Environmental enteric dysfunction (EED) affects 50-90% of children in low-income countries and is likely an important factor in child stunting as it impedes efficient nutrient uptake in the small intestine. EED is suspected to be the result of persistent exposure to enteric pathogens, although it has not been correlated with any specific pathogen. My research explores the interplay of gut microbiota, including enteric pathogens, and the host immune system with a focus on understanding EED so we can rationally design treatments and preventive measures.

Honors & Awards

  • NIH NRSA Ruth L. Kirschstein F32 Individual Postdoctoral Fellowship, NIH/ NIDDK (2022-2025)
  • Dr. George Rosenkranz Prize, Freeman Spogli Institute for International Studies and Stanford Health Policy (2021)
  • School of Medicine Dean's Postdoctoral Fellowship, Stanford University (2021)
  • Stanford Interdisciplinary Graduate Fellowship, Stanford University (2015-2018)
  • Graduate Research Fellowship, National Science Foundation (2011-2015)

Boards, Advisory Committees, Professional Organizations

  • Global Health Postdoctoral Affiliate, Center for Innovations in Global Health (2022 - Present)
  • Member, Stanford Military-Affiliated Advisory Committee (2019 - Present)
  • Member, American Society of Tropical Medicine and Hygiene (2014 - Present)
  • Member, American Society for Microbiology (2009 - Present)

Professional Education

  • Bachelor of Science, United States Military Academy, Environmental Engineering (2001)
  • Master of Science, Pennsylvania State University, Environmental Engineering (2011)
  • PhD, Stanford University (2019)
  • MS, Penn State University (2011)
  • BS, United States Military Academy at West Point (2001)

Stanford Advisors

Lab Affiliations

All Publications

  • Influence of hydrometeorological risk factors on child diarrhea and enteropathogens in rural Bangladesh. PLoS neglected tropical diseases Grembi, J. A., Nguyen, A. T., Riviere, M., Heitmann, G. B., Patil, A., Athni, T. S., Djajadi, S., Ercumen, A., Lin, A., Crider, Y., Mertens, A., Karim, M. A., Islam, M. O., Miah, R., Famida, S. L., Hossen, M. S., Mutsuddi, P., Ali, S., Rahman, M. Z., Hussain, Z., Shoab, A. K., Haque, R., Rahman, M., Unicomb, L., Luby, S. P., Arnold, B. F., Bennett, A., Benjamin-Chung, J. 2024; 18 (5): e0012157


    A number of studies have detected relationships between weather and diarrhea. Few have investigated associations with specific enteric pathogens. Understanding pathogen-specific relationships with weather is crucial to inform public health in low-resource settings that are especially vulnerable to climate change.Our objectives were to identify weather and environmental risk factors associated with diarrhea and enteropathogen prevalence in young children in rural Bangladesh, a population with high diarrheal disease burden and vulnerability to weather shifts under climate change.We matched temperature, precipitation, surface water, and humidity data to observational longitudinal data from a cluster-randomized trial that measured diarrhea and enteropathogen prevalence in children 6 months-5.5 years from 2012-2016. We fit generalized additive mixed models with cubic regression splines and restricted maximum likelihood estimation for smoothing parameters.Comparing weeks with 30°C versus 15°C average temperature, prevalence was 3.5% higher for diarrhea, 7.3% higher for Shiga toxin-producing Escherichia coli (STEC), 17.3% higher for enterotoxigenic E. coli (ETEC), and 8.0% higher for Cryptosporidium. Above-median weekly precipitation (median: 13mm; range: 0-396mm) was associated with 29% higher diarrhea (adjusted prevalence ratio 1.29, 95% CI 1.07, 1.55); higher Cryptosporidium, ETEC, STEC, Shigella, Campylobacter, Aeromonas, and adenovirus 40/41; and lower Giardia, sapovirus, and norovirus prevalence. Other associations were weak or null.Higher temperatures and precipitation were associated with higher prevalence of diarrhea and multiple enteropathogens; higher precipitation was associated with lower prevalence of some enteric viruses. Our findings emphasize the heterogeneity of the relationships between hydrometeorological variables and specific enteropathogens, which can be masked when looking at composite measures like all-cause diarrhea. Our results suggest that preventive interventions targeted to reduce enteropathogens just before and during the rainy season may more effectively reduce child diarrhea and enteric pathogen carriage in rural Bangladesh and in settings with similar meteorological characteristics, infrastructure, and enteropathogen transmission.

    View details for DOI 10.1371/journal.pntd.0012157

    View details for PubMedID 38739632

  • Influence of Temperature and Precipitation on the Effectiveness of Water, Sanitation, and Handwashing Interventions against Childhood Diarrheal Disease in Rural Bangladesh: A Reanalysis of the WASH Benefits Bangladesh Trial. Environmental health perspectives Nguyen, A. T., Grembi, J. A., Riviere, M., Barratt Heitmann, G., Hutson, W. D., Athni, T. S., Patil, A., Ercumen, A., Lin, A., Crider, Y., Mertens, A., Unicomb, L., Rahman, M., Luby, S. P., Arnold, B. F., Benjamin-Chung, J. 2024; 132 (4): 47006


    Diarrheal disease is a leading cause of childhood morbidity and mortality globally. Household water, sanitation, and handwashing (WASH) interventions can reduce exposure to diarrhea-causing pathogens, but meteorological factors may impact their effectiveness. Information about effect heterogeneity under different weather conditions is critical to refining these targeted interventions.We aimed to determine whether temperature and precipitation modified the effect of low-cost, point-of-use WASH interventions on child diarrhea.We analyzed data from a trial in rural Bangladesh that compared child diarrhea prevalence between clusters (N=720) that were randomized to different WASH interventions between 2012 and 2016 (NCT01590095). We matched temperature and precipitation measurements to diarrhea outcomes (N=12,440 measurements, 6,921 children) by geographic coordinates and date. We estimated prevalence ratios (PRs) using generative additive models and targeted maximum likelihood estimation to assess the effectiveness of each WASH intervention under different weather conditions.Generally, WASH interventions most effectively prevented diarrhea during monsoon season, particularly following weeks with heavy rain or high temperatures. The PR for diarrhea in the WASH interventions group compared with the control group was 0.49 (95% CI: 0.35, 0.68) after 1 d of heavy rainfall, with a less-protective effect [PR=0.87 (95% CI: 0.60, 1.25)] when there were no days with heavy rainfall. Similarly, the PR for diarrhea in the WASH intervention group compared with the control group was 0.60 (95% CI: 0.48, 0.75) following above-median temperatures vs. 0.91 (95% CI: 0.61, 1.35) following below-median temperatures. The influence of precipitation and temperature varied by intervention type; for precipitation, the largest differences in effectiveness were for the sanitation and combined WASH interventions.WASH intervention effectiveness was strongly influenced by precipitation and temperature, and nearly all protective effects were observed during the rainy season. Future implementation of these interventions should consider local environmental conditions to maximize effectiveness, including targeted efforts to maintain latrines and promote community adoption ahead of monsoon seasons.

    View details for DOI 10.1289/EHP13807

    View details for PubMedID 38602833

    View details for PubMedCentralID PMC11008709

  • Treatment Heterogeneity of Water, Sanitation, Hygiene, and Nutrition Interventions on Child Growth by Environmental Enteric Dysfunction and Pathogen Status for Young Children in Bangladesh. medRxiv : the preprint server for health sciences Butzin-Dozier, Z., Ji, Y., Coyle, J., Malenica, I., McQuade, E. T., Grembi, J. A., Platts-Mills, J. A., Houpt, E. R., Graham, J. P., Ali, S., Rahman, M. Z., Alauddin, M., Famida, S. L., Akther, S., Hossen, M. S., Mutsuddi, P., Shoab, A. K., Rahman, M., Islam, M. O., Miah, R., Taniuchi, M., Liu, J., Alauddin, S., Stewart, C. P., Luby, S. P., Colford, J. M., Hubbard, A. E., Mertens, A. N., Lin, A. 2024


    Water, sanitation, hygiene (WSH), nutrition (N), and combined (N+WSH) interventions are often implemented by global health organizations, but WSH interventions may insufficiently reduce pathogen exposure, and nutrition interventions may be modified by environmental enteric dysfunction (EED), a condition of increased intestinal permeability and inflammation. This study investigated the heterogeneity of these treatments' effects based on individual pathogen and EED biomarker status with respect to child linear growth.We applied cross-validated targeted maximum likelihood estimation and super learner ensemble machine learning to assess the conditional treatment effects in subgroups defined by biomarker and pathogen status. We analyzed treatment (N+WSH, WSH, N, or control) randomly assigned in-utero, child pathogen and EED data at 14 months of age, and child LAZ at 28 months of age. We estimated the difference in mean child length for age Z-score (LAZ) under the treatment rule and the difference in stratified treatment effect (treatment effect difference) comparing children with high versus low pathogen/biomarker status while controlling for baseline covariates.We analyzed data from 1,522 children, who had median LAZ of -1.56. We found that myeloperoxidase (N+WSH treatment effect difference 0.0007 LAZ, WSH treatment effect difference 0.1032 LAZ, N treatment effect difference 0.0037 LAZ) and Campylobacter infection (N+WSH treatment effect difference 0.0011 LAZ, WSH difference 0.0119 LAZ, N difference 0.0255 LAZ) were associated with greater effect of all interventions on growth. In other words, children with high myeloperoxidase or Campylobacter infection experienced a greater impact of the interventions on growth. We found that a treatment rule that assigned the N+WSH (LAZ difference 0.23, 95% CI (0.05, 0.41)) and WSH (LAZ difference 0.17, 95% CI (0.04, 0.30)) interventions based on EED biomarkers and pathogens increased predicted child growth compared to the randomly allocated intervention.These findings indicate that EED biomarker and pathogen status, particularly Campylobacter and myeloperoxidase (a measure of gut inflammation), may be related to impact of N+WSH, WSH, and N interventions on child linear growth.

    View details for DOI 10.1101/2024.03.21.24304684

    View details for PubMedID 38585931

    View details for PubMedCentralID PMC10996736

  • 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


    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

  • Micronutrient status during pregnancy is associated with child immune status in rural Bangladesh. Current developments in nutrition Jung, D. K., Tan, S. T., Hemlock, C., Mertens, A. N., Stewart, C. P., Rahman, M. Z., Ali, S., Raqib, R., Grembi, J. A., Karim, M. R., Shahriar, S., Roy, A. K., Abdelrahman, S., Shoab, A. K., Famida, S. L., Hossen, M. S., Mutsuddi, P., Akther, S., Rahman, M., Unicomb, L., Hester, L., Granger, D. A., Erhardt, J., Naved, R. T., Al Mamun, M. M., Parvin, K., Colford, J. M., Fernald, L. C., Luby, S. P., Dhabhar, F. S., Lin, A. 2023; 7 (8): 101969


    Background: Poor immune function increases children's risk of infection and mortality. Several maternal factors during pregnancy may affect infant immune function during the postnatal period.Objectives: We aimed to evaluate whether maternal micronutrients, stress, estriol, and immune status during the first or second trimester of pregnancy were associated with child immune status in the first two years after birth.Methods: We conducted observational analyses within the water, sanitation, and hygiene (WASH) Benefits Bangladesh randomized controlled trial. We measured biomarkers in 575 pregnant women and postnatally in their children. Maternal biomarkers measured during the first and second trimester of pregnancy included nutrition status via vitamin D (25-hydroxy-D [25(OH)D]), ferritin, soluble transferrin receptor (sTfR), and retinol-binding protein (RBP); cortisol; estriol. Immune markers were assessed in pregnant women at enrollment and their children at ages 14 and 28 mo, including C-reactive protein (CRP), alpha-1-acid glycoprotein (AGP), and 13 cytokines (including IFN-gamma). We generated a standardized sum score of log-transformed cytokines. We analyzed IFN-gamma individually because it is a critical immunoregulatory cytokine. All outcomes were prespecified. We used generalized additive models and reported the mean difference and 95% confidence intervals at the 25th and 75th percentiles of exposure distribution.Results: At child age 14 mo, concentrations of maternal RBP were inversely associated with the cytokine sum score in children (-0.34 adjusted difference between the 25th and 75th percentile [95% confidence interval -0.61, -0.07]), and maternal vitamin A deficiency was positively associated with the cytokine sum score in children (1.02 [0.13, 1.91]). At child age of 28 mo, maternal RBP was positively associated with IFN-gamma in children (0.07 [0.01, 0.14]), whereas maternal vitamin A deficiency was negatively associated with child AGP (-0.07 [-0.13, -0.02]). Maternal iron deficiency was associated with higher AGP concentrations in children at age 14 mo (0.13 [0.04, 0.23]), and maternal sTfR concentrations were positively associated with child CRP concentrations at age 28 mo (0.18 [0, 0.36]).Conclusion: Maternal deficiencies in vitamin A or iron during the first 2 trimesters of pregnancy may shape the trajectory of a child's immune status.

    View details for DOI 10.1016/j.cdnut.2023.101969

    View details for PubMedID 37560460

  • Profiling the human intestinal environment under physiological conditions. Nature Shalon, D., Culver, R. N., Grembi, J. A., Folz, J., Treit, P. V., Shi, H., Rosenberger, F. A., Dethlefsen, L., Meng, X., Yaffe, E., Aranda-Diaz, A., Geyer, P. E., Mueller-Reif, J. B., Spencer, S., Patterson, A. D., Triadafilopoulos, G., Holmes, S. P., Mann, M., Fiehn, O., Relman, D. A., Huang, K. C. 2023


    The spatiotemporal structure of the human microbiome1,2, proteome3 and metabolome4,5 reflects and determines regional intestinal physiology and may have implications for disease6. Yet, little is known about the distribution of microorganisms, their environment and their biochemical activity in the gut because of reliance on stool samples and limited access to only some regions of the gut using endoscopy in fasting or sedated individuals7. To address these deficiencies, we developed an ingestible device that collects samples from multiple regions of the human intestinal tract during normal digestion. Collection of 240 intestinal samples from 15 healthy individuals using the device and subsequent multi-omics analyses identified significant differences between bacteria, phages, host proteins and metabolites in the intestines versus stool. Certain microbial taxa were differentially enriched and prophage induction was more prevalent in the intestines than in stool. The host proteome and bile acid profiles varied along the intestines and were highly distinct from those of stool. Correlations between gradients in bile acid concentrations and microbial abundance predicted species that altered the bile acid pool through deconjugation. Furthermore, microbially conjugated bile acid concentrations exhibited amino acid-dependent trends that were not apparent in stool. Overall, non-invasive, longitudinal profiling of microorganisms, proteins and bile acids along the intestinal tract under physiological conditions can help elucidate the roles of the gut microbiome and metabolome in human physiology and disease.

    View details for DOI 10.1038/s41586-023-05989-7

    View details for PubMedID 37165188

  • Human metabolome variation along the upper intestinal tract. Nature metabolism Folz, J., Culver, R. N., Morales, J. M., Grembi, J., Triadafilopoulos, G., Relman, D. A., Huang, K. C., Shalon, D., Fiehn, O. 2023


    Most processing of the human diet occurs in the small intestine. Metabolites in the small intestine originate from host secretions, plus the ingested exposome1 and microbial transformations. Here we probe the spatiotemporal variation of upper intestinal luminal contents during routine daily digestion in 15 healthy male and female participants. For this, we use a non-invasive, ingestible sampling device to collect and analyse 274 intestinal samples and 60 corresponding stool homogenates by combining five mass spectrometry assays2,3 and 16S rRNA sequencing. We identify 1,909 metabolites, including sulfonolipids and fatty acid esters of hydroxy fatty acids (FAHFA) lipids. We observe that stool and intestinal metabolomes differ dramatically. Food metabolites display trends in dietary biomarkers, unexpected increases in dicarboxylic acids along the intestinal tract and a positive association between luminal keto acids and fruit intake. Diet-derived and microbially linked metabolites account for the largest inter-individual differences. Notably, two individuals who had taken antibiotics within 6 months before sampling show large variation in levels of bioactive FAHFAs and sulfonolipids and other microbially related metabolites. From inter-individual variation, we identify Blautia species as a candidate to be involved in FAHFA metabolism. In conclusion, non-invasive, in vivo sampling of the human small intestine and ascending colon under physiological conditions reveals links between diet, host and microbial metabolism.

    View details for DOI 10.1038/s42255-023-00777-z

    View details for PubMedID 37165176

  • 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


    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

  • Introducing riskCommunicator: An R package to obtain interpretable effect estimates for public health. PloS one Grembi, J. A., Rogawski McQuade, E. T. 2022; 17 (7): e0265368


    Common statistical modeling methods do not necessarily produce the most relevant or interpretable effect estimates to communicate risk. Overreliance on the odds ratio and relative effect measures limit the potential impact of epidemiologic and public health research. We created a straightforward R package, called riskCommunicator, to facilitate the presentation of a variety of effect measures, including risk differences and ratios, number needed to treat, incidence rate differences and ratios, and mean differences. The riskCommunicator package uses g-computation with parametric regression models and bootstrapping for confidence intervals to estimate effect measures in time-fixed data. We demonstrate the utility of the package using data from the Framingham Heart Study to estimate the effect of prevalent diabetes on the 24-year risk of cardiovascular disease or death. The package promotes the communication of public-health relevant effects and is accessible to a broad range of epidemiologists and health researchers with little to no expertise in causal inference methods or advanced coding.

    View details for DOI 10.1371/journal.pone.0265368

    View details for PubMedID 35849588

  • Advantageous microbial community development and improved performance of pilot-scale field systems treating high-risk acid mine drainage with crab shell. Journal of hazardous materials Lin, Y., Grembi, J. A., Goots, S. S., Sebastian, A., Albert, I., Brennan, R. A. 2021; 420: 126665


    Microbial communities are crucial to the effectiveness and stability of bioremediation systems treating acid mine drainage (AMD); however, little research has addressed how they correlate to system performance under changing environmental conditions. In this study, 16S rRNA gene sequencing and quantitative PCR (qPCR) were used to characterize microbial communities within different substrate combinations of crab shell (CS) and spent mushroom compost (SMC) and their association with chemical performance in pilot-scale vertical flow ponds (VFPs) treating high risk AMD in central Pennsylvania over 643 days of operation. As compared to a control containing SMC, VFPs containing CS sustained higher alkalinity, higher sulfate-reducing rates, and more thorough metals removal (>90% for Fe and Al, >50% for Mn and Zn). Correspondingly, CS VFPs supported the growth of microorganisms in key functional groups at increasing abundance and diversity over time, especially more diverse sulfate-reducing bacteria. Through changing seasonal and operational conditions over almost two years, the relative abundance of the core phyla shifted in all reactors, but the smallest changes in functional gene copies were observed in VFPs containing CS. These results suggest that the high diversity and stability of microbial communities associated with CS are consistent with effective AMD treatment.

    View details for DOI 10.1016/j.jhazmat.2021.126665

    View details for PubMedID 34351284

  • High-throughput low-cost nl-qPCR for enteropathogen detection: A proof-of-concept among hospitalized patients in Bangladesh. PloS one Flaherty, K. E., Grembi, J. A., Ramachandran, V. V., Haque, F., Khatun, S., Rahman, M., Maples, S., Becker, T. K., Spormann, A. M., Schoolnik, G. K., Hryckowian, A. J., Nelson, E. J. 2021; 16 (10): e0257708


    BACKGROUND: Diarrheal disease is a leading cause of morbidity and mortality globally, especially in low- and middle-income countries. High-throughput and low-cost approaches to identify etiologic agents are needed to guide public health mitigation. Nanoliter-qPCR (nl-qPCR) is an attractive alternative to more expensive methods yet is nascent in application and without a proof-of-concept among hospitalized patients.METHODS: A census-based study was conducted among diarrheal patients admitted at two government hospitals in rural Bangladesh during a diarrheal outbreak period. DNA was extracted from stool samples and assayed by nl-qPCR for common bacterial, protozoan, and helminth enteropathogens as the primary outcome.RESULTS: A total of 961 patients were enrolled; stool samples were collected from 827 patients. Enteropathogens were detected in 69% of patient samples; More than one enteropathogen was detected in 32%. Enteropathogens most commonly detected were enteroaggregative Escherichia coli (26.0%), Shiga toxin-producing E.coli (18.3%), enterotoxigenic E. coli (15.5% heat stable toxin positive, 2.2% heat labile toxin positive), Shigella spp. (14.8%), and Vibrio cholerae (9.0%). Geospatial analysis revealed that the median number of pathogens per patient and the proportion of cases presenting with severe dehydration were greatest amongst patients residing closest to the study hospitals."CONCLUSIONS: This study demonstrates a proof-of-concept for nl-qPCR as a high-throughput low-cost method for enteropathogen detection among hospitalized patients.

    View details for DOI 10.1371/journal.pone.0257708

    View details for PubMedID 34597302

  • Effect of water, sanitation, handwashing and nutrition interventions on enteropathogens in children 14 months old: a cluster-randomized controlled trial in rural Bangladesh. The Journal of infectious diseases Grembi, J. A., Lin, A., Karim, M. A., Islam, M. O., Miah, R., Arnold, B. F., McQuade, E. T., Ali, S., Rahman, M. Z., Hussain, Z., Shoab, A. K., Famida, S. L., Hossen, M. S., Mutsuddi, P., Rahman, M., Unicomb, L., Haque, R., Taniuchi, M., Liu, J., Platts-Mills, J. A., Holmes, S. P., Stewart, C. P., Benjamin-Chung, J., Colford, J. M., Houpt, E. R., Luby, S. P. 2020


    BACKGROUND: We evaluated the impact of low-cost water, sanitation, handwashing (WSH) and child nutrition interventions on enteropathogen carriage in the WASH Benefits cluster-randomized controlled trial in rural Bangladesh.METHODS: We analyzed 1411 routine fecal samples from children 14±2 months old in the WSH (n = 369), nutrition counseling plus lipid-based nutrient supplement (n = 353), nutrition plus WSH (n = 360), and control (n = 329) arms for 34 enteropathogens using quantitative PCR. Outcomes included the number of co-occurring pathogens; cumulative quantity of four stunting-associated pathogens; and prevalence and quantity of individual pathogens. Masked analysis was by intention-to-treat.RESULTS: 326 (99.1%) control children had one or more enteropathogens detected (mean 3.8±1.8). Children receiving WSH interventions had lower prevalence and quantity of individual viruses than controls (prevalence difference for norovirus: -11% [95% confidence interval [CI], -5 to -17%]; sapovirus: -9% [95%CI, -3 to -15%]; and adenovirus 40/41: -9% [95%CI, -2 to - 15%]). There was no difference in bacteria, parasites, or cumulative quantity of stunting-associated pathogens between controls and any intervention arm.CONCLUSIONS: WSH interventions were associated with fewer enteric viruses in children aged 14 months. Different strategies are needed to reduce enteric bacteria and parasites at this critical young age.

    View details for DOI 10.1093/infdis/jiaa549

    View details for PubMedID 32861214

  • Gold-standard cholera diagnostics are tarnished by lytic bacteriophage and antibiotics. Journal of clinical microbiology Nelson, E. J., Grembi, J. A., Chao, D. L., Andrews, J. R., Alexandrova, L., Rodriguez, P. H., Ramachandran, V. V., Sayeed, M. A., Wamala, J. F., Debes, A. K., Sack, D. A., Hryckowian, A. J., Haque, F., Khatun, S., Rahman, M., Chien, A., Spormann, A. M., Schoolnik, G. K. 2020


    A fundamental, clinical and scientific concern is how lytic bacteriophage, as well as antibiotics, impact diagnostic positivity. Cholera was chosen as a model disease to investigate this important question because cholera outbreaks enable large enrollment, field methods are well established, and the predatory relationship between lytic bacteriophage and the etiologic agent Vibrio cholerae share commonalities across bacterial taxa. Patients with diarrheal disease were enrolled at two remote hospitals in Bangladesh. Diagnostic performance was assessed as a function of lytic bacteriophage detection and exposure to the first-line antibiotic azithromycin detected in stool samples by mass spectrometry. Among diarrheal samples positive by nanoliter quantitative PCR for V. cholerae (n=78/849), the odds that a rapid diagnostic test (RDT) or qPCR was positive was reduced by 89% (OR 0.108; 95%CI 0.002-0.872) and 87% (OR 0.130; 95%CI 0.022-0.649) when lytic bacteriophage were detected, respectively. The odds that a rapid diagnostic test (RDT) or qPCR was positive was reduced by more than 99% (OR 0.00; 95% CI: 0.00-0.28) and 89% (OR 0.11; 95% CI: 0.03-0.44) when azithromycin was detected, respectively. Analysis of additional samples from South Sudan found similar phage effects on RDTs; antibiotics were not assayed. Cholera burden estimates may improve by accommodating for the negative effects of lytic bacteriophage and antibiotic exposure on diagnostic positivity. One accommodation is using bacteriophage detection as proxy for pathogen detection. These findings have relevance for other diagnostic settings where bacterial pathogens are vulnerable to lytic bacteriophage predation.

    View details for DOI 10.1128/JCM.00412-20

    View details for PubMedID 32611794

  • Effects of Water, Sanitation, Handwashing, and Nutritional Interventions on Environmental Enteric Dysfunction in Young Children: A Cluster-randomized, Controlled Trial in Rural Bangladesh CLINICAL INFECTIOUS DISEASES Lin, A., Ali, S., Arnold, B. F., Rahman, M., Alauddin, M., Grembi, J., Mertens, A. N., Famida, S. L., Akther, S., Hossen, M., Mutsuddi, P., Shoab, A. K., Hussain, Z., Rahman, M., Unicomb, L., Ashraf, S., Naser, A., Parvez, S. M., Ercumen, A., Benjamin-Chung, J., Haque, R., Ahmed, T., Hossain, M., Choudhury, N., Jannat, K., Alauddin, S. T., Minchala, S. G., Cekovic, R., Hubbard, A. E., Stewart, C. P., Dewey, K. G., Colford, J. M., Luby, S. P. 2020; 70 (5): 738–47

    View details for DOI 10.1093/cid/ciz291

    View details for Web of Science ID 000520551800008

  • Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention Scientific Reports Grembi, J. A., Nguyen, L. H., Haggerty, T. D., Gardner, C. D., Holmes, S. P., Parsonnet, J. 2020; 10
  • High-Throughput Multiparallel Enteropathogen Detection via Nano-Liter qPCR. Frontiers in cellular and infection microbiology Grembi, J. A., Mayer-Blackwell, K. n., Luby, S. P., Spormann, A. M. 2020; 10: 351


    Quantitative molecular diagnostic methods can effectively detect pathogen-specific nucleic acid sequences, but costs associated with multi-pathogen panels hinder their widespread use in research trials. Nano-liter qPCR (nL-qPCR) is a miniaturized tool for quantification of multiple targets in large numbers of samples based on assay parallelization on a single chip, with potentially significant cost-savings due to rapid throughput and reduced reagent volumes. We evaluated a suite of novel and published assays to detect 17 enteric pathogens using a commercially available nL-qPCR technology. Amplification efficiencies ranged from 88 to 98% (mean 91%) and were reproducible across four operators at two separate facilities. When applied to fecal material, assays were sensitive and selective (99.8% of DNA amplified were genes from the target organism). Due to nanofluidic volumes, detection limits were 1-2 orders of magnitude less sensitive for nL-qPCR than an enteric TaqMan Array Card (TAC). However, higher detection limits do not hinder detection of diarrhea-causing pathogen concentrations. Compared to TAC, nL-qPCR displayed 99% (95% CI 0.98, 0.99) negative percent agreement and 62% (95% CI 0.59, 0.65) overall positive percent agreement for presence of pathogens across diarrheal and non-diarrheal fecal samples. Positive percent agreement was 89% among samples with concentrations above the nL-qPCR detection limits. nL-qPCR assays showed an underestimation bias of 0.34 log10 copies/gram of stool [IQR -0.40, -0.28] compared with TAC. With 12 times higher throughput for a sixth of the per-sample cost of the enteric TAC, the nL-qPCR chip is a viable alternative for enteropathogen quantification for studies where other technologies are cost-prohibitive.

    View details for DOI 10.3389/fcimb.2020.00351

    View details for PubMedID 32766166

    View details for PubMedCentralID PMC7381150

  • Shared bacterial communities between soil, stored drinking water, and hands in rural Bangladeshi households. Water research X Fuhrmeister, E. R., Ercumen, A. n., Grembi, J. A., Islam, M. n., Pickering, A. J., Nelson, K. L. 2020; 9: 100056


    Understanding household-level transmission pathways of fecal pathogens can provide insight for developing effective strategies to reduce diarrheal illness in low- and middle-income countries. We applied whole bacterial community analysis to investigate pathways of bacterial transmission in 50 rural Bangladeshi households. SourceTracker was used to quantify the shared microbial community in household reservoirs (stored drinking water, soil, and hands) and estimate the percentage of fecal-associated bacteria from child and mothers' feces in these reservoirs. Among the reservoirs studied, most bacterial transfer occurred between mothers' and children's hands and between mothers' hands and stored water. The relative percentage of human fecal-associated bacteria in all household reservoirs was low. We also quantified the number of identical amplicon sequence variants within and between individual households to assess bacterial community exchange in the domestic environment. Intra-household sharing of bacteria between mothers' and children's hands and between hands and soil was significantly greater than inter-household sharing.

    View details for DOI 10.1016/j.wroa.2020.100056

    View details for PubMedID 32529181

    View details for PubMedCentralID PMC7276488

  • Effects of water, sanitation, handwashing, and nutritional interventions on environmental enteric dysfunction in young children: a cluster-randomized controlled trial in rural Bangladesh. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America Lin, A., Ali, S., Arnold, B. F., Rahman, M. Z., Alauddin, M., Grembi, J., Mertens, A. N., Famida, S. L., Akther, S., Hossen, M. S., Mutsuddi, P., Shoab, A. K., Hussain, Z., Rahman, M., Unicomb, L., Ashraf, S., Naser, A. M., Parvez, S. M., Ercumen, A., Benjamin-Chung, J., Haque, R., Ahmed, T., Hossain, M. I., Choudhury, N., Jannat, K., Alauddin, S. T., Minchala, S. G., Cekovic, R., Hubbard, A. E., Stewart, C. P., Dewey, K. G., Colford, J. M., Luby, S. P. 2019


    BACKGROUND: We hypothesized that drinking water, sanitation, handwashing (WSH) and nutritional interventions would improve environmental enteric dysfunction (EED), a potential contributor to stunting.METHODS: Within a subsample of a cluster-randomized controlled trial in rural Bangladesh, we enrolled pregnant women in four arms: control, combined WSH, child nutrition counseling plus lipid-based nutrient supplements (N), and combined nutrition plus WSH (N+WSH). Among the birth cohort, we measured biomarkers of gut inflammation (myeloperoxidase, neopterin), permeability (alpha-1-antitrypsin, lactulose, mannitol), and repair (regenerating gene 1beta) at median ages 3, 14, and 28 months. Analysis was intention-to-treat.RESULTS: We assessed 1512 children. At age 3 months, compared to controls, neopterin was reduced by nutrition (-0.21 log nmol/L, CI -0.37, -0.05) and N+WSH (-0.20 log nmol/L, CI -0.34, -0.06) interventions; similar reductions were observed at 14 months. At 3 months, all interventions reduced lactulose and mannitol (-0.60 to -0.69 log mmol/L). At 28 months, myeloperoxidase was elevated in the WSH (0.23 log ng/ml, CI 0.06, 0.39) and nutrition (0.27 log ng/ml, CI 0.07, 0.47) arms and lactulose was higher in the WSH arm (0.30 log mmol/L, CI 0.07, 0.53).CONCLUSIONS: Reductions in permeability and inflammation at ages 3 and 14 months suggest that the interventions promoted healthy intestinal maturation; however, by 28 months the WSH and nutrition arms showed elevated EED biomarkers. These results underscore the importance of better understanding the pathophysiology of EED and targeting interventions early in childhood during the critical period when they are likely to have the largest benefit to intestinal health.( NCT01590095).

    View details for PubMedID 30963177

  • Identification of widespread antibiotic exposure in cholera patients correlates with clinically relevant microbiota changes. The Journal of infectious diseases Alexandrova, L. n., Haque, F. n., Rodriguez, P. n., Marrazzo, A. C., Grembi, J. A., Ramachandran, V. n., Hryckowian, A. J., Adams, C. M., Siddique, M. S., Khan, A. I., Qadri, F. n., Andrews, J. R., Rahman, M. n., Spormann, A. M., Schoolnik, G. K., Chien, A. n., Nelson, E. J. 2019


    A first step to combating antimicrobial resistance in enteric pathogens is to establish an objective assessment of antibiotic exposure. Our goal was to develop and evaluate a liquid chromatography-ion trap mass spectrometry (LC/MS) method to determine antibiotic exposure in cholera patients.A priority list for targeted LC/MS was generated from medication vendor surveys in Bangladesh. A study of cholera and non-cholera patients was conducted to collect and analyze paired urine and stool samples.Among 845 patients, 11% (n=90) were Vibrio cholerae positive; at least one antibiotic was detected in 86% and at least two in 52% of cholera stools. Among paired urine and stool (n=44), at least one antibiotic was detected in 98% and at least two in 84%, despite 55% self-reporting medication use. Compared to LC/MS, a low-cost antimicrobial detection bio-assay lacked sufficient negative predictive value (10%; 95% CI 6-16). Detection of guideline-recommended antibiotics in stool did (azithromycin; p=0.040) and did not (ciprofloxacin) correlate with V. cholerae suppression. A non-recommended antibiotic (metronidazole) was associated with decreases in anaerobes (Prevotella; p<0.001).The findings suggest there may be no true negative control group when attempting to account for antibiotic exposure in settings like those in this study.

    View details for DOI 10.1093/infdis/jiz299

    View details for PubMedID 31192364

  • Effects of lipid-based nutrient supplements and infant and young child feeding counseling with or without improved water, sanitation, and hygiene (WASH) on anemia and micronutrient status: results from 2 cluster-randomized trials in Kenya and Bangladesh AMERICAN JOURNAL OF CLINICAL NUTRITION Stewart, C. P., Dewey, K. G., Lin, A., Pickering, A. J., Byrd, K. A., Jannat, K., Ali, S., Rao, G., Dentz, H. N., Kiprotich, M., Arnold, C. D., Arnold, B. F., Allen, L. H., Shahab-Ferdows, S., Ercumen, A., Grembi, J. A., Naser, A., Rahman, M., Unicomb, L., Colford, J. M., Luby, S. P., Null, C. 2019; 109 (1): 148–64
  • Remediation of High-Strength Mine-Impacted Water with Mixed Organic Substrates Containing Crab Shell and Spent Mushroom Compost JOURNAL OF ENVIRONMENTAL ENGINEERING Grembi, J. A., Sick, B. A., Brennan, R. A. 2016; 142 (2)