor contribution to bacterial levels in the water. Molecular source tracking methods indicate the FIB at the beach is of human and bird origin. The microbial source tracking (MST) approach presented here provides a framework for future efforts.

  View details for DOI 10.1021/es402303w

  View details for PubMedID 23924260

• Conducting nanosponge electroporation for affordable and high-efficiency disinfection of bacteria and viruses in water. Nano letters Liu, C., Xie, X., Zhao, W., Liu, N., Maraccini, P. A., Sassoubre, L. M., Boehm, A. B., Cui, Y. 2013; 13 (9): 4288-4293

  Abstract

  High-efficiency, affordable, and low energy water disinfection methods are in great need to prevent diarrheal illness, which is one of the top five leading causes of death over the world. Traditional water disinfection methods have drawbacks including carcinogenic disinfection byproducts formation, energy and time intensiveness, and pathogen recovery. Here, we report an innovative method that achieves high-efficiency water disinfection by introducing nanomaterial-assisted electroporation implemented by a conducting nanosponge filtration device. The use of one-dimensional (1D) nanomaterials allows electroporation to occur at only several volts, which is 2 to 3 orders of magnitude lower than that in traditional electroporation applications. The disinfection mechanism of electroporation prevents harmful byproduct formation and ensures a fast treatment speed of 15 000 L/(h·m(2)), which is equal to a contact time of 1 s. The conducting nanosponge made from low-cost polyurethane sponge coated with carbon nanotubes and silver nanowires ensures the device's affordability. This method achieves more than 6 log (99.9999%) removal of four model bacteria, including Escherichia coli, Salmonella enterica Typhimirium, Enterococcus faecalis, and Bacillus subtilis, and more than 2 log (99%) removal of one model virus, bacteriophage MS2, with a low energy consumption of only 100 J/L.

  View details for DOI 10.1021/nl402053z

  View details for PubMedID 23987737

• Mechanisms of post-supply contamination of drinking water in Bagamoyo, Tanzania. Journal of water and health Harris, A. R., Davis, J., Boehm, A. B. 2013; 11 (3): 543-554

  Abstract

  Access to household water connections remains low in sub-Saharan Africa, representing a public health concern. Previous studies have shown water stored in the home to be more contaminated than water at the source; however, the mechanisms of post-supply contamination remain unclear. Using water quality measurements and structured observations of households in Bagamoyo, Tanzania, this study elucidates the causal mechanisms of the microbial contamination of drinking water after collection from a communal water source. The study identifies statistically significant loadings of fecal indicator bacteria (FIB) occurring immediately after filling the storage container at the source and after extraction of the water from the container in the home. Statistically significant loadings of FIB also occur with various water extraction methods, including decanting from the container and use of a cup or ladle. Additionally, pathogenic genes of Escherichia coli were detected in stored drinking water but not in the source from which it was collected, highlighting the potential health risks of post-supply contamination. The results of the study confirm that storage containers and extraction utensils introduce microbial contamination into stored drinking water, and suggest that further research is needed to identify methods of water extraction that prevent microbial contamination of drinking water.

  View details for DOI 10.2166/wh.2013.023

  View details for PubMedID 23981881

• Enterococcus spp on fomites and hands indicate increased risk of respiratory illness in child care centers AMERICAN JOURNAL OF INFECTION CONTROL Julian, T. R., Pickering, A. J., Leckie, J. O., Boehm, A. B. 2013; 41 (8): 728-733

  Abstract

  BACKGROUND: Surface-mediated transmission is a potential route for respiratory disease in child care centers, but evidence of its importance relative to other routes (eg, airborne) is limited. METHODS: We tracked respiratory disease and monitored bacteria contamination on hands and fomites over 4 months during 64 visits at 2 child care centers. Staff monitored health daily by recording respiratory symptoms. We measured concentrations of Escherichia coli, Enterococcus spp, and fecal coliform in hand rinses and on select fomites. RESULTS: We demonstrated that symptomatic respiratory illness was positively associated with microbial contamination on hands and fomites, as measured using Enterococcus spp. Enterococcus spp were 0.28 (95% confidence interval: 0.08-0.48)-log(10) (colony-forming units per 2 hands) higher when an individual had symptomatic respiratory illness. Susceptible individuals were 1.62 (95% confidence interval: 1.06-2.46) times more likely to develop respiratory illness within 4 days with every log(10) increase of Enterococcus spp on hands. CONCLUSION: The findings imply that hand contamination as measured using Enterococcus spp is a risk factor for onset of respiratory illness and highlight the utility of fecal indicator bacteria as a metric for hand and fomite contamination.

  View details for DOI 10.1016/j.ajic.2012.10.013

  View details for Web of Science ID 000322641100014

  View details for PubMedID 23394857

• Engineered Infiltration Systems for Urban Stormwater Reclamation ENVIRONMENTAL ENGINEERING SCIENCE Grebel, J. E., Mohanty, S. K., Torkelson, A. A., Boehm, A. B., Higgins, C. P., Maxwell, R. M., Nelson, K. L., Sedlak, D. L. 2013; 30 (8): 437-454

  View details for DOI 10.1089/ees.2012.0312

  View details for Web of Science ID 000323206400005

• Salmonella enterica Diversity in Central Californian Coastal Waterways. Applied and environmental microbiology Walters, S. P., González-Escalona, N., Son, I., Melka, D. C., Sassoubre, L. M., Boehm, A. B. 2013; 79 (14): 4199-4209

  Abstract

  Salmonella enterica is one of the most important bacterial enteric pathogens worldwide, however, little is known about its distribution and diversity in the environment. The present study explored the diversity of 104 strains of Salmonella enterica isolated over two years from twelve coastal waterways in central California. Pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were used to probe species diversity. Seventy-four PFGE patterns and 38 sequence types (STs) were found including 18 newly described ST. Nineteen of 25 PFGE patterns were indistinguishable from those of clinical isolates in PulseNet. The most common ST was consistent with S. enterica serovar Typhimurium; other frequently detected STs were associated with serovars Heidelberg and Enteritidis - all important etiologies of salmonellosis. An investigation into S. enterica biogeography was conducted at the level of ST and subspecies. At the ST and subspecies level, we found a taxa-time relationship, but no taxa-area or taxa-environmental distance relationships. STs collected during wet versus dry conditions tended to be more similar; however, STs collected from waterways adjacent to watersheds with similar land covers did not tend to be similar. The results suggest lack of dispersal limitation may be an important factor affecting the diversity of S. enterica in the region.

  View details for DOI 10.1128/AEM.00930-13

  View details for PubMedID 23624479

• Sunlight Inactivation of Human Viruses and Bacteriophages in Coastal Waters Containing Natural Photosensitizers ENVIRONMENTAL SCIENCE & TECHNOLOGY Silverman, A. I., Peterson, B. M., Boehm, A. B., McNeill, K., Nelson, K. L. 2013; 47 (4): 1870-1878

  Abstract

  Sunlight inactivation of poliovirus type 3 (PV3), adenovirus type 2 (HAdV2), and two bacteriophage (MS2 and PRD1) was investigated in an array of coastal waters to better understand solar inactivation mechanisms and the effect of natural water constituents on observed inactivation rates (k(obs)). Reactor scale inactivation experiments were conducted using a solar simulator, and k(obs) for each virus was measured in a sensitizer-free control and five unfiltered surface water samples collected from different sources. k(obs) values varied between viruses in the same water matrix, and for each virus in different matrices, with PV3 having the fastest and MS2 the slowest k(obs) in all waters. When exposed to full-spectrum sunlight, the presence of photosensitizers increased k(obs) of HAdV2, PRD1 and MS2, but not PV3, which provides evidence that the exogenous sunlight inactivation mechanism, involving damage by exogenously produced reactive intermediates, played a greater role for these viruses. While PV3 inactivation was observed to be dominated by endogenous mechanisms, this may be due to a masking of exogenous k(obs) by significantly faster endogenous k(obs). Results illustrate that differences in water composition can shift absolute and relative inactivation rates of viruses, which has important implications for natural wastewater treatment systems, solar disinfection (SODIS), and the use of indicator organisms for monitoring water quality.

  View details for DOI 10.1021/es3036913

  View details for Web of Science ID 000315326700012

  View details for PubMedID 23384052

• Hands and Water as Vectors of Diarrhea! Pathogens in Bagannoyo, Tanzania ENVIRONMENTAL SCIENCE & TECHNOLOGY Mattioli, M. C., Pickering, A. J., Gilsdorf, R. J., Davis, J., Boehm, A. B. 2013; 47 (1): 355-363

  Abstract

  Diarrheal disease is a leading cause of under-five childhood mortality worldwide, with at least half of these deaths occurring in sub-Saharan Africa. Transmission of diarrheal pathogens occurs through several exposure routes including drinking water and hands, but the relative importance of each route is not well understood. Using molecular methods, this study examines the relative importance of different exposure routes by measuring enteric bacteria (pathogenic Escherichia coli) and viruses (rotavirus, enterovirus, adenovirus) in hand rinses, stored water, and source waters in Bagamoyo, Tanzania. Viruses were most frequently found on hands, suggesting that hands are important vectors for viral illness. The occurrence of E. coli virulence genes (ECVG) was equivalent across all sample types, indicating that both water and hands are important for bacterial pathogen transmission. Fecal indicator bacteria and turbidity were good predictors of ECVG, whereas turbidity and human-specific Bacteroidales were good predictors of viruses. ECVG were more likely found in unimproved water sources, but both ECVG and viral genes were detected in improved water sources. ECVG were more likely found in stored water of households with unimproved sanitation facilities. The results provide insights into the distribution of pathogens in Tanzanian households and offer evidence that hand-washing and improved water management practices could alleviate viral and bacterial diarrhea.

  View details for DOI 10.1021/es303878d

  View details for Web of Science ID 000313220300046

  View details for PubMedID 23181394

• Mechanisms of post-supply contamination of drinking water in Bagamoyo Tanzania. Journal of Water & Health Harris, A., R., Davis, J., Boehm, A., B. 2013; 3 (11): 543-54

  Abstract

  Access to household water connections remains low in sub-Saharan Africa, representing a public health concern. Previous studies have shown water stored in the home to be more contaminated than water at the source; however, the mechanisms of post-supply contamination remain unclear. Using water quality measurements and structured observations of households in Bagamoyo, Tanzania, this study elucidates the causal mechanisms of the microbial contamination of drinking water after collection from a communal water source. The study identifies statistically significant loadings of fecal indicator bacteria (FIB) occurring immediately after filling the storage container at the source and after extraction of the water from the container in the home. Statistically significant loadings of FIB also occur with various water extraction methods, including decanting from the container and use of a cup or ladle. Additionally, pathogenic genes of Escherichia coli were detected in stored drinking water but not in the source from which it was collected, highlighting the potential health risks of post-supply contamination. The results of the study confirm that storage containers and extraction utensils introduce microbial contamination into stored drinking water, and suggest that further research is needed to identify methods of water extraction that prevent microbial contamination of drinking water.

  View details for DOI 10.2166/wh.2013.023

• Recommendations following a multi-laboratory comparison of microbial source tracking methods. Water Research. Stewart, J., Boehm, A., B, Dubinsky, E., A., Fong, T., T., Goodwin, K., D., Griffith, J., F. 2013; 47: 6829-6838
• Performance of Viruses and Bacteriophages for Fecal Source Determination in a Multi-Laboratory, Comparative Study. Water Research. Harwood, V., J., Boehm, A., B., Sassoubre, L., M., Kannappan, V., Stewart, J., R., Fong, T., T. 2013; 47: 6929-6943
• Multi-Laboratory Evaluations of the Performance of Catellicoccus marimamm\ alium PCR Assays Developed to Target Gull Fecal Sources Water Research. Sinigalliano, C., D., Ervin, J., Van De Werfhorst, L., Badgley, B., Balleste, E., Bartkowiak, J., Boehm, A. 2013; 47: 6883-6896
• Fecal indicator bacteria on fomites and hands are associated with increased risk of respiratory illness in day care centers. American Journal of Infection Control Julian, T., R., Pickering, A., J., Leckie, J., O., Boehm., A., B. 2013; 41: 728-733
• Evaluation of the repeatability and reproducibility of a suite of qPCR-based microbial source tracking methods. Water Research. Ebentier, D., L., Hanley, K., T., Cao, Y., Badgley, B., D., Boehm, A., B., Ervin, J., S. 2013; 47: 6839-6848
• Characterization of fecal concentrations in human and other animal sources by physical, cutlure, and quantitative real-time PCR methods. Water Research. Ervin, J., S., Russell, T., L, Layton, B., A., Yamahara, K., M., Wang, D., Sassoubre, L., M., Boehm, A. 2013; 47: 6873-6882
• A simple estimate of entrainment rate of pollutants from a coastal discharge into the surf zone. Environmental Science & Technology Wong, S.H., C., Monismith, S., G., Boehm, A., B. 2013; 47: 11554-11561
• Performance of human fecal-associated PCR-based assays: an international source identificiaiton method evaluation. Water Research. Layton, B., Cao, Y., Ebentie, D., L., Hanley, K., T., Van De Werfhorst, L., Wang, D., Boehm, A. 2013; 47: 6897-6908
• Enterococcus and Escherichia coli fecal source apportionment with microbial source tracking genetic markers -- Is it feasible? Water Research. Wang, D., Farnleitner, A., H., Field, K., G., Green, H., C., Shanks, O., C., Boehm., A., B. 2013; 47: 6849-6861
• Comparison of PCR and quantitative real-time PCR methods for the characterization of ruminant and cattle fecal pollution sources. Water Research. Raith, M., Kelty, C., A., Griffith, J., F., Schriewer, A., Wuertz, S., Mieszkin, S., Boehm, A. 2013; 47: 6921-6928
• Mechanisms for Photoinactivation of Enterococcus faecalis in Seawater APPLIED AND ENVIRONMENTAL MICROBIOLOGY Sassoubre, L. M., Nelson, K. L., Boehm, A. B. 2012; 78 (21): 7776-7785

  Abstract

  Field studies in fresh and marine waters consistently show diel fluctuations in concentrations of enterococci, indicators of water quality. We investigated sunlight inactivation of Enterococcus faecalis to gain insight into photoinactivation mechanisms and cellular responses to photostress. E. faecalis bacteria were exposed to natural sunlight in clear, filtered seawater under both oxic and anoxic conditions to test the relative importance of oxygen-mediated and non-oxygen-mediated photoinactivation mechanisms. Multiple methods were used to assess changes in bacterial concentration, including cultivation, quantitative PCR (qPCR), propidium monoazide (PMA)-qPCR, LIVE/DEAD staining using propidium iodide (PI), and cellular activity, including ATP concentrations and expression of the superoxide dismutase-encoding gene, sodA. Photoinactivation, based on numbers of cultivable cells, was faster in oxic than in anoxic microcosms exposed to sunlight, suggesting that oxygen-mediated photoinactivation dominated. There was little change in qPCR signal over the course of the experiment, demonstrating that the nucleic acid targets were not damaged to a significant extent. The PMA-qPCR signal was also fairly stable, consistent with the observation that the fraction of PI-permeable cells was constant. Thus, damage to the membrane was minimal. Microbial ATP concentrations decreased in all microcosms, particularly the sunlit oxic microcosms. The increase in relative expression of the sodA gene in the sunlit oxic microcosms suggests that cells were actively responding to oxidative stress. Dark repair was not observed. This research furthers our understanding of photoinactivation mechanisms and the conditions under which diel fluctuations in enterococci can be expected in natural and engineered systems.

  View details for DOI 10.1128/AEM.02375-12

  View details for Web of Science ID 000309678600032

  View details for PubMedID 22941072

  View details for PubMedCentralID PMC3485734

• Comparison of enterovirus and adenovirus concentration and enumeration methods in seawater from Southern California, USA and Baja Malibu, Mexico JOURNAL OF WATER AND HEALTH Sassoubre, L. M., Love, D. C., Silverman, A. I., Nelson, K. L., Boehm, A. B. 2012; 10 (3): 419-430

  Abstract

  Despite being important etiological agents of waterborne illness, the sources, transport and decay of human viruses in recreational waters are not well understood. This study examines enterovirus and adenovirus concentrations in coastal water samples collected from four beaches impacted by microbial pollution: (1) Malibu Lagoon, Malibu; (2) Tijuana River, Imperial Beach; (3) Baja Malibu, Baja California; and (4) Punta Bandera, Baja California. Water samples were concentrated using a flocculation-based skim milk method and dead-end membrane filtration (MF). Viruses were enumerated using cell culture infectivity assays and reverse transcription quantitative polymerase chain reaction (RT-QPCR). Across concentration and quantification methods, enteroviruses were detected more often than adenoviruses. For both viruses, MF followed by (RT)QPCR yielded higher concentrations than skim milk flocculation followed by (RT)QPCR or cell culture assays. Samples concentrated by skim milk flocculation and enumerated by (RT)QPCR agreed more closely with concentrations enumerated by cell culture assays than MF followed by (RT)QPCR. The detection of viruses by MF and (RT)QPCR was positively correlated with the presence of infectious viruses. Further research is needed to determine if detection of viruses by rapid methods such as (RT)QPCR can be a useful water quality monitoring tool to assess health risks in recreational waters.

  View details for DOI 10.2166/wh.2012.011

  View details for Web of Science ID 000309490300009

  View details for PubMedID 22960486

• Mobilization and Transport of Naturally Occurring Enterococci in Beach Sands Subject to Transient Infiltration of Seawater ENVIRONMENTAL SCIENCE & TECHNOLOGY Russell, T. L., Yamahara, K. M., Boehm, A. B. 2012; 46 (11): 5988-5996

  Abstract

  This study explores the transport of enterococci (ENT) from naturally contaminated beach sands to the groundwater table via infiltrating seawater using field, laboratory, and modeling experiments. ENT were readily mobilized and transported through the unsaturated zone during infiltration events in both the field and laboratory column experiments. Detachment mechanisms were investigated using a modified version of HYDRUS-1D. Three models for detachment kinetics were tested. Detachment kinetics that are first order with respect to the rate of change in the water content and attached surface bacterial concentrations were found to provide a best fit between predicted and observed data. From these experimental and model results we conclude that detachment mechanisms associated with the rapid increases in pore water content such as air-water interface scouring and thin film expansion are likely drivers of ENT mobilization in the investigated system. These findings suggest that through-beach transport of ENT may be an important pathway through which ENT from beach sands are transported to beach groundwater where they may be discharged to coastal waters via submarine groundwater discharge.

  View details for DOI 10.1021/es300408z

  View details for Web of Science ID 000304783000046

  View details for PubMedID 22533299

• Fecal Contamination and Diarrheal Pathogens on Surfaces and in Soils among Tanzanian Households with and without Improved Sanitation ENVIRONMENTAL SCIENCE & TECHNOLOGY Pickering, A. J., Julian, T. R., Marks, S. J., Mattioli, M. C., Boehm, A. B., Schwab, K. J., Davis, J. 2012; 46 (11): 5736-5743

  Abstract

  Little is known about the extent or pattern of environmental fecal contamination among households using low-cost, on-site sanitation facilities, or what role environmental contamination plays in the transmission of diarrheal disease. A microbial survey of fecal contamination and selected diarrheal pathogens in soil (n = 200), surface (n = 120), and produce samples (n = 24) was conducted in peri-urban Bagamoyo, Tanzania, among 20 households using private pit latrines. All samples were analyzed for E. coli and enterococci. A subset was analyzed for enterovirus, rotavirus, norovirus GI, norovirus GII, diarrheagenic E. coli, and general and human-specific Bacteroidales fecal markers using molecular methods. Soil collected from the house floor had significantly higher concentrations of E. coli and enterococci than soil collected from the latrine floor. There was no significant difference in fecal indicator bacteria levels between households using pit latrines with a concrete slab (improved sanitation) versus those without a slab. These findings imply that the presence of a concrete slab does not affect the level of fecal contamination in the household environment in this setting. Human Bacteroidales, pathogenic E. coli, enterovirus, and rotavirus genes were detected in soil samples, suggesting that soil should be given more attention as a transmission pathway of diarrheal illness in low-income countries.

  View details for DOI 10.1021/es300022c

  View details for Web of Science ID 000304783000017

  View details for PubMedID 22545817

• Occurrence and Persistence of Bacterial Pathogens and Indicator Organisms in Beach Sand along the California Coast APPLIED AND ENVIRONMENTAL MICROBIOLOGY Yamahara, K. M., Sassoubre, L. M., Goodwin, K. D., Boehm, A. B. 2012; 78 (6): 1733-1745

  Abstract

  This report documents the presence of fecal indicators and bacterial pathogens in sand at 53 California marine beaches using both culture-dependent and -independent (PCR and quantitative PCR [QPCR]) methods. Fecal indicator bacteria were widespread in California beach sand, with Escherichia coli and enterococci detected at 68% and 94% of the beaches surveyed, respectively. Somatic coliphages and a Bacteroidales human-specific fecal marker were detected at 43% and 13% of the beaches, respectively. Dry sand samples from almost 30% of the beaches contained at least one of the following pathogens: Salmonella spp., Campylobacter spp., Staphylococcus aureus, and methicillin-resistant Staphylococcus aureus (MRSA), which were detected at 15%, 13%, 14%, and 3% of tested beaches, respectively. Fecal indicators and pathogens were poorly correlated to one another and to land cover. Sands were dry at the time of collection, and those with relatively high moisture tended to have higher concentrations or a more frequent occurrence of both indicators and pathogens. Using culture-dependent assays, fecal indicators decayed faster than pathogens in microcosm experiments using unaltered beach sand seeded with sewage and assessed by culture-dependent assays. The following order of persistence was observed (listed from most to least persistent): Campylobacter > Salmonella > somatic coliphages > enterococci > E. coli > F(+) phages. In contrast, pathogens decayed faster than fecal indicators in culture-independent assays: enterococci > Bacteroidales human-specific marker > Salmonella > Campylobacter. Microcosm experiments demonstrated that both indicators and pathogens were mobilized by wetting with seawater. Decay rates measured by QPCR were lower than those measured with culture-dependent methods. Enterococcal persistence and possible growth were observed for wetted microcosms relative to unwetted controls.

  View details for DOI 10.1128/AEM.06185-11

  View details for Web of Science ID 000300629800014

  View details for PubMedID 22247142

  View details for PubMedCentralID PMC3298156

• Coupled physical, chemical, and microbiological measurements suggest a connection between internal waves and surf zone water quality in the Southern California Bight CONTINENTAL SHELF RESEARCH Wong, S. H., Santoro, A. E., Nidzieko, N. J., Hench, J. L., Boehm, A. B. 2012; 34: 64-78

  View details for DOI 10.1016/j.csr.2011.12.005

  View details for Web of Science ID 000300033000008

• Solar inactivation of four Salmonella serovars in fresh and marine waters JOURNAL OF WATER AND HEALTH Boehm, A. B., Soetjipto, C., Wang, D. 2012; 10 (4): 504-510

  Abstract

  Sunlight-mediated disinfection of water is of interest to both the drinking and recreational water quality community of researchers due to its potential to reduce microbial contamination and waterborne illness. Photo-inactivation of enteric bacteria has primarily been investigated using Escherichia coli and laboratory strains of model bacteria. The present study sought to document the photo-inactivation of environmental isolates of Salmonella in filter-sterilized natural seawater and freshwater and to test the hypothesis that diverse Salmonella serovars decay at similar rates both within and between water matrices. The inactivation of Salmonella enterica Typhimurium LT2, Typhimurium ST19, Heidelberg, and Mbandaka was examined in sunlit and dark microcosms. First order decay was observed in sunlit microcosms; the time until 90% inactivation was of the order of 10 min. A significant shoulder, of the order of 1 hr in length, was observed in the freshwater microcosms during which concentrations were stable. Serovar Mdandaka decayed more slowly than other serovars in both seawater and freshwater. The serovars were extremely stable in the dark microcosms showing little to no decay over 53 days. The results document intra-species variation in photo-inactivation, likely owing to differences in intracellular concentrations of photo-sensitizing molecules or molecules that quench reactive species.

  View details for DOI 10.2166/wh.2012.084

  View details for Web of Science ID 000311341300002

  View details for PubMedID 23165707

• Marine and Freshwater Fecal Indicators and Source Identification. Encyclopedia of Sustainability Science and Technology McLellan, S., L., Boehm, A., B., Shanks, O., C. edited by Grimes, D., J. 2012
• Photoinactivation mechanisms of Enterococcus faecalis in seawater. Applied and Environmental Microbiology Sassoubre, L., M., Nelson, K., L., Boehm., A., B. 2012; 78: 7776-7785
• Diurnal Variation in Enterococcus Species Composition in Polluted Ocean Water and a Potential Role for the Enterococcal Carotenoid in Protection against Photoinactivation APPLIED AND ENVIRONMENTAL MICROBIOLOGY Maraccini, P. A., Ferguson, D. M., Boehm, A. B. 2012; 78 (2): 305-310

  Abstract

  Enterococcus species composition was determined each hour for 72 h at a polluted marine beach in Avalon, Santa Catalina Island, CA. Species composition during the day was significantly different from that at night, based on an analysis of similarity. Enterococcus faecium and E. faecalis were more prevalent at night than during the day, while E. hirae and other Enterococcus species were more prevalent during the day than the night. Enterococcus spp. containing a yellow pigment were more common during the day than the night, suggesting that the pigmented phenotype may offer a competitive advantage under sunlit conditions. A laboratory microcosm experiment established that the pigmented E. casseliflavus isolate and a pigmented E. faecalis isolate recovered from the field site decay slower than a nonpigmented E. faecalis isolate in a solar simulator in simulated, clear seawater. This further supports the idea that the yellow carotenoid pigment in Enterococcus provides protection under sunlit conditions. The findings are in accordance with previous work with other carotenoid-containing nonphotosynthetic and photosynthetic bacteria that suggests that the carotenoid is able to quench reactive oxygen species capable of causing photoinactivation and photostress. The results suggest that using enterococcal species composition as a microbial source tracking tool may be hindered by the differential environmental persistence of pigmented and nonpigmented enterococci.

  View details for DOI 10.1128/AEM.06821-11

  View details for Web of Science ID 000299018800002

  View details for PubMedID 22081569

  View details for PubMedCentralID PMC3255750

• Quantitative PCR-based detection of pathogenic Leptospira in Hawai'ian coastal streams JOURNAL OF WATER AND HEALTH Viau, E. J., Boehm, A. B. 2011; 9 (4): 637-646

  Abstract

  Pathogenic Leptospira, the causative agents of leptospirosis, are mainly associated with tropical freshwaters, but little is known about their fate in the environment. This study analyzed the distribution of pathogenic Leptospira genomes in 22 tropical coastal streams using quantitative polymerase chain reaction (qPCR). Statistical analyses were conducted to understand pathogenic Leptospira associations with water quality parameters, land use, microbial source tracking (MST) markers, and fecal indicators. Results indicated that pathogenic Leptospira genomes were widespread in O'ahu coastal streams during the Hawai'ian rainy season, with slightly higher concentrations in December when compared with March. Leptospira showed a strong positive association to turbidity, a finding consistent with studies showing increased Leptospira survival when aggregated to particles. Positive correlations to salinity may also indicate survival of Leptospira in relatively saline stream waters. A positive association to the human Bacteroidales fecal marker, no correlation to pig or cow Bacteroidales markers, and a negative association to agricultural land coverage may suggest human or other non-agricultural animal sources of Leptospira (e.g., rats or dogs). Future studies of Leptospira in the Hawai'ian environment are recommended to investigate Leptospira survival in saline waters, to determine both primary and secondary Hawai'ian animal hosts of Leptospira, and to correlate environmental exposures with epidemiological studies of leptospirosis.

  View details for DOI 10.2166/wh.2011.064

  View details for Web of Science ID 000297599300003

  View details for PubMedID 22048423

• Effective detection of human noroviruses in Hawaiian waters using enhanced RT-PCR methods WATER RESEARCH Tong, H., Connell, C., Boehm, A. B., Lu, Y. 2011; 45 (18): 5837-5848

  Abstract

  The current recreational water quality criteria using growth-based measurements of fecal indicator bacteria (FIB) concentration have their limitations for swimmer protection. To evaluate the possible use of enteric viruses as an improved indicator of human sewage contamination in recreational waters for enhanced health risk assessment, human norovirus (huNoV) was tested as a model in this study. To establish a highly sensitive protocol for effective huNoV detection in waters, 16 published and newly designed reverse transcription polymerase chain reaction (RT-PCR) primer pairs specific for huNoV genogroup I (GI) and genogroup II (GII) were comparatively evaluated side-by-side using single sources of huNoV RNA stock extracted from local clinical isolates. Under optimized conditions, these RT-PCR protocols shared a very different pattern of detection sensitivity for huNoV. The primer sets COG2F/COG2R and QNIF4/NV1LCR were determined to be the most sensitive ones for huNoV GII and GI, respectively, with up to 10(5)- and 10(6)-fold more sensitive as compared to other sets tested. These two sensitive protocols were validated by positive detection of huNoV in untreated and treated urban wastewater samples. In addition, these RT-PCR protocols enabled detection of the prevalence of huNoV in 5 (GI) and 10 (GII) of 16 recreational water samples collected around the island of O'ahu, which was confirmed by DNA sequencing and sequence analysis. Findings from this study support the possible use of enteric viral pathogens for environmental monitoring and argue the importance and essentiality for such monitoring activity to ensure a safe use of recreational waters.

  View details for DOI 10.1016/j.watres.2011.08.030

  View details for Web of Science ID 000296826200003

  View details for PubMedID 21945082

• Comparison of Surface Sampling Methods for Virus Recovery from Fomites APPLIED AND ENVIRONMENTAL MICROBIOLOGY Julian, T. R., Tamayo, F. J., Leckie, J. O., Boehm, A. B. 2011; 77 (19): 6918-6925

  Abstract

  The role of fomites in infectious disease transmission relative to other exposure routes is difficult to discern due, in part, to the lack of information on the level and distribution of virus contamination on surfaces. Comparisons of studies intending to fill this gap are difficult because multiple different sampling methods are employed and authors rarely report their method's lower limit of detection. In the present study, we compare a subset of sampling methods identified from a literature review to demonstrate that sampling method significantly influences study outcomes. We then compare a subset of methods identified from the review to determine the most efficient methods for recovering virus from surfaces in a laboratory trial using MS2 bacteriophage as a model virus. Recoveries of infective MS2 and MS2 RNA are determined using both a plaque assay and quantitative reverse transcription-PCR, respectively. We conclude that the method that most effectively recovers virus from nonporous fomites uses polyester-tipped swabs prewetted in either one-quarter-strength Ringer's solution or saline solution. This method recovers a median fraction for infective MS2 of 0.40 and for MS2 RNA of 0.07. Use of the proposed method for virus recovery in future fomite sampling studies would provide opportunities to compare findings across multiple studies.

  View details for DOI 10.1128/AEM.05709-11

  View details for Web of Science ID 000295123300023

  View details for PubMedID 21821742

  View details for PubMedCentralID PMC3187074

• Swimmer Risk of Gastrointestinal Illness from Exposure to Tropical Coastal Waters Impacted by Terrestrial Dry-Weather Runoff ENVIRONMENTAL SCIENCE & TECHNOLOGY Viau, E. J., Lee, D., Boehm, A. B. 2011; 45 (17): 7158-7165

  Abstract

  This study used molecular methods to measure concentrations of four enteric viruses (adenovirus, enterovirus, norovirus GI, and norovirus GII) and fecal source tracking markers (human, ruminant, and pig Bacteroidales) in land-based runoff from 22 tropical streams on O'ahu, Hawai'i. Each stream was sampled twice in the morning and afternoon during dry weather. Viruses and human Bacteroidales were widespread in the streams. Watershed septic tank densities were positively associated with higher occurrence of human Bacteroidales and norovirus. There were no associations between occurrence of viruses and fecal indicator concentrations. Virus concentrations and previously reported culturable Salmonella and Campylobacter were used as inputs to a quantitative microbial risk assessment (QMRA) model to estimate the risk of acquiring gastrointestinal (GI) illness from swimming in tropical marine waters adjacent to discharging streams. Monte Carlo methods were used to incorporate uncertainties in the dilution of stream discharge with seawater, swimmer ingestion volumes, pathogen concentrations, and dose-response parameters into the model. Median GI illness risk to swimmers from exposure to coastal waters adjacent to the 22 streams ranged from 0 to 21/1000. GI illness risks from viral exposures were generally orders of magnitude greater than bacterial exposures. Swimming adjacent to streams positive for norovirus or adenovirus resulted in the highest risks. The median risk adjacent to each stream was positively, significantly correlated to the concentration of Clostridium perfringens in the stream. Although a number of important assumptions were made to complete the QMRA, results suggest land-based runoff in the tropics as a potential source of GI illness risk, with pathogens coming from both human and nonhuman nonpoint sources including septic tanks.

  View details for DOI 10.1021/es200984b

  View details for Web of Science ID 000294373400012

  View details for PubMedID 21780808

• Dissolved Inorganic Nitrogen, Soluble Reactive Phosphorous, and Microbial Pollutant Loading from Tropical Rural Watersheds in Hawai'i to the Coastal Ocean During Non-Storm Conditions ESTUARIES AND COASTS Boehm, A. B., Yamahara, K. M., Walters, S. P., Layton, B. A., Keymer, D. P., Thompson, R. S., Knee, K. L., Rosener, M. 2011; 34 (5): 925-936

  View details for DOI 10.1007/s12237-010-9352-8

  View details for Web of Science ID 000293185800004

• Using radium isotopes to characterize water ages and coastal mixing rates: A sensitivity analysis LIMNOLOGY AND OCEANOGRAPHY-METHODS Knee, K. L., Garcia-Solsona, E., Garcia-Orellana, J., Boehm, A. B., Paytan, A. 2011; 9: 380-395

  View details for DOI 10.4319/lom.2011.9.380

  View details for Web of Science ID 000300377600003

• Sources and fate of Salmonella and fecal indicator bacteria in an urban creek JOURNAL OF ENVIRONMENTAL MONITORING Sassoubre, L. M., Walters, S. P., Russell, T. L., Boehm, A. B. 2011; 13 (8): 2206-2212

  Abstract

  This research aimed to understand the sources and fate of Salmonella and fecal bacteria in urban surface waters. An urban creek (San Pedro Creek, California, USA) that had unusually high levels of Salmonella and fecal bacteria relative to other nearby waterbodies was chosen as a model field site. State of the art microbiological methods were used in concert with modeling to investigate Salmonella and fecal bacteria sources, and determine field-relevant dark inactivation and photoinactivation rates. Three along-creek surveys that spanned reaches adjacent to both urban and forested land covers were conducted to measure Salmonella, enterococci, Escherichia coli, and horse- and human-specific Bacteroidales. Salmonella were detected adjacent to and downstream of urban land cover, but not adjacent to forested land cover. No human or horse-specific Bacteroidales fecal markers were detected implicating other urban animal sources of bacteria. Two locations along the creek where Salmonella was consistently detected were sampled hourly for 25 hours and a mass-balance model was applied to determine field-relevant light and dark inactivation rates for Salmonella, enterococci, and E. coli. Sunlight inactivation did not appear to be important in modulating concentrations of Salmonella, but was important in modulating both enterococci and E. coli concentrations. Dark inactivation was important for all three organisms. This is the first study to quantitatively examine the fate of Salmonella within an urban surface water. Although the work is carried out at a single site, the methodologies are extendable to source tracking in other waterbodies. Additionally, the rate constants determined through the modeling will be useful for modeling these organisms in other surface waters, and represent useful benchmarks for comparison to laboratory-derived inactivation rates.

  View details for DOI 10.1039/c1em10213c

  View details for Web of Science ID 000293502600012

  View details for PubMedID 21687857

• Wrack promotes the persistence of fecal indicator bacteria in marine sands and seawater FEMS MICROBIOLOGY ECOLOGY Imamura, G. J., Thompson, R. S., Boehm, A. B., Jay, J. A. 2011; 77 (1): 40-49

  Abstract

  Algae on freshwater beaches can serve as reservoirs for fecal indicator bacteria (FIB). Wrack (especially kelp) at marine beaches might sustain FIB as well. This study examines the relationship between beach wrack, FIB, and surrounding water and sediment at marine beaches along the California coast. Surveys of southern and central California beaches were conducted to observe environmental wrack-associated FIB concentrations. FIB concentrations normalized to dry weight were the highest in stranded dry wrack, followed by stranded wet and suspended 'surf' wrack. Laboratory microcosms were conducted to examine the effect of wrack on FIB persistence in seawater and sediment. Indigenous enterococci and Escherichia coli incubated in a seawater microcosm containing wrack showed increased persistence relative to those incubated in a microcosm without wrack. FIB concentrations in microcosms containing wrack-covered sand were significantly higher than those in uncovered sand after several days. These findings implicate beach wrack as an important FIB reservoir. The presence of wrack may increase water and sediment FIB levels, altering the relationship between FIB levels and actual health risk while possibly leading to beach closures. Further work will need to investigate the possibility of FIB growth on wrack and the potential for pathogen presence.

  View details for DOI 10.1111/j.1574-6941.2011.01082.x

  View details for Web of Science ID 000291312500004

  View details for PubMedID 21385189

• Bacterial pathogens in Hawaiian coastal streams-Associations with fecal indicators, land cover, and water quality WATER RESEARCH Viau, E. J., Goodwin, K. D., Yamahara, K. M., Layton, B. A., Sassoubre, L. M., Burns, S. L., Tong, H., Wong, S. H., Lu, Y., Boehm, A. B. 2011; 45 (11): 3279-3290

  Abstract

  This work aimed to understand the distribution of five bacterial pathogens in O'ahu coastal streams and relate their presence to microbial indicator concentrations, land cover of the surrounding watersheds, and physical-chemical measures of stream water quality. Twenty-two streams were sampled four times (in December and March, before sunrise and at high noon) to capture seasonal and time of day variation. Salmonella, Campylobacter, Staphylococcus aureus, Vibrio vulnificus, and V. parahaemolyticus were widespread -12 of 22 O'ahu streams had all five pathogens. All stream waters also had detectable concentrations of four fecal indicators and total vibrio with log mean ± standard deviation densities of 2.2 ± 0.8 enterococci, 2.7 ± 0.7 Escherichia coli, 1.1 ± 0.7 Clostridium perfringens, 1.2 ± 0.8 F(+) coliphages, and 3.6 ± 0.7 total vibrio per 100 ml. Bivariate associations between pathogens and indicators showed enterococci positively associated with the greatest number of bacterial pathogens. Higher concentrations of enterococci and higher incidence of Campylobacter were found in stream waters collected before sunrise, suggesting these organisms are sensitive to sunlight. Multivariate regression models of microbes as a function of land cover and physical-chemical water quality showed positive associations between Salmonella and agricultural and forested land covers, and between S. aureus and urban and agricultural land covers; these results suggested that sources specific to those land covers may contribute these pathogens to streams. Further, significant associations between some microbial targets and physical-chemical stream water quality (i.e., temperature, nutrients, turbidity) suggested that organism persistence may be affected by stream characteristics. Results implicate streams as a source of pathogens to coastal waters. Future work is recommended to determine infectious risks of recreational waterborne illness related to O'ahu stream exposures and to mitigate these risks through control of land-based runoff sources.

  View details for DOI 10.1016/j.watres.2011.03.033

  View details for Web of Science ID 000291499100002

  View details for PubMedID 21492899

• Submarine Groundwater Discharge to a High-Energy Surf Zone at Stinson Beach, California, Estimated Using Radium Isotopes ESTUARIES AND COASTS de Sieyes, N. R., Yamahara, K. M., Paytan, A., Boehm, A. B. 2011; 34 (2): 256-268

  View details for DOI 10.1007/s12237-010-9305-2

  View details for Web of Science ID 000287146900005

• Impact of urbanization and agriculture on the occurrence of bacterial pathogens and stx genes in coastal waterbodies of central California WATER RESEARCH Walters, S. P., Thebo, A. L., Boehm, A. B. 2011; 45 (4): 1752-1762

  Abstract

  Fecal pollution enters coastal waters through multiple routes, many of which originate from land-based activities. Runoff from pervious and impervious land surfaces transports pollutants from land to sea and can cause impairment of coastal ocean waters. To understand how land use practices and water characteristics influence concentrations of fecal indicator bacteria (FIB) and pathogens in natural waters, fourteen coastal streams, rivers, and tidal lagoons, surrounded by variable land use and animal densities, were sampled every six weeks over two years (2008 & 2009). Fecal indicator bacteria (FIB; Escherichia coli and Enterococci) and Salmonella concentrations, the occurrence of Bacteroidales human, ruminant, and pig-specific fecal markers, E. coli O157:H7, and Shiga toxin (stx) genes present in E. coli, were measured. In addition, environmental and climatic variables (e.g., temperature, salinity, rainfall), as well as human and livestock population densities and land cover were quantified. Concentrations of FIB and Salmonella were correlated with each other, but the occurrence of host-specific Bacteroidales markers did not correlate with FIB or pathogens. FIB and Salmonella concentrations, as well as the occurrence of E. coli harboring stx genes, were positively associated with the fraction of the surrounding subwatershed that was urban, while the occurrence of E. coli O157:H7 was positively associated with the agricultural fraction. FIB and Salmonella concentrations were negatively correlated to salinity and temperature, and positively correlated to rainfall. Areal loading rates of FIB, Salmonella and E. coli O157:H7 to the coastal ocean were calculated for stream and river sites and varied with land cover, salinity, temperature, and rainfall. Results suggest that FIB and pathogen concentrations are influenced, in part, by their flux from the land, which is exacerbated during rainfall; once waterborne, bacterial persistence is affected by water temperature and salinity.

  View details for DOI 10.1016/j.watres.2010.11.032

  View details for Web of Science ID 000286995000025

  View details for PubMedID 21168181

• The Effects of Informational Interventions on Household Water Management, Hygiene Behaviors, Stored Drinking Water Quality, and Hand Contamination in Peri-Urban Tanzania AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE Davis, J., Pickering, A. J., Rogers, K., Mamuya, S., Boehm, A. B. 2011; 84 (2): 184-191

  Abstract

  Safe water storage and hand hygiene have been shown to reduce fecal contamination and improve health in experimental settings; however, triggering and sustaining such behaviors is challenging. This study investigates the extent to which personalized information about Escherichia coli contamination of stored water and hands influenced knowledge, reported behaviors, and subsequent contamination levels among 334 households with less than 5-year-old children in peri-urban Dar es Salaam, Tanzania. One-quarter of the study participants received information about strategies to reduce risk of water- and sanitation-related illness. Respondents in another three study cohorts received this same information, along with their household's water and/or hand-rinse test results. Findings from this study suggest that additional work is needed to elucidate the conditions under which such testing represents a cost-effective strategy to motivate improved household water management and hand hygiene.

  View details for DOI 10.4269/ajtmh.2011.10-0126

  View details for Web of Science ID 000287003900002

  View details for PubMedID 21292883

  View details for PubMedCentralID PMC3029166

• Bacterial hand contamination among Tanzanian mothers varies temporally and following household activities TROPICAL MEDICINE & INTERNATIONAL HEALTH Pickering, A. J., Julian, T. R., Mamuya, S., Boehm, A. B., Davis, J. 2011; 16 (2): 233-239

  Abstract

  To characterize mechanisms of hand contamination with faecal indicator bacteria and to assess the presence of selected pathogens on mothers' hands in Tanzania.A household observational study combined with repeated microbiological hand rinse sampling was conducted among 119 mothers in Dar es Salaam, Tanzania. All hand rinse samples were analysed for enterococci and Escherichia coli, and selected samples were analysed for genetic markers of Bacteroidales, enterovirus and pathogenic E. coli.Using the toilet, cleaning up a child's faeces, sweeping, cleaning dishes, preparing food and bathing were all found to increase faecal indicator bacterial levels on hands. Geometric mean increases in colony forming units per two hands ranged from 50 (cleaning dishes) to 6310 (food preparation). Multivariate modelling of hand faecal indicator bacteria as a function of activities recently performed shows that food handling, exiting the household premises and longer time since last handwashing with soap are positively associated with bacterial levels on hands, while bathing is negatively associated. Genetic markers of Bacteroidales, enterovirus and pathogenic E. coli were each detected on a subset of mothers' hands.Escherichia coli and enterococci on hands can be significantly increased by various household activities, including those involving the use of soap and water. Thus, faecal indicator bacteria should be considered highly variable when used as indicators of handwashing behaviour. This work corroborates hands as important vectors of disease among Tanzanian mothers and highlights the difficulty of good personal hygiene in an environment characterized by the lack of networked sanitation and water supply services.

  View details for DOI 10.1111/j.1365-3156.2010.02677.x

  View details for Web of Science ID 000286116500015

  View details for PubMedID 21091858

• Recombination Shapes the Structure of an Environmental Vibrio cholerae Population APPLIED AND ENVIRONMENTAL MICROBIOLOGY Keymer, D. P., Boehm, A. B. 2011; 77 (2): 537-544

  Abstract

  Vibrio cholerae consists of pathogenic strains that cause sporadic gastrointestinal illness or epidemic cholera disease and nonpathogenic strains that grow and persist in coastal aquatic ecosystems. Previous studies of disease-causing strains have shown V. cholerae to be a primarily clonal bacterial species, but isolates analyzed have been strongly biased toward pathogenic genotypes, while representing only a small sample of the vast diversity in environmental strains. In this study, we characterized homologous recombination and structure among 152 environmental V. cholerae isolates and 13 other putative Vibrio isolates from coastal waters and sediments in central California, as well as four clinical V. cholerae isolates, using multilocus sequence analysis of seven housekeeping genes. Recombinant regions were identified by at least three detection methods in 72% of our V. cholerae isolates. Despite frequent recombination, significant linkage disequilibrium was still detected among the V. cholerae sequence types. Incongruent but nonrandom associations were observed for maximum likelihood topologies from the individual loci. Overall, our estimated recombination rate in V. cholerae of 6.5 times the mutation rate is similar to those of other sexual bacteria and appears frequently enough to restrict selection from purging much of the neutral intraspecies diversity. These data suggest that frequent recombination among V. cholerae may hinder the identification of ecotypes in this bacterioplankton population.

  View details for DOI 10.1128/AEM.02062-10

  View details for Web of Science ID 000286147300019

  View details for PubMedID 21075874

• CLASSICAL AND MOLECULAR METHODS TO MEASURE FECAL BACTERIA FECAL BACTERIA Edge, T. A., Boehm, A. B., Sadowsky, M. J., Whitman, R. L. 2011: 241–73

  View details for Web of Science ID 000285533600011

• MODELING FATE AND TRANSPORT OF FECAL BACTERIA IN SURFACE WATER FECAL BACTERIA Nevers, M. B., Boehm, A. B., Sadowsky, M. J., Whitman, R. L. 2011: 165–88

  View details for Web of Science ID 000285533600008

• Beaches and Coastal Environments MICROBIAL SOURCE TRACKING: METHODS, APPLICATIONS, AND CASE STUDIES Solo-Gabriele, H. M., Boehm, A. B., Scott, T. M., Sinigalliano, C. D., Hagedorn, C., Blanch, A. R., Harwood, V. J. 2011: 451–83

  View details for DOI 10.1007/978-1-4419-9386-1_20

  View details for Web of Science ID 000292530800020

• Case Studies: Beach Environments. Microbial Source Tracking: Methods, Applications, and Case Studies Solo-Gabriele, H., M., Boehm, A., B., Scott, T., M., Sinigalliano, C. edited by Hagedorn, C., Blanch, A., Harwood, J. Springer. 2011
• Recreational Water risk: Pathogens and Fecal Indicators. Encyclopedia of Sustainability Science and Technology Boehm, A., B., Soller, J., A. edited by Meyers, R., A. Springer. 2011

  View details for DOI 10.1007/978-1-14419-0851-3

• Oceans and human health. Encyclopedia of Environmental Health Boehm, A., B., Bischel, H., N. edited by Nriagu, J. Burlington, Elsevier.. 2011: 223–230
• Beach wrack is a reservoir for faecal indicator bacteria along the California coast FEMS Microbiology Ecology Imamura, G., Strickfaden, R., M., Boehm, A., B., Jay., J., A. 2011; 77: 40-49
• A comparison of surface sampling methods for virus recovery from fomites. Applied and Environmental Microbiology Julian, T., R., Tamayo, F., J., Leckie, J., O., Boehm, A., B. 2011; 77: 6918-6925
• Prominent human health impacts from several marine microbes: History, ecology, and public health implications. International Journal of Microbiology Bienfang, P., K., DeFelice, S., V., Laws, E., A., Brand, L., E., Bidigare, R., R., Christensen, S., Boehm, A. 2011

  View details for DOI 10.1155/2011/152815

• Hand fecal contamination among Tanzanian mothers varies temporally and following household activities. Tropical Medicine and International Health Pickering, A., J., Julian, T., R., Mamuya, S., Boehm, A., B., Davis, J. 2011; 16: 233-239
• Contributions of Foot Traffic and Outdoor Concentrations to Indoor Airborne Aspergillus AEROSOL SCIENCE AND TECHNOLOGY Goebes, M. D., Boehm, A. B., Hildemann, L. M. 2011; 45 (3): 352-363

  View details for DOI 10.1080/02786826.2010.537712

  View details for Web of Science ID 000286655700006

• Efficacy of alcohol-based hand sanitizer on hands soiled with dirt and cooking oil JOURNAL OF WATER AND HEALTH Pickering, A. J., Davis, J., Boehm, A. B. 2011; 9 (3): 429-433

  Abstract

  Handwashing education and promotion are well established as effective strategies to reduce diarrhea and respiratory illness in countries around the world. However, access to reliable water supplies has been identified as an important barrier to regular handwashing in low-income countries. Alcohol-based hand sanitizer (ABHS) is an effective hand hygiene method that does not require water, but its use is not currently recommended when hands are visibly soiled. This study evaluated the efficacy of ABHS on volunteers' hands artificially contaminated with Escherichia coli in the presence of dirt (soil from Tanzania) and cooking oil. ABHS reduced levels of E. coli by a mean of 2.33 log colony forming units (CFU) per clean hand, 2.32 log CFU per dirt-covered hand, and 2.13 log CFU per oil-coated hand. No significant difference in efficacy was detected between hands that were clean versus dirty or oily. ABHS may be an appropriate hand hygiene method for hands that are moderately soiled, and an attractive option for field settings in which access to water and soap is limited.

  View details for DOI 10.2166/wh.2011.138

  View details for Web of Science ID 000293624300001

  View details for PubMedID 21976190

• Virus transfer between fingerpads and fomites JOURNAL OF APPLIED MICROBIOLOGY JULIAN, T. R., Leckie, J. O., Boehm, A. B. 2010; 109 (6): 1868-1874

  Abstract

  Virus transfer between individuals and fomites is an important route of transmission for both gastrointestinal and respiratory illness. The present study examines how direction of transfer, virus species, time since last handwashing, gender, and titre affect viral transfer between fingerpads and glass.Six hundred fifty-six total transfer events, performed by 20 volunteers using MS2, φX174, and fr indicated 0·23 ± 0·22 (mean and standard deviation) of virus is readily transferred on contact. Virus transfer is significantly influenced by virus species and time since last handwashing. Transfer of fr bacteriophage is significantly higher than both MS2 and φX174. Virus transfer between surfaces is reduced for recently washed hands.Viruses are readily transferred between skin and surfaces on contact. The fraction of virus transferred is dependent on multiple factors including virus species, recently washing hands, and direction of transfer likely because of surface physicochemical interactions.The study is the first to provide a large data set of virus transfer events describing the central tendency and distribution of fraction virus transferred between fingers and glass. The data set from the study, along with the quantified effect sizes of the factors explored, inform studies examining role of fomites in disease transmission.

  View details for DOI 10.1111/j.1365-2672.2010.04814.x

  View details for Web of Science ID 000284170300002

  View details for PubMedID 20659186

• Enterococcus species distribution among human and animal hosts using multiplex PCR JOURNAL OF APPLIED MICROBIOLOGY Layton, B. A., Walters, S. P., Lam, L. H., Boehm, A. B. 2010; 109 (2): 539-547

  Abstract

  This study evaluated the use of Enterococcus species differentiation as a tool for microbial source tracking (MST) in recreational waters.Avian, mammalian and human faecal samples were screened for the occurrence of Enterococcus avium, Enterococcus casseliflavus, Enterococcus durans, Enterococcus gallinarum, Enterococcus faecium, Enterococcus faecalis, Enterococcus hirae and Enterococcus saccharolyticus using multiplex PCR. Host-specific patterns of Enterococcus species presence were observed only when data for multiple Enterococcus species were considered in aggregate.The results suggest that no single Enterococcus species is a reliable indicator of the host faecal source. However, Enterococcus species composite 'fingerprints' may offer auxiliary evidence for bacterial source identification.This study presents novel information on the enterococci species assemblages present in avian and mammalian hosts proximate to the nearshore ocean. These data will aid the development of appropriate MST strategies, and the approach used in this study could potentially assist in the identification of faecal pollution sources.

  View details for DOI 10.1111/j.1365-2672.2010.04675.x

  View details for Web of Science ID 000279733700016

  View details for PubMedID 20132375

• Caffeine and agricultural pesticide concentrations in surface water and groundwater on the north shore of Kauai (Hawaii, USA) MARINE POLLUTION BULLETIN Knee, K. L., Gossett, R., Boehm, A. B., Paytan, A. 2010; 60 (8): 1376-1382

  Abstract

  Caffeine has been associated with wastewater pollution in temperate and subtropical locations, but environmental caffeine concentrations in tropical locations have not been reported. The objectives of this study were to measure caffeine and agricultural pesticide (carbaryl, metalaxyl, and metribuzin) concentrations in environmental waters on the tropical north shore of Kauai (Hawaii, USA) and assess whether patterns in caffeine concentration were consistent with a wastewater caffeine source. Groundwater, river, stream and coastal ocean samples were collected in August 2006 and February 2007. Caffeine was detected in all August 2006 samples and in 33% of February 2007 samples at concentrations up to 88ngL(-1). Metribuzin was detected in five samples collected in February 2007. Carbaryl and metalaxyl were not detected in any sample. Caffeine was not detected in offshore ocean samples or river samples upstream of human development. A positive correlation between caffeine and enterococci suggested a possible wastewater caffeine source.

  View details for DOI 10.1016/j.marpolbul.2010.04.019

  View details for Web of Science ID 000281474000039

  View details for PubMedID 20557899

• Relationship and Variation of qPCR and Culturable Enterococci Estimates in Ambient Surface Waters Are Predictable ENVIRONMENTAL SCIENCE & TECHNOLOGY Whitman, R. L., Ge, Z., Nevers, M. B., Boehm, A. B., Chern, E. C., Haugland, R. A., Lukasik, A. M., Molina, M., Przybyla-Kelly, K., Shively, D. A., White, E. M., Zepp, R. G., Byappanahalli, M. N. 2010; 44 (13): 5049-5054

  Abstract

  The quantitative polymerase chain reaction (qPCR) method provides rapid estimates of fecal indicator bacteria densities that have been indicated to be useful in the assessment of water quality. Primarily because this method provides faster results than standard culture-based methods, the U.S. Environmental Protection Agency is currently considering its use as a basis for revised ambient water quality criteria. In anticipation of this possibility, we sought to examine the relationship between qPCR-based and culture-based estimates of enterococci in surface waters. Using data from several research groups, we compared enterococci estimates by the two methods in water samples collected from 37 sites across the United States. A consistent linear pattern in the relationship between cell equivalents (CCE), based on the qPCR method, and colony-forming units (CFU), based on the traditional culturable method, was significant (P < 0.05) at most sites. A linearly decreasing variance of CCE with increasing CFU levels was significant (P < 0.05) or evident for all sites. Both marine and freshwater sites under continuous influence of point-source contamination tended to reveal a relatively constant proportion of CCE to CFU. The consistency in the mean and variance patterns of CCE versus CFU indicates that the relationship of results based on these two methods is more predictable at high CFU levels (e.g., log(10)CFU > 2.0/100 mL) while uncertainty increases at lower CFU values. It was further noted that the relative error in replicated qPCR estimates was generally higher than that in replicated culture counts even at relatively high target levels, suggesting a greater need for replicated analyses in the qPCR method to reduce relative error. Further studies evaluating the relationship between culture and qPCR should take into account analytical uncertainty as well as potential differences in results of these methods that may arise from sample variability, different sources of pollution, and environmental factors.

  View details for DOI 10.1021/es9028974

  View details for Web of Science ID 000279304700038

  View details for PubMedID 20527919

• Nutrient inputs to the coastal ocean from submarine groundwater discharge in a groundwater-dominated system: Relation to land use (Kona coast, Hawaii, USA) LIMNOLOGY AND OCEANOGRAPHY Knee, K. L., Street, J. H., Grossman, E. E., Boehm, A. B., Paytan, A. 2010; 55 (3): 1105-1122

  View details for DOI 10.4319/lo.2010.55.3.1105

  View details for Web of Science ID 000277650900013

• Hands, Water, and Health: Fecal Contamination in Tanzanian Communities with Improved, Non-Networked Water Supplies ENVIRONMENTAL SCIENCE & TECHNOLOGY Pickering, A. J., Davis, J., Walters, S. P., Horak, H. M., Keymer, D. P., Mushi, D., Strickfaden, B., Chynoweth, J. S., Liu, J., Blum, A., Rogers, K., Boehm, A. B. 2010; 44 (9): 3267-3272

  Abstract

  Almost half of the world's population relies on non-networked water supply services, which necessitates in-home water storage. It has been suggested that dirty hands play a role in microbial contamination of drinking water during collection, transport, and storage. However, little work has been done to evaluate quantitatively the association between hand contamination and stored water quality within households. This study measured levels of E. coli, fecal streptococci, and occurrence of the general Bacteroidales fecal DNA marker in source water, in stored water, and on hands in 334 households among communities in Dar es Salaam, Tanzania, where residents use non-networked water sources. Levels of fecal contamination on hands of mothers and children were positively correlated to fecal contamination in stored drinking water within households. Household characteristics associated with hand contamination included mother's educational attainment, use of an improved toilet, an infant in the household, and dissatisfaction with the quantity of water available for hygiene. In addition, fecal contamination on hands was associated with the prevalence of gastrointestinal and respiratory symptoms within a household. The results suggest that reducing fecal contamination on hands should be investigated as a strategy for improving stored drinking water quality and health among households using non-networked water supplies.

  View details for DOI 10.1021/es903524m

  View details for Web of Science ID 000277067000014

  View details for PubMedID 20222746

• Efficacy of Waterless Hand Hygiene Compared with Handwashing with Soap: A Field Study in Dar es Salaam, Tanzania AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE Pickering, A. J., Boehm, A. B., Mwanjali, M., Davis, J. 2010; 82 (2): 270-278

  Abstract

  Effective handwashing with soap requires reliable access to water supplies. However, more than three billion persons do not have household-level access to piped water. This research addresses the challenge of improving hand hygiene within water-constrained environments. The antimicrobial efficacy of alcohol-based hand sanitizer, a waterless hand hygiene product, was evaluated and compared with handwashing with soap and water in field conditions in Dar es Salaam, Tanzania. Hand sanitizer use by mothers resulted in 0.66 and 0.64 log reductions per hand of Escherichia coli and fecal streptococci, respectively. In comparison, handwashing with soap resulted in 0.50 and 0.25 log reductions per hand of E. coli and fecal streptococci, respectively. Hand sanitizer was significantly better than handwashing with respect to reduction in levels of fecal streptococci (P = 0.01). The feasibility and health impacts of promoting hand sanitizer as an alternative hand hygiene option for water-constrained environments should be assessed.

  View details for DOI 10.4269/ajtmh.2010.09-0220

  View details for Web of Science ID 000274263300018

  View details for PubMedID 20134005

  View details for PubMedCentralID PMC2813169

• Contrasting spring and summer phytoplankton dynamics in the nearshore Southern California Bight LIMNOLOGY AND OCEANOGRAPHY Santoro, A. E., Nidzieko, N. J., Van Dijken, G. L., Arrigo, K. R., Boehm, A. B. 2010; 55 (1): 264-278

  View details for Web of Science ID 000272759900015

• Classical and Molecular Methods to Measure Fecal Bacteria. The Fecal Indicator Bacteria Edge, T., A., Boehm, A., B. edited by Sadowsky, M., Whitman, R. ASM Press. 2010: 328
• Modeling Fate and Transport of Fecal Bacteria in Surface Water. The Fecal Indicator Bacteria Nevers, M., N., Boehm, A., B. edited by Sadowsky, M., Whitman, R. ASM Press. 2010: 328
• Microbial and metal water quality in rain catchments compared with traditional drinking water sources in the East Sepik Province, Papua New Guinea JOURNAL OF WATER AND HEALTH Horak, H. M., Chynoweth, J. S., Myers, W. P., Davis, J., Fendorf, S., Boehm, A. B. 2010; 8 (1): 126-138

  Abstract

  In Papua New Guinea, a significant portion of morbidity and mortality is attributed to water-borne diseases. To reduce incidence of disease, communities and non-governmental organizations have installed rain catchments to provide drinking water of improved quality. However, little work has been done to determine whether these rain catchments provide drinking water of better quality than traditional drinking water sources, and if morbidity is decreased in villages with rain catchments. The specific aim of this study was to evaluate the quality of water produced by rain catchments in comparison with traditional drinking water sources in rural villages in the East Sepik Province. Fifty-four water sources in 22 villages were evaluated for enterococci and Escherichia coli densities as well as 14 health-relevant metals. In addition, we examined how the prevalence of diarrhoeal illness in villages relates to the type of primary drinking water source. The majority of tested metals were below World Health Organization safety limits. Catchment water sources had lower enterococci and E. coli than other water sources. Individuals in villages using Sepik River water as their primary water source had significantly higher incidence of diarrhoea than those primarily using other water sources (streams, dug wells and catchments).

  View details for Web of Science ID 000275310700014

  View details for PubMedID 20009255

• Persistence of nucleic acid markers of health-relevant organisms in seawater microcosms: Implications for their use in assessing risk in recreational waters WATER RESEARCH Walters, S. P., Yamahara, K. M., Boehm, A. B. 2009; 43 (19): 4929-4939

  Abstract

  In the last decade, the use of culture-independent methods for detecting indicator organisms and pathogens in recreational waters has increased and has led to heightened interest in their use for routine water quality monitoring. However, a thorough understanding of the persistence of genetic markers in environmental waters is lacking. In the present study, we evaluate the persistence of enterococci, enterovirus, and human-specific Bacteroidales in seawater microcosms. Two microcosms consisted of seawater seeded with human sewage. Two additional seawater microcosms were seeded with naked Enterococcus faecium DNA and poliovirus RNA. One of each replicate microcosm was exposed to natural sunlight; the other was kept in complete darkness. In the sewage microcosms, concentrations of enterococci and enterovirus were measured using standard culture-dependent methods as well as QPCR and RT-QPCR respectively. Concentrations of human-specific Bacteroidales were determined with QPCR. In the naked-genome microcosms, enterococci and enterovirus markers were enumerated using QPCR and RT-QPCR, respectively. In the sewage microcosm exposed to sunlight, concentrations of culturable enterococci fell below the detection limit within 5 days, but the QPCR signal persisted until the end of the experiment (day 28). Culturable enterococci did not persist as long as infectious enteroviruses. The ability to culture enteroviruses and enterococci was lost before detection of the genetic markers was lost, but the human-specific Bacteroidales QPCR signal persisted for a similar duration as infectious enteroviruses in the sewage microcosm exposed to sunlight. In the naked-genome microcosms, DNA and RNA from enterococci and enterovirus, respectively, persisted for over 10d and did not vary between the light and dark treatments. These results indicate differential persistence of genetic markers and culturable organisms of public health relevance in an environmental matrix and have important management implications.

  View details for DOI 10.1016/j.watres.2009.05.047

  View details for Web of Science ID 000272057000017

  View details for PubMedID 19616273

• Faecal indicator bacteria enumeration in beach sand: a comparison study of extraction methods in medium to coarse sands JOURNAL OF APPLIED MICROBIOLOGY Boehm, A. B., Griffith, J., Mcgee, C., Edge, T. A., Solo-Gabriele, H. M., Whitman, R., Cao, Y., Getrich, M., Jay, J. A., Ferguson, D., Goodwin, K. D., Lee, C. M., Madison, M., Weisberg, S. B. 2009; 107 (5): 1740-1750

  Abstract

  The absence of standardized methods for quantifying faecal indicator bacteria (FIB) in sand hinders comparison of results across studies. The purpose of the study was to compare methods for extraction of faecal bacteria from sands and recommend a standardized extraction technique.Twenty-two methods of extracting enterococci and Escherichia coli from sand were evaluated, including multiple permutations of hand shaking, mechanical shaking, blending, sonication, number of rinses, settling time, eluant-to-sand ratio, eluant composition, prefiltration and type of decantation. Tests were performed on sands from California, Florida and Lake Michigan. Most extraction parameters did not significantly affect bacterial enumeration. anova revealed significant effects of eluant composition and blending; with both sodium metaphosphate buffer and blending producing reduced counts.The simplest extraction method that produced the highest FIB recoveries consisted of 2 min of hand shaking in phosphate-buffered saline or deionized water, a 30-s settling time, one-rinse step and a 10 : 1 eluant volume to sand weight ratio. This result was consistent across the sand compositions tested in this study but could vary for other sand types.Method standardization will improve the understanding of how sands affect surface water quality.

  View details for DOI 10.1111/j.1365-2672.2009.04440.x

  View details for PubMedID 19659700

• Covariation and Photoinactivation of Traditional and Novel Indicator Organisms and Human Viruses at a Sewage-Impacted Marine Beach ENVIRONMENTAL SCIENCE & TECHNOLOGY Boehm, A. B., Yamahara, K. M., Love, D. C., Peterson, B. M., McNeill, K., Nelson, K. L. 2009; 43 (21): 8046-8052

  Abstract

  Sunlight modulates concentrations of Escherichia coli and enterococci in marine waters. However, the mechanism of photoinactivation is poorly understood. Additionally, little is known about photoinactivation of other fecal indicators and human viruses in recreational waters. We sampled nearshore waters at Avalon Beach, California hourly for 72 h for reactive oxygen species (ROS), traditional indicator bacteria (E. coli and enterococci, and QPCR-based detection of enterococci), F+ (DNA and RNA) and somatic coliphages, the human-specific marker in Bacteroidales (HF marker), human enterovirus, and human adenovirus. E. coli and enterococci (regardless of measurement technique) covaried with each other and the coliphages suggesting similar sources and fates. The occurrence of the HF and enterovirus markers was correlated, but their occurrence was not positively correlated with the other indicators. Lower concentrations or occurrence of all microbes, excluding the HF and enterovirus markers, were observed during sunlit as opposed to dark hours, pointing to the importance of photoinactivation. Empirical-deterministic models for a subset of microbial indicators were created to determine field-relevant sunlight inactivation rates while accounting for time dependent sources and sinks. Photoinactivation rates of enterococci and E. coli, enterococci measured by QPCR, and somatic coliphage were estimated at 7, 6, 3, and 28 d(-1) I(-1), respectively, where I is UVB intensity in W/m(2). Average H(2)O(2) was 183 nM and the maximum singlet oxygen steady state concentration was 6.6 fM. Given the clarity of the water, direct genomic damage of bacteria and coliphage, as well as indirect endogenous damage of bacteria, were likely the most important inactivation mechanisms, but we cannot rule out a contribution by indirect mechanisms involving the H(2)O(2) and singlet oxygen produced exogenously.

  View details for DOI 10.1021/es9015124

  View details for Web of Science ID 000271106300015

  View details for PubMedID 19924921

• Distribution and diversity of the enterococcal surface protein (esp) gene in animal hosts and the Pacific coast environment JOURNAL OF APPLIED MICROBIOLOGY Layton, B. A., Walters, S. P., Boehm, A. B. 2009; 106 (5): 1521-1531

  Abstract

  This study sought to evaluate the distribution of the enterococcal surface protein (esp) gene in Enterococcus faecium in the Pacific coast environment as well as the distribution and diversity of the gene in Northern California animal hosts.Over 150 environmental samples from the Pacific coast environment (sand, surf zone, fresh/estuarine, groundwater, and storm drain) were screened for the esp gene marker in E. faecium, and the marker was found in 37% of the environmental samples. We examined the host specificity of the gene by screening various avian and mammalian faecal samples, and found the esp gene to be widespread in nonhuman animal faeces. DNA sequence analysis performed on esp polymerase chain reaction amplicons revealed that esp gene sequences were not divergent between hosts.Our data confirm recent findings that the E. faecium variant of the esp gene is not human-specific.Our results suggest that the use of the esp gene for microbial source tracking applications may not be appropriate at all recreational beaches.

  View details for DOI 10.1111/j.1365-2672.2008.04113.x

  View details for Web of Science ID 000264958000012

  View details for PubMedID 19187132

• Growth of Enterococci in Unaltered, Unseeded Beach Sands Subjected to Tidal Wetting (vol 75, pg 1517, 2009) APPLIED AND ENVIRONMENTAL MICROBIOLOGY Yamahara, K. M., Walters, S. P., Boehm, A. B. 2009; 75 (9): 2997-2997

  View details for DOI 10.1128/AEM.00551-09

  View details for Web of Science ID 000265586900054

• A Model of Exposure to Rotavirus from Nondietary Ingestion Iterated by Simulated Intermittent Contacts RISK ANALYSIS Julian, T. R., Canales, R. A., Leckie, J. O., Boehm, A. B. 2009; 29 (5): 617-632

  Abstract

  Existing microbial risk assessment models rarely incorporate detailed descriptions of human interaction with fomites. We develop a stochastic-mechanistic model of exposure to rotavirus from nondietary ingestion iterated by simulated intermittent fomes-mouth, hand-mouth, and hand-fomes contacts typical of a child under six years of age. This exposure is subsequently translated to risk using a simple static dose-response relationship. Through laboratory experiments, we quantified the mean rate of inactivation for MS2 phage on glass (0.0052/hr) and mean transfer between fingertips and glass (36%). Simulations using these parameters demonstrated that a child's ingested dose from a rotavirus-contaminated ball ranges from 2 to 1,000 virus over a period of one hour, with a median value of 42 virus. These results were heavily influenced by selected values of model parameters, most notably the concentration of rotavirus on fomes, frequency of fomes-mouth contacts, frequency of hand-mouth contacts, and virus transferred from fomes to mouth. The model demonstrated that mouthing of fomes is the primary exposure route, with hand mouthing contributions accounting for less than one-fifth of the child's dose over the first 10 minutes of interaction.

  View details for DOI 10.1111/j.1539-6924.2008.01193.x

  View details for Web of Science ID 000264892100002

  View details for PubMedID 19187484

• Biogeographic Patterns in Genomic Diversity among a Large Collection of Vibrio cholerae Isolates APPLIED AND ENVIRONMENTAL MICROBIOLOGY Keymer, D. P., Lam, L. H., Boehm, A. B. 2009; 75 (6): 1658-1666

  Abstract

  Vibrio cholerae strains are capable of inhabiting multiple niches in the aquatic environment and in some cases cause disease in humans. However, the ecology and biodiversity of these bacteria in environmental settings remains poorly understood. We used the genomic fingerprinting technique enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) to profile 835 environmental isolates from waters and sediments obtained at nine sites along the central California coast. We identified 115 ERIC-PCR genotypes from 998 fingerprints, with a reproducibility of 98.5% and a discriminatory power of 0.971. When the temporal dynamics at a subset of sampling sites were explored, several genotypes provided evidence for cosmopolitan or geographically restricted distributions, and other genotypes displayed nonrandom patterns of cooccurrence. Partial Mantel tests confirmed that genotypic similarity of isolates across all sampling events was correlated with environmental similarity (0.04 < or = r < or = 0.05), temporal proximity (r = 0.09), and geographic distance (r = 0.09). A neutral community model for all sampling events explained 61% of the variation in genotype abundance. Cooccurrence indices (C-score, C-board, and Combo) were significantly different than expected by chance, suggesting that the V. cholerae population may have a competitive structure, especially at the regional scale. Even though stochastic processes are undoubtedly important in generating biogeographic patterns in diversity, deterministic factors appear to play a significant, albeit small, role in shaping the V. cholerae population structure in this system.

  View details for DOI 10.1128/AEM.01304-08

  View details for Web of Science ID 000263920900024

  View details for PubMedID 19139224

  View details for PubMedCentralID PMC2655455

• A sea change ahead for recreational water quality criteria JOURNAL OF WATER AND HEALTH Boehm, A. B., Ashbolt, N. J., Colford, J. M., Dunbar, L. E., Fleming, L. E., Gold, M. A., Hansel, J. A., Hunter, P. R., Ichida, A. M., McGee, C. D., Soller, J. A., Weisberg, S. B. 2009; 7 (1): 9-20

  Abstract

  The United States Environmental Protection Agency is committed to developing new recreational water quality criteria for coastal waters by 2012 to provide increased protection to swimmers. We review the uncertainties and shortcomings of the current recreational water quality criteria, describe critical research needs for the development of new criteria, as well as recommend a path forward for new criteria development. We believe that among the most needed research needs are the completion of epidemiology studies in tropical waters and in waters adversely impacted by urban runoff and animal feces, as well as studies aimed to validate the use of models for indicator and pathogen concentration and health risk predictions.

  View details for DOI 10.2166/wh.2009.122

  View details for Web of Science ID 000264052900002

  View details for PubMedID 18957771

• Growth of Enterococci in Unaltered, Unseeded Beach Sands Subjected to Tidal Wetting APPLIED AND ENVIRONMENTAL MICROBIOLOGY Yamahara, K. M., Walters, S. P., Boehm, A. B. 2009; 75 (6): 1517-1524

  Abstract

  Enterococci are indicator bacteria used to assess the risk of acquiring enteric disease from swimming in marine waters. Previous work identified beach sands as reservoirs of enterococci which can be transported from the sand to the sea, where they may instigate beach advisories. The present study establishes that naturally occurring enterococci can replicate in beach sands under environmentally relevant conditions. In unseeded, nonsterile microcosm experiments, it was shown that intermittent wetting of sands by seawater, like that which would occur at the high tide line, stimulates the transient replication of enterococci at rates of 0.20 to 0.63 per day (equivalent to doubling times of 1.1 to 3.5 days). Replication was not observed in control microcosms that were not subjected to wetting. Enterococci were enumerated using both culture-dependent (membrane filtration and mEI media) and culture-independent (quantitative PCR [QPCR], 23S rRNA gene based) techniques, which allowed tracking of both culturable and total enterococcus populations. Inhibition of QPCR and DNA extraction efficiencies were accounted for in the interpretation of the QPCR results. The results provide evidence that enterococci may not be an appropriate indicator of enteric disease risk at recreational beaches subject to nonpoint sources of pollution.

  View details for DOI 10.1128/AEM.02278-08

  View details for Web of Science ID 000263920900006

  View details for PubMedID 19151188

  View details for PubMedCentralID PMC2655449

• Sources of nutrients and fecal indicator bacteria to nearshore waters on the north shore of Kauai (Hawaii, USA) ESTUARIES AND COASTS Knee, K. L., Layton, B. A., Street, J. H., Boehm, A. B., Paytan, A. 2008; 31 (4): 607-622

  View details for DOI 10.1007/s12237-008-9055-6

  View details for Web of Science ID 000258153200001

• Submarine discharge of nutrient-enriched fresh groundwater at Stinson Beach, California is enhanced during neap tides LIMNOLOGY AND OCEANOGRAPHY de Sieyes, N. R., Yamahara, K. M., Layton, B. A., Joyce, E. H., Boehm, A. B. 2008; 53 (4): 1434-1445

  View details for Web of Science ID 000257773700021

• Fecal indicator bacteria and Salmonella in ponds managed as bird habitat, San Francisco Bay, California, USA WATER RESEARCH Shellenbarger, G. G., Athearn, N. D., Takekawa, J. Y., Boehm, A. B. 2008; 42 (12): 2921-2930

  Abstract

  Throughout the world, coastal resource managers are encouraging the restoration of previously modified coastal habitats back into wetlands and managed ponds for their ecosystem value. Because many coastal wetlands are adjacent to urban centers and waters used for human recreation, it is important to understand how wildlife can affect water quality. We measured fecal indicator bacteria (FIB) concentrations, presence/absence of Salmonella, bird abundance, and physico-chemical parameters in two coastal, managed ponds and adjacent sloughs for 4 weeks during the summer and winter in 2006. We characterized the microbial water quality in these waters relative to state water-quality standards and examined the relationship between FIB, bird abundance, and physico-chemical parameters. A box model approach was utilized to determine the net source or sink of FIB in the ponds during the study periods. FIB concentrations often exceeded state standards, particularly in the summer, and microbial water quality in the sloughs was generally lower than in ponds during both seasons. Specifically, the inflow of water from the sloughs to the ponds during the summer, more so than waterfowl use, appeared to increase the FIB concentrations in the ponds. The box model results suggested that the ponds served as net wetland sources and sinks for FIB, and high bird abundances in the winter likely contributed to net winter source terms for two of the three FIB in both ponds. Eight serovars of the human pathogen Salmonella were isolated from slough and pond waters, although the source of the pathogen to these wetlands was not identified. Thus, it appeared that factors other than bird abundance were most important in modulating FIB concentrations in these ponds.

  View details for DOI 10.1016/j.watres.2008.03.006

  View details for Web of Science ID 000257649100009

  View details for PubMedID 18457857

• Shifts in the relative abundance of ammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterranean estuary ENVIRONMENTAL MICROBIOLOGY Santoro, A. E., Francis, C. A., de Sieyes, N. R., Boehm, A. B. 2008; 10 (4): 1068-1079

  Abstract

  Submarine groundwater discharge to coastal waters can be a significant source of both contaminants and biologically limiting nutrients. Nitrogen cycling across steep gradients in salinity, oxygen and dissolved inorganic nitrogen in sandy 'subterranean estuaries' controls both the amount and form of nitrogen discharged to the coastal ocean. We determined the effect of these gradients on betaproteobacterial ammonia-oxidizing bacteria (beta-AOB) and ammonia-oxidizing archaea (AOA) in a subterranean estuary using the functional gene encoding ammonia monooxygenase subunit A (amoA). The abundance of beta-AOB was dramatically lower in the freshwater stations compared with saline stations, while AOA abundance remained nearly constant across the study site. This differing response to salinity altered the ratio of beta-AOB to AOA such that bacterial amoA was 30 times more abundant than crenarchaeal amoA at the oxic marine station, but nearly 10 times less abundant at the low-oxygen fresh and brackish stations. As the location of the brackish mixing zone within the aquifer shifted from landward in winter to oceanward in summer, the location of the transition from a beta-AOB-dominated to an AOA-dominated community also shifted, demonstrating the intimate link between microbial communities and coastal hydrology. Analysis of ammonia-oxidizing enrichment cultures at a range of salinities revealed that AOA persisted solely in the freshwater enrichments where they actively express amoA. Diversity (as measured by total richness) of crenarchaeal amoA was high at all stations and time points, in sharp contrast to betaproteobacterial amoA for which only two sequence types were found. These results offer new insights into the ecology of AOA and beta-AOB by elucidating conditions that may favour the numerical dominance of beta-AOB over AOA in coastal sediments.

  View details for DOI 10.1111/j.1462-2920.2007.01547.x

  View details for Web of Science ID 000254124100023

  View details for PubMedID 18266758

• Enterococci concentrations in diverse coastal environments exhibit extreme variability ENVIRONMENTAL SCIENCE & TECHNOLOGY Boehm, A. B. 2007; 41 (24): 8227-8232

  Abstract

  Fecal indicator bacteria (FIB) concentrations in a single grab sample of water are used to notify the public about the safety of swimming in coastal waters. If concentrations are over a single-sample standard, waters are closed or placed under an advisory. Previous work has shown that notification errors occur often because FIB vary more quickly than monitoring results can be obtained (typically 24 h). Rapid detection technologies (such as quantitative polymerase chain reaction) that allow FIB quantification in hours have been suggested as a solution to notification errors. In the present study, I explore variability of enterococci (ENT) over time scales less than a day that might affect interpretation of FIB concentrations from a single grab sample, even if obtained rapidly. Five new data sets of ENT collected at 10 and 1 min periodicities for 24 and 1 h, respectively, are presented. Data sets are collected in diverse marine environments from a turbulent surf zone to a quiescent bay. ENT vary with solar and tidal cycles, as has been observed in previous studies. Over short time scales, ENT are extremely variable in each environment even the quiescent bay. Changes in ENT concentrations between consecutive samples (1 or 10 min apart) greater than the single-sample standard (104 most probable number per 100 mL) are not unusual. Variability, defined as the change in concentration between consecutive samples, is not distinct between environments. ENT change by 60% on average between consecutive samples, and by as much as 700%. Spectral analyses reveal no spectral peaks, but power-law decline of spectral density with frequency. Power-law exponents are close to 1 suggesting ENT time series share properties with 1/f noise and are fractal in nature. Since fractal time series have no characteristic time scale associated with them, it is not obvious how the fractal nature of ENT can be exploited for adaptive sampling or management. Policy makers, as well as scientists designing field campaigns for microbial source tracking and epidemiology studies, are cautioned that a single sample of water reveals little about the true water quality at a beach. Multiple samples must be taken to gain a snapshot into the patchy structure of microbial water quality and associated human health risk.

  View details for DOI 10.1021/es071807v

  View details for Web of Science ID 000251582800007

  View details for PubMedID 18200844

• Frequent occurrence of the human-specific Bacteroides fecal marker at an open coast marine beach: relationship to waves, tides and traditional indicators ENVIRONMENTAL MICROBIOLOGY Santoro, A. E., Boehm, A. B. 2007; 9 (8): 2038-2049

  Abstract

  Molecular genetic markers, such as those from fecal Bacteroides microorganisms, can link microbial pollution with its source, and have been used successfully in studies of sheltered aquatic environments. Their applicability to wave-driven, open coast environments has not been tested. We assessed the contribution of a tidal outlet to surf zone water quality in coastal Orange County, California, USA by measuring three traditional culture-based fecal indicator bacteria (FIB) as well as the human-specific Bacteroides molecular marker (HF marker) at four shoreline locations. We found that total and fecal coliform levels were higher during low tides than high tides at two of the four stations, and that this effect was strongest at the mouth of the tidal lagoon and decayed with distance from the outlet. The HF marker was detected in 23% and 47% of samples from the tidal outlet and 26% and 41% of samples from an adjacent recreational beach in 2005 and 2006 respectively. Surprisingly, the station farthest from the tidal outlet had the highest occurrence of the HF marker. We found no relationship between FIB abundance and occurrence of the HF marker for individual samples, but that when the data were considered together by year, higher FIB abundance was correlated with a higher incidence of the HF marker. DNA sequences of the HF marker recovered from this site were > 99% similar to those recovered from other states and countries, suggesting low global diversity of this marker. These data provide strong support for the idea that multiple time points and physical conditions should be considered when assessing coastal water quality.

  View details for DOI 10.1111/j.1462-2920.2007.01319.x

  View details for Web of Science ID 000248451600014

  View details for PubMedID 17635548

• Beach sands along the California coast are diffuse sources of fecal bacteria to coastal waters ENVIRONMENTAL SCIENCE & TECHNOLOGY Yamahara, K. M., Layton, B. A., Santoro, A. E., Boehm, A. B. 2007; 41 (13): 4515-4521

  Abstract

  Fecal indicator bacteria (FIB) are nearly ubiquitous in California (CA) beach sands. Sands were collected from 55 beaches along the CA coast. Ninety-one percent of the beaches had detectable enterococci (ENT) while 62% had detectable E. coli (EC) in their sands. The presence of a putative bacterial source (such as a river), the degree of wave shelter, and surrounding land use explained a significant (p < 0.05) fraction of the variation in both ENT and EC densities between beaches. Sand characteristics including moisture content, organic carbon, and percentfines, significantly (p < 0.05) influenced only EC densities in beach sand. We assayed 34 of 163 sand samples for salmonellae, but did not detect this bacterial pathogen. The potential for FIB to be transported from the sand to sea was investigated at a single wave-sheltered beach with high densities of ENT in beach sand: Lovers Point, CA (LP). We collected samples of exposed and submerged sands as well as water over a 24 h period in order to compare the disappearance or appearance of ENT in sand and the water column. Exposed sands had significantly higher densities of ENT than submerged sands with the highest densities located near the high tide line. Water column ENT densities began low, increased sharply during the first flood tide and slowly decreased over the remainder of the study. During the first flood tide, the number of ENT that entered the water column was nearly equivalent to the number of ENT lost from exposed sands when they were submerged by seawater. The decrease in nearshore ENT concentrations after the initial influx can be explained by ENT die-off and dilution with clean ocean water. While some ENT in the water and sand at LP might be of human origin because they were positive for the esp gene, others lacked the esp gene and were therefore equivocal with respect to their origin. Follow-up sampling at LP revealed the presence of the human specific Bacteroides marker in water and sand.

  View details for DOI 10.1021/es062822n

  View details for Web of Science ID 000247782500014

  View details for PubMedID 17695890

• Detection and transformation of genome segments that differ within a coastal population of Vibrio cholerae strains APPLIED AND ENVIRONMENTAL MICROBIOLOGY Miller, M. C., Keymer, D. P., Avelar, A., Boehm, A. B., Schoolnik, G. K. 2007; 73 (11): 3695-3704

  Abstract

  Vibrio cholerae is an autochthonous member of diverse aquatic ecosystems around the globe. Collectively, the genomes of environmental V. cholerae strains comprise a large repository of encoded functions which can be acquired by individual V. cholerae lineages through uptake and recombination. To characterize the genomic diversity of environmental V. cholerae, we used comparative genome hybridization to study 41 environmental strains isolated from diverse habitats along the central California coast, a region free of endemic cholera. These data were used to classify genes of the epidemic V. cholerae O1 sequenced strain N16961 as conserved, variably present, or absent from the isolates. For the most part, absent genes were restricted to large mobile elements and have known functions in pathogenesis. Conversely, genes present in some, but not all, California isolates were in smaller contiguous clusters and were less likely to be near genes with functions in DNA mobility. Two such clusters of variable genes encoding different selectable metabolic phenotypes (mannose and diglucosamine utilization) were transformed into the genomes of environmental isolates by chitin-dependent competence, indicating that this mechanism of general genetic exchange is conserved among V. cholerae. The transformed DNA had an average size of 22.7 kbp, demonstrating that natural competence can mediate the movement of large chromosome fragments. Thus, whether variable genes arise through the acquisition of new sequences by horizontal gene transfer or by the loss of preexisting DNA though deletion, natural transformation provides a mechanism by which V. cholerae clones can gain access to the V. cholerae pan-genome.

  View details for DOI 10.1128/AEM.02735-06

  View details for PubMedID 17449699

• Genomic and phenotypic diversity of coastal Vibrio cholerae strains is linked to environmental factors APPLIED AND ENVIRONMENTAL MICROBIOLOGY Keymer, D. P., Miller, M. C., Schoolnik, G. K., Boehm, A. B. 2007; 73 (11): 3705-3714

  Abstract

  Studies of Vibrio cholerae diversity have focused primarily on pathogenic isolates of the O1 and O139 serotypes. However, autochthonous environmental isolates of this species routinely display more extensive genetic diversity than the primarily clonal pathogenic strains. In this study, genomic and metabolic profiles of 41 non-O1/O139 environmental isolates from central California coastal waters and four clinical strains are used to characterize the core genome and metabolome of V. cholerae. Comparative genome hybridization using microarrays constructed from the fully sequenced V. cholerae O1 El Tor N16961 genome identified 2,787 core genes that approximated the projected species core genome within 1.6%. Core genes are almost universally present in strains with widely different niches, suggesting that these genes are essential for persistence in diverse aquatic environments. In contrast, the dispensable genes and phenotypic traits identified in this study should provide increased fitness for certain niche environments. Environmental parameters, measured in situ during sample collection, are correlated to the presence of specific dispensable genes and metabolic capabilities, including utilization of mannose, sialic acid, citrate, and chitosan oligosaccharides. These results identify gene content and metabolic pathways that are likely selected for in certain coastal environments and may influence V. cholerae population structure in aquatic environments.

  View details for DOI 10.1128/AEM.02736-06

  View details for PubMedID 17449702

• Now-casting recreational water quality. Statistical Framework for Water Quality Criteria and Monitoring Boehm, A., B., Whitman, R., L., Nevers, M., B., Hou, D., Weisberg, S., B. edited by Wymer, L., Dufour, A. 2007
• Beach sands along the California coast are diffuse sources of fecal bacteria to coastal waters. Environmental Science & Technology Yamahara, K., M., Layton, B., A., Santoro, A., E., Boehm., A., B. 2007; 41: 4515-4521
• Human development is linked to multiple water body impairments along the California coast ESTUARIES AND COASTS Handler, N. B., Payran, A., Higgins, C. P., Luthy, R. G., Boehm, A. B. 2006; 29 (5): 860-870

  View details for Web of Science ID 000241837400015

• Regional public health cost estimates of contaminated coastal waters: A case study of gastroenteritis at southern california beaches ENVIRONMENTAL SCIENCE & TECHNOLOGY Given, S., Pendleton, L. H., Boehm, A. B. 2006; 40 (16): 4851-4858

  Abstract

  We present estimates of annual public health impacts, both illnesses and cost of illness, attributable to excess gastrointestinal illnesses caused by swimming in contaminated coastal waters at beaches in southern California. Beach-specific enterococci densities are used as inputs to two epidemiological dose-response models to predict the risk of gastrointestinal illness at 28 beaches spanning 160 km of coastline in Los Angeles and Orange Counties. We use attendance data along with the health cost of gastrointestinal illness to estimate the number of illnesses among swimmers and their likely economic impact. We estimate that between 627,800 and 1,479,200 excess gastrointestinal illnesses occur at beaches in Los Angeles and Orange Counties each year. Using a conservative health cost of gastroenteritis, this corresponds to an annual economic loss of dollars 21 or dollars 51 million depending upon the underlying epidemiological model used (in year 2000 dollars). Results demonstrate that improving coastal water quality could result in a reduction of gastrointestinal illnesses locally and a concurrent savings in expenditures on related health care costs.

  View details for DOI 10.1021/es060679s

  View details for Web of Science ID 000239684900012

  View details for PubMedID 16955877

• Enterococci predictions from partial least squares regression models in conjunction with a single-sample standard improve the efficacy of beach management advisories ENVIRONMENTAL SCIENCE & TECHNOLOGY Hou, D., Rabinovici, S. J., Boehm, A. B. 2006; 40 (6): 1737-1743

  Abstract

  Beach health advisories are issued if enterococci (ENT) densities exceed the 30-d geometric mean or single-sample water quality criteria. Current ENT enumeration procedures require 1 day of incubation; therefore, beach managers make policy decisions using 1-day-old data. This is tantamount to using a model that assumes ENT density on day t is equal to ENT density on day t-1. Research has shown that ENT densities vary over time scales shorterthan a day, calling into question the usefulness of the current model for decision-making. We created Dynamic Partial Least Square Regression (DPLSR) models for ENT at water quality monitoring stations within two adjacent marine recreational sites, Huntington State Beach (HSB) and Huntington City (HCB) Beach, California, using publicly available environmental data and tested whether these models overcome the drawbacks of the current model. The DPLSR models provide a better prediction of ENT than the current models based on comparisons of root-mean-square errors of prediction and the numbers of type 1 and 2 errors. We compared outcomes in terms of predicted illness, swimmers deterred from entering the water, and net benefits to swimmers for hypothetical management scenarios where beach advisories were issued based on (a) the previously collected sample's ENT density in conjunction with the two water quality criteria, and (b) predictions from DPLSR models in conjunction with the single-sample standard. At both HSB and HCB the DPLSR scenario produced a more favorable balance between illness prevention and recreational access. The results call into question the current method of beach management and show that model-informed decision-making and elimination of the geometric mean standard will aid beach managers in achieving more favorable outcomes in terms of illness and access than are presently achieved using 1-day-old measurements, especially at beaches where water quality problems are chronic.

  View details for DOI 10.1021/es0515250

  View details for Web of Science ID 000236213900005

  View details for PubMedID 16570591

• Composition and flux of groundwater from a California beach aquifer: Implications for nutrient supply to the surf zone (vol 26, pg 269, 2006) CONTINENTAL SHELF RESEARCH Boehm, A., Paytan, A., Shellenbarger, G. G., Davis, K. A. 2006; 26 (4): 554-554

  View details for DOI 10.1016/j.csr.2006.01.005

  View details for Web of Science ID 000236661200008

• Denitrifier community composition along a nitrate and salinity gradient in a coastal aquifer APPLIED AND ENVIRONMENTAL MICROBIOLOGY Santoro, A. E., Boehm, A. B., Francis, C. A. 2006; 72 (3): 2102-2109

  Abstract

  Nitrogen flux into the coastal environment via submarine groundwater discharge may be modulated by microbial processes such as denitrification, but the spatial scales at which microbial communities act and vary are not well understood. In this study, we examined the denitrifying community within the beach aquifer at Huntington Beach, California, where high-nitrate groundwater is a persistent feature. Nitrite reductase-encoding gene fragments (nirK and nirS), responsible for the key step in the denitrification pathway, were PCR amplified, cloned, and sequenced from DNAs extracted from aquifer sediments collected along a cross-shore transect, where groundwater ranged in salinity from 8 to 34 practical salinity units and in nitrate concentration from 0.5 to 330 muM. We found taxonomically rich and novel communities, with all nirK clones exhibiting <85% identity and nirS clones exhibiting <92% identity at the amino acid level to those of cultivated denitrifiers and other environmental clones in the database. Unique communities were found at each site, despite being located within 40 m of each other, suggesting that the spatial scale at which denitrifier diversity and community composition vary is small. Statistical analyses of nir sequences using the Monte Carlo-based program integral-Libshuff confirmed that some populations were indeed distinct, although further sequencing would be required to fully characterize the highly diverse denitrifying communities at this site.

  View details for DOI 10.1128/AEM.72.3.2102-2109.2006

  View details for Web of Science ID 000236069200045

  View details for PubMedID 16517659

  View details for PubMedCentralID PMC1393195

• Composition and flux of groundwater from a California beach aquifer: Implications for nutrient supply to the surf zone CONTINENTAL SHELF RESEARCH Boehm, A. B., Paytan, A., Shellenbarger, G. G., Davis, K. A. 2006; 26 (2): 269-282

  View details for DOI 10.1016/j.csr.2005.11.008

  View details for Web of Science ID 000235251400009

• An analytical model of enterococci inactivation, grazing, and transport in the surf zone of a marine beach WATER RESEARCH Boehm, A. B., Keymer, D. P., Shellenbarger, G. G. 2005; 39 (15): 3565-3578

  Abstract

  An analytical model of enterococci (ENT) concentrations in the surf zone of a long sandy beach is constructed considering the physical processes of dilution by rip currents and alongshore littoral drift, and the biological processes of inactivation and mortality by grazing. The solution is used to construct an expression for the length of shoreline adversely impacted by ENT from a point source. Two non-dimensional parameters are developed whose magnitude can be used to ascertain whether dilution, inactivation, or grazing is the dominant sink for ENT in the surf zone. The model is applied to beaches in southern California, USA. Model input parameters related to physical processes and inactivation are compiled from the literature. Laboratory experiments are conducted to determine grazing mortality rates of ENT (6.5 x 10(-6) s(-1)). Results indicate that at the field sites, between 1000 and 5000 m of shoreline are typically impacted by a continuous point source of ENT. Dilution is the primary cause of decline in ENT concentrations within the surf zone, with inactivation secondary and grazing tertiary. Results recommend strategic positioning of point sources and timing of effluent releases to take advantage of high dilution conditions. Our estimates for grazing mortality rates are within the same order of magnitude as some published inactivation rates, thus we cannot rule out the possibility that grazing is an important sink for ENT, especially in low dilution environments like enclosed bays.

  View details for Web of Science ID 000232417800014

  View details for PubMedID 16095656

• Tidal forcing of enterococci at marine recreational beaches at fortnightly and semidiurnal frequencies ENVIRONMENTAL SCIENCE & TECHNOLOGY Boehm, A. B., Weisberg, S. B. 2005; 39 (15): 5575-5583

  Abstract

  Marine beach water quality is typically monitored in early morning once a week without respect to tidal condition. To assess the effect of tide on this public health warning system, we analyzed enterococci (ENT) data from 60 southern California marine beaches with differing geomorphology, orientation, and proximity to runoff sources. ENT concentrations during spring tides were significantly higher (p < 0.1) than those during neap tides at 50 of the beaches, and at the majority of these, water samples were also more than twice as likely to be out of compliance with the ENT single-sample standard during spring tides compared to neap tides. When tide range (spring/neap) and tide stage (ebb/flood) conditions were considered together, spring-ebb tides yielded the highest ENT concentrations and the greatest chance of exceeding the single-sample standard at the majority of beaches. The proximity to a terrestrial runoff source, the slope of the runoff source, the slope of the beach, and the orientation of the beach had minimal influence on the tidal modulation of ENT concentrations. The presence of spring and spring-ebb tide signals at such a great percentage of beaches suggests that tide should be considered in the design and interpretation of beach monitoring program data. It also suggests that ENT delivered by tidally forced sources other than terrestrial surficial runoff are widespread. Possibilities include ENT-laden groundwater (saline and fresh) from the beach aquifer as well as ENT-enriched sands, decaying wrack, and bird feces near the high water line.

  View details for DOI 10.1021/es048175m

  View details for Web of Science ID 000230919800020

  View details for PubMedID 16124289

• Groundwater discharge: Potential association with fecal indicator bacteria in the surf zone ENVIRONMENTAL SCIENCE & TECHNOLOGY Boehm, A. B., Shellenbarger, G. G., Paytan, A. 2004; 38 (13): 3558-3566

  Abstract

  Short-lived radium isotopes (223Ra and 224Ra) are used to investigate the potential association between groundwater discharge and microbial pollution at Huntington Beach, CA. We establish the tidally driven exchange of groundwater from the surficial beach aquifer across the beach face. Groundwater is found to be a source of nutrients (silica, inorganic nitrogen, and orthophosphate) to the surf zone, and these nutrients could possibly provide an environment for enhanced growth or increased persistence of fecal indicator bacteria (FIB). Ammonium and ortho-phosphate explain up to 12-20% of the variance in FIB levels in the surf zone. Elevated levels of FIB were only found in 1 of the 26 groundwater samples. However, FIB in the surf zone covary with radium at fortnightly, diurnal, and semi-diurnal tidal periods. In addition, radium accounts for up to 38% of the variance in log-FIB levels in the surf zone. A column experiment illustrates that Enterococcus suspended in Huntington Beach saline groundwater is not significantly filtered by sand collected from the field. This work establishes a mechanism for the subterranean delivery of FIB pollution to the surf zone from the surficial aquifer and presents evidence that supports an association between groundwater discharge and FIB.

  View details for DOI 10.1021/es035385a

  View details for Web of Science ID 000222396400021

  View details for PubMedID 15296305

• Scaling and management of fecal indicator bacteria in runoff from a coastal urban watershed in southern California ENVIRONMENTAL SCIENCE & TECHNOLOGY Reeves, R. L., Grant, S. B., Mrse, R. D., Oancea, C. M., Sanders, B. F., Boehm, A. B. 2004; 38 (9): 2637-2648

  Abstract

  This paper describes a series of field studies aimed at identifying the spatial distribution and flow forcing of fecal indicator bacteria in dry and wet weather runoff from the Talbert watershed, a highly urbanized coastal watershed in southern California. Runoff from this watershed drains through tidal channels to a popular public beach, Huntington State Beach, which has experienced chronic surf zone water quality problems over the past several years. During dry weather, concentrations of fecal indicator bacteria are highest in inland urban runoff, intermediate in tidal channels harboring variable mixtures of urban runoff and ocean water, and lowest in ocean water at the base of the watershed. This inland-to-coastal gradient is consistent with the hypothesis that urban runoff from the watershed contributes to coastal pollution. On a year round basis, the vast majority (>99%) of fecal indicator bacteria loading occurs during storm events when runoff diversions, the management approach of choice, are not operating. During storms, the load of fecal indicator bacteria in runoff follows a power law of the form L approximately Qn, where L is the loading rate (in units of fecal indicator bacteria per time), Q is the volumetric flow rate (in units of volume per time), and the exponent n ranges from 1 to 1.5. This power law and the observed range of exponent values are consistent with the predictions of a mathematical model that assumes fecal indicator bacteria in storm runoff originate from the erosion of contaminated sediments in drainage channels or storm sewers. The theoretical analysis, which is based on a conventional model for the shear-induced erosion of particles from land and channel-bed surfaces, predicts that the magnitude of the exponent n reflects the geometry of the stormwater conveyance system from which the pollution derives. This raises the possibility that the scaling properties of pollutants in stormwater runoff (i.e., the value of n) may harbor information about the origin of nonpoint source pollution.

  View details for Web of Science ID 000221189900029

  View details for PubMedID 15180060

• Covariation of coastal water temperature and microbial pollution at interannual to tidal periods GEOPHYSICAL RESEARCH LETTERS Boehm, A. B., Lluch-Cota, D. B., Davis, K. A., Winant, C. D., Monismith, S. G. 2004; 31 (6)

  View details for DOI 10.1029/2003GL019122

  View details for Web of Science ID 000220743300005

• Bacterial Contamination and Submarine Groundwater Discharge-A Possible Link ENVIRONMENTAL CHEMISTRY Paytan, A., Boehm, A. B., Shellenbarger, G. G. 2004; 1 (1): 29-30

  View details for DOI 10.1071/EN04002

  View details for Web of Science ID 000207050400009

• Sources, management, and scaling of fecal indicator bacteria in runoff from a coastal urban watershed in Southern California. Environmental Science and Technology Reeves, R., L., Grant, S., B., Mrse, R., D., Oancea, C., M. C., Sanders, B., F., Boehm., A., B. 2004; 38: 2637-2648
• Model of microbial transport and inactivation in the surf zone and application to field measurements of total coliform in Northern Orange County, California ENVIRONMENTAL SCIENCE & TECHNOLOGY Boehm, A. B. 2003; 37 (24): 5511-5517

  Abstract

  The classic model of pollutant transport in the surf zone of a long, sandy beach developed by Inman et al. (J. Geophys. Res. 1971, 76, 3493) is altered to account for first-order pollutant inactivation in an effort to understand how rip cell dilution and bacterial inactivation control the length of shoreline adversely impacted by microbial pollution from a point source. A dimensionless number gamma dictates whether physical processes (dilution of microbes in the surf zone by rip cell mixing) or biological processes (microbial inactivation) control the distribution of pollution along the shoreline. Estimates of gamma for beaches in Northern Orange County, California, indicate that dilution is the primary factor controlling total coliform levels surrounding two drains that release nuisance runoff directly onto the beach. It is also shown that, even when alongshore currents are fast, pollutant levels will drop e-fold at distances under 4000 m from the point source due to dilution alone. Because dilution is ultimately controlled by wave climate and shoreline morphology, the results suggest the strategic position of drains and other point sources in high dilution wave environments will reduce potential adverse effects on beach water quality. In addition, the results stress the importance of understanding hydrodynamics when conducting microbial source tracking at wave-dominated marine beaches.

  View details for DOI 10.1021/es034321x

  View details for Web of Science ID 000187248000006

  View details for PubMedID 14717158

• Tiered approach for identification of a human fecal pollution source at a recreational beach: Case study at Avalon Cay, Catalina Island, California ENVIRONMENTAL SCIENCE & TECHNOLOGY Boehm, A. B., Fuhrman, J. A., Mrse, R. D., Grant, S. B. 2003; 37 (4): 673-680

  Abstract

  Recreational marine beaches in California are posted as unfit for swimming when the concentration of fecal indicator bacteria (FIB) exceeds any of seven concentration standards. Finding and mitigating sources of shoreline FIB is complicated by the many potential human and nonhuman sources of these organisms and the complex fate and transport processes that control their concentrations. In this study, a three-tiered approach is used to identify human and nonhuman sources of FIB in Avalon Bay, a popular resort community on Catalina Island in southern California. The first and second tiers utilize standard FIB tests to spatially isolate the FIB signal, to characterize the variability of FIB over a range of temporal scales, and to measure FIB concentrations in potential sources of these organisms. In the third tier, water samples from FIB "hot spots" and sources are tested for human-specific bacteria Bacteroides/Prevotella and enterovirus to determine whether the FIB are from human sewage or from nonhuman sources such as bird feces. FIB in Avalon Bay appear to be from multiple, primarily land-based, sources including bird droppings, contaminated subsurface water, leaking drains, and runoff from street wash-down actvities. Multiple shoreline samples and two subsurface water samples tested positive for human-specific bacteria and enterovirus, suggesting that at least a portion of the FIB contamination is from human sewage.

  View details for DOI 10.1021/es025934x

  View details for Web of Science ID 000181067100003

  View details for PubMedID 12636264

• A model of microbial transport and inactivation in the surf zone and application to field measurements of total coliform in Northern Orange County, California. Environmental Science and Technology Boehm., A., B. 2003; 37: 5511-5517
• A tiered approach for identification of a human fecal pollution source at a recreational beach: Case study at Avalon Bay, Catalina Island, California, USA. Environmental Science and Technology Boehm., A., B., Fuhrman, J., A., Mrse, R., D., Grant., S., B. 2003; 37: 673-680
• A scaling theory for number-flux distributions generated during steady-state coagulation and settling and application to particles in Lake Zurich, Switzerland JOURNAL OF COLLOID AND INTERFACE SCIENCE Boehm, A. B. 2002; 254 (2): 266-273

  Abstract

  In this study, we extend the established scaling theory for cluster size distributions generated during unsteady coagulation to number-flux distributions that arise during steady-state coagulation and settling in an unmixed water mass. The scaling theory predicts self-similar number-flux distributions and power-law decay of total number flux with depth. The shape of the number-flux distributions and the power-law exponent describing the decay of the total number flux are shown to depend on the homogeneity and small i/j limit of the coagulation kernel and the exponent kappa, which describes the variation in settling velocity with cluster volume. Particle field measurements from Lake Zurich, collected by U. Weilenmann and co-workers (Limnol. Oceanogr.34, 1 (1989)), are used to illustrate how the scaling predictions can be applied to a natural system. This effort indicates that within the mid-depth region of Lake Zurich, clusters of the same size preferentially interact and large clusters react with one another more quickly than small ones, indicative of clusters coagulating in a reaction-limited regime.

  View details for DOI 10.1006/jcis.2002.8599

  View details for Web of Science ID 000178935400009

  View details for PubMedID 12702397

• Decadal and shorter period variability of surf zone water quality at Huntington Beach, California ENVIRONMENTAL SCIENCE & TECHNOLOGY Boehm, A. B., Grant, S. B., Kim, J. H., Mowbray, S. L., McGee, C. D., Clark, C. D., Foley, D. M., Wellman, D. E. 2002; 36 (18): 3885-3892

  Abstract

  The concentration of fecal indicator bacteria in the surf zone at Huntington Beach, CA, varies over time scales that span at least 7 orders of magnitude, from minutes to decades. Sources of this variability include historical changes in the treatment and disposal of wastewater and dry weather runoff, El Niño events, seasonal variations in rainfall, spring-neap tidal cycles, sunlight-induced mortality of bacteria, and nearshore mixing. On average, total coliform concentrations have decreased over the past 43 years, although point sources of shoreline contamination (storm drains, river outlets, and submarine outfalls) continue to cause transiently poor water quality. These transient point sources typically persist for 5-8 yr and are modulated by the phase of the moon, reflecting the influence of tides on the sourcing and transport of pollutants in the coastal ocean. Indicator bacteria are very sensitive to sunlight therefore, the time of day when samples are collected can influence the outcome of water quality testing. These results demonstrate that coastal water quality is forced by a complex combination of local and external processes and raise questions about the efficacy of existing marine bathing water monitoring and reporting programs.

  View details for DOI 10.1021/es020524u

  View details for Web of Science ID 000178016600001

  View details for PubMedID 12269739

• Cross-shelf transport at Huntington Beach. Implications for the fate of sewage discharged through an offshore ocean outfall ENVIRONMENTAL SCIENCE & TECHNOLOGY Boehm, A. B., Sanders, B. F., Winant, C. D. 2002; 36 (9): 1899-1906

  Abstract

  In this study, we evaluate the potential for internal tides to transport wastewater effluent from the Orange County Sanitation District (OCSD) ocean outfall toward Huntington Beach. Results of plume tracking studies show that OCSD effluent occasionally moves shoreward into water less than 20 m deep. Analyses of current and temperature observations indicate cold water is regularly advected cross-shelf, in to and out of the nearshore, at both semi-diurnal and diurnal frequencies. Isotherms typically associated with the waste field near the outfall are observed just outside the Huntington Beach surf zone, where the total depth is less than 6 m, highlighting the extent of the cross-shelf transport. This advection is attributed to a mode 1 internal motion, or internal tide. On the basis of the analyses presented here, the OCSD plume cannot be ruled out as a contributor to poor bathing-water quality at Huntington Beach.

  View details for DOI 10.1021/es0111986

  View details for Web of Science ID 000175311900010

  View details for PubMedID 12026969

• Decadal and shorter period variability of surf zone water quality at Huntington Beach, California. Environmental Science and Technology Boehm., A., B., Grant, S., B., Kim, J., H., Mowbray, S., L., McGee, C., D., Clark, C., D. 2002; 36: 3885-3892
• Cross-shelf transport at Huntington Beach -Implications for the fate of sewage discharged through an offshore ocean outfall. Environmental Science and Technology Boehm., A., B., Sanders, B., F., Winant., C., D. 2002; 36: 1899-1906
• A steady state model of particulate organic carbon flux below the mixed layer and application to the Joint Global Ocean Flux Study JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS Boehm, A. B., Grant, S. B. 2001; 106 (C12): 31227-31237

  View details for Web of Science ID 000173402400023

• Generation of enterococci bacteria in a coastal saltwater marsh and its impact on surf zone water quality ENVIRONMENTAL SCIENCE & TECHNOLOGY Grant, S. B., Sanders, B. F., Boehm, A. B., Redman, J. A., Kim, J. H., Mrse, R. D., Chu, A. K., Gouldin, M., McGee, C. D., Gardiner, N. A., Jones, B. H., Svejkovsky, J., Leipzig, G. V. 2001; 35 (12): 2407-2416

  Abstract

  Elevated levels of enterococci bacteria, an indicator of fecal pollution, are routinely detected in the surf zone at Huntington State and City Beaches in southern California. A multidisciplinary study was carried out to identify sources of enterococci bacteria landward of the coastline. We find that enterococci bacteria are present at high concentrations in urban runoff, bird feces, marsh sediments, and on marine vegetation. Surprisingly, urban runoff appears to have relatively little impact on surf zone water quality because of the long time required for this water to travel from its source to the ocean. On the other hand, enterococci bacteria generated in a tidal saltwater marsh located near the beach significantly impact surf zone water quality. This study identifies a potential tradeoff between restoring coastal wetlands and protecting beach water quality and calls into question the use of ocean bathing water standards based on enterococci at locations near coastal wetlands.

  View details for Web of Science ID 000169343700002

  View details for PubMedID 11432541

• A steady-state model of particulate organic carbon flux below the mixed layer and application to the Joint Global Ocean Flux Study. Journal of Geophysical Research-Oceans Boehm, A., B., Grant., S., B. 2001; 106: 31227-21237
• Generation of enterococci bacteria in a coastal saltwater marsh and its impact on surf zone water quality. Environmental Science & Technology Grant, S., B., Sanders, B., F., Boehm, A., B., Redman, J., A., Kim, J., H., Mrse, R., D. 2001; 35: 2407-2416
• Particle coagulation and the memory of initial conditions JOURNAL OF PHYSICS A-MATHEMATICAL AND GENERAL Boehm, A. B., Poor, C., Grant, S. B. 1998; 31 (46): 9241-9254

  View details for Web of Science ID 000077247700014

• Influence of coagulation, sedimentation, and grazing by zooplankton on phytoplankton aggregate distributions in aquatic systems JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS Boehm, A. B., Grant, S. B. 1998; 103 (C8): 15601-15612

  View details for Web of Science ID 000074741000006

• Particle coagulation and the memory of initial conditions Journal of Physics A: Mathematics and General Boehm, A., B., Poor, C., Grant., S., B. 1998; 31: 9241-9254
• The influence of coagulation, sedimentation, and grazing by zooplankton on phytoplankton aggregate size distributions in aquatic systems. Journal of Geophysical Research-Oceans Boehm, A., B., Grant., S., B. 1998; 103: 15601-15612