Sheena Conforti

All Publications

• Enterovirus D68 in United States wastewater: a longitudinal surveillance study integrating climatic, demographic, and clinical data. Lancet regional health. Americas Conforti, S., Zulli, A., Boehm, A. B. 2026; 57: 101446

  Abstract

  Enterovirus D68 (EV-D68) can cause severe respiratory illness and acute flaccid myelitis (AFM), but limited clinical testing and sparse surveillance data hinder the ability to address epidemiological questions about its circulation. This study aimed to characterize EV-D68 seasonality across the U.S. using wastewater data, evaluate the influence of climatic and sociodemographic factors, and compare trends with symptom-based clinical indicators.We analyzed 43,876 samples collected from 147 wastewater treatment plants across 40 U.S. states between July 2023 and July 2025 to quantify EV-D68 RNA in wastewater solids and estimate the seasonal peak and season duration. We evaluated climatic and sociodemographic drivers of variation and compared wastewater trends with symptom-based clinical diagnoses for AFM, wheezing, and enterovirus retrieved from Epic Cosmos, a nationwide electronic health record-based research network, representing 4.5 billion encounters during the same study period.We observed a biennial EV-D68 pattern with a national peak in September 2024 and an extended 20-month period of detection in California. Seasonal peaks occurred 28-31 days earlier in regions with 5 °C higher temperatures or dew points. Season duration was longer by 7-11 weeks in dense, urban catchments with more childcare facilities, crowded households, hospitals, and nursing homes. Wastewater concentrations correlated positively with enterovirus diagnoses (Spearman ρ = 0.34, p = 0.01) and negatively with wheezing in adults ≥65 years (ρ = -0.49, p < 0.0001).Wastewater surveillance can generate epidemiological metrics for EV-D68 without clinical surveillance data, identify where and when activity increases, and reveal the environmental and demographic factors driving these patterns. Wastewater surveillance offers high-resolution data for pathogens with diagnostic testing constraints and provides information that can strengthen epidemiological modeling and support preparedness for future disease waves.Sergey Brin Family Foundation.

  View details for DOI 10.1016/j.lana.2026.101446

  View details for PubMedID 41853773

  View details for PubMedCentralID PMC12993338

• From clinics to sewers: leveraging environmental surveillance and whole genome sequencing to inform transmission of ESBL-Escherichia coli in Switzerland. Applied and environmental microbiology Conforti, S., du Plessis, L., Bagutti, C., Becker, J., Brugger, S. D., Cusini, A., Egli, A., Gaia, V., Greub, G., Guler, C., Huisman, J. S., Kocher, C., Kouyos, R. D., Leuzinger, K., Maffioli, C., Neacșu, M., Nolte, O., Ramette, A., Seiffert, S. N., Tschudin-Sutter, S., Zumthor, J. P., Stadler, T., Julian, T. R. 2026: e0184825

  Abstract

  Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-E. coli) is a major antimicrobial resistance concern spreading across human, animal, and environmental domains. To assess between-source transitions, we analyzed 762 ESBL-E. coli genomes collected from wastewater (used as a community shedding indicator), clinical settings, cattle, and wildlife across Switzerland (2021-2023). ST131 was the most prevalent sequence type (ST), and 76% of isolates carried resistance to at least two antibiotic classes in addition to β-lactams. Phylogenetic analysis showed isolates were interspersed across sources, yet genetically similar strains were more common within compartments. Clonal isolates (0 SNPs) were rarely shared (n = 2) between wastewater and corresponding clinics. Ancestral state reconstruction revealed compartmentalization of isolates between wastewater and clinics across the whole phylogeny. However, this pattern disappears within human-associated ST131, ST69, and ST1193, highlighting exchange between clinics and communities. These findings show that wastewater surveillance captures community circulation of ESBL-E. coli, which overlaps with circulating clinically relevant strains.Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-E. coli) is a major antimicrobial resistance concern globally, with ready transmission between people, animals, and the environment. Understanding transmission patterns among reservoirs can help inform risks and inform intervention strategies. To date, surveillance is heavily reliant on aggregation of clinical data, resulting in limited insights on ESBL-E. coli circulation in the population. Wastewater-based surveillance has emerged as a powerful tool to understand epidemiology of antimicrobial resistance circulating in communities, thereby complementing clinical surveillance approaches. Here, we demonstrate integrated surveillance of ESBL-E. coli isolates across sectors using whole genome sequencing, providing an opportunity to understand exchange of bacterial isolates between clinics, communities, livestock, and wildlife.

  View details for DOI 10.1128/aem.01848-25

  View details for PubMedID 41940667

• Strengthening Policy Relevance of Wastewater-Based Surveillance for Antimicrobial Resistance. Environmental science & technology Conforti, S., Pruden, A., Acosta, N., Anderson, C., Buergmann, H., Calabria De Araujo, J., Cristobal, J. R., Drigo, B., Ellison, C., Francis, Z., Frigon, D., Gaenzle, M., Vierheilig, J., Julian, T. R., Klümper, U., Ma, L., Mangat, C., Nadimpalli, M., Nakashita, M., Osena, G., Rathinavelu, S., Reid-Smith, R., Saldana, M., Schmitt, H., Li, S., Singer, A. C., Tran, T. T., Yanac, K., Ybazeta, G., Harnisz, M. 2025; 59 (5): 2339-2343

  View details for DOI 10.1021/acs.est.4c09663

  View details for PubMedID 39874274

  View details for PubMedCentralID PMC11823445

• Monitoring ESBL-Escherichia coli in Swiss wastewater between November 2021 and November 2022: insights into population carriage. mSphere Conforti, S., Holschneider, A., Sylvestre, É., Julian, T. R. 2024; 9 (5): e0076023

  Abstract

  Antimicrobial resistance (AMR) poses a global health threat, causing millions of deaths annually, with expectations of increased impact in the future. Wastewater surveillance offers a cost-effective, non-invasive tool to understand AMR carriage trends within a population. We monitored extended-spectrum β-lactamase producing Escherichia coli (ESBL-E. coli) weekly in influent wastewater from six wastewater treatment plants (WWTPs) in Switzerland (November 2021 to November 2022) to investigate spatio-temporal variations, explore correlations with environmental variables, develop a predictive model for ESBL-E. coli carriage in the community, and detect the most prevalent ESBL-genes. We cultured total and ESBL-E. coli in 300 wastewater samples to quantify daily loads and percentage of ESBL-E. coli. Additionally, we screened 234 ESBL-E. coli isolates using molecular methods for the presence of 18 ESBL-gene families. We found a population-weighted mean percentage of ESBL-E. coli of 1.9% (95% confidence interval: 1.8-2%) across all sites and weeks, which can inform ESBL-E. coli carriage. Concentrations of ESBL-E. coli varied across WWTPs and time, with higher values observed in WWTPs serving larger populations. Recent precipitations (previous 24/96 h) showed no significant association with ESBL-E. coli, while temperature occasionally had a moderate impact (P < 0.05, correlation coefficients approximately 0.40) in some locations. We identified blaCTX-M-1, blaCTX-M-9, and blaTEM as the predominant ESBL-gene families. Our study demonstrates that wastewater-based surveillance of culturable ESBL-E. coli provides insights into AMR trends in Switzerland and may also inform resistance. These findings establish a foundation for long term, nationally established monitoring protocols and provide information that may help inform targeted public health interventions.Antimicrobial resistance (AMR) is a global health threat and is commonly monitored in clinical settings, given its association with the risk of antimicrobial-resistant infections. Nevertheless, tracking AMR within a community proves challenging due to the substantial sample size required for a representative population, along with high associated costs and privacy concerns. By investigating high resolution temporal and geographic trends in extended-spectrum beta-lactamase producing Escherichia coli in wastewater, we provide an alternative approach to monitor AMR dynamics, distinct from the conventional clinical settings focus. Through this approach, we develop a mechanistic model, shedding light on the relationship between wastewater indicators and AMR carriage in the population. This perspective contributes valuable insights into trends of AMR carriage, emphasizing the importance of wastewater surveillance in informing effective public health interventions.

  View details for DOI 10.1128/msphere.00760-23

  View details for PubMedID 38606968

  View details for PubMedCentralID PMC11328990

• High-Throughput Multiplex Detection of Antibiotic-Resistant Genes and Virulence Factors in Escherichia coli Using Digital Multiplex Ligation Assay. The Journal of molecular diagnostics : JMD Conforti, S., Rossi Orts, P., Tamminen, M., Julian, T. R. 2025; 27 (6): 511-524

  Abstract

  Escherichia coli causes >400,000 annual deaths in children aged <5 years worldwide, with morbidity and mortality exacerbated by antimicrobial-resistant strains. A high-throughput multiplexing assay called digital multiplex ligation assay (dMLA) was developed to detect simultaneously 43 priority genes in E. coli related to the following: antibiotic resistance (n = 19), virulence factors (n = 16), and phylogroup markers (n = 6) with controls (uidA, gapdh). Genes are detected via PCR amplification of adjacent probe pairs that ligate in the presence of target gene-specific DNA, followed by sequencing of amplicons on short-read sequencers. The assay was tested in technical replicates on 63 synthetic DNA controls, and applied to 58 E. coli, 2 Staphylococcus aureus, 2 Klebsiella pneumoniae, 1 Klebsiella oxytoca, 1 Vibrio cholera, 1 Pseudomonas lurida, and 1 Salmonella enterica isolates in duplicate. Whole-genome sequencing was used to assess specificity and sensitivity. dMLA showed 100% sensitivity and >99.9% specificity and balanced accuracy on synthetic DNA. Balanced accuracy, calculated as the average of sensitivity and specificity, accounts for imbalanced data sets where negative outcomes are significantly more prevalent than positive ones. dMLA achieved a balanced accuracy of 90% for bacterial isolates. The results underline dMLA's effectiveness in high-throughput characterization of E. coli libraries for antimicrobial resistance genes and virulence factors, leveraging sequencing for massively parallel multiplexing of gene regions on multiple samples simultaneously, and are extendable to targets beyond E. coli.

  View details for DOI 10.1016/j.jmoldx.2025.03.003

  View details for PubMedID 40239804

• Monitoring an Emergent Pathogen at Low Incidence in Wastewater Using qPCR: Mpox in Switzerland. Food and environmental virology Julian, T. R., Devaux, A. J., Brülisauer, L., Conforti, S., Rusch, J. C., Gan, C., Bagutti, C., Stadler, T., Kohn, T., Ort, C. 2024; 16 (3): 269-279

  Abstract

  Wastewater-based epidemiology offers a complementary approach to clinical case-based surveillance of emergent diseases and can help identify regions with infected people to prioritize clinical surveillance strategies. However, tracking emergent diseases in wastewater requires reliance on novel testing assays with uncertain sensitivity and specificity. Limited pathogen shedding may cause detection to be below the limit of quantification or bordering the limit of detection. Here, we investigated how the definition of limit of detection for quantitative polymerase chain reaction (qPCR) impacts epidemiological insights during an mpox outbreak in Switzerland. 365 wastewater samples from three wastewater treatment plants in Switzerland from 9 March through 31 October 2022 were analyzed for mpox DNA using qPCR. We detected mpox DNA in 22% (79 of 365) wastewater samples based on a liberal definition of qPCR detection as any exponentially increasing fluorescence above the threshold. Based on a more restrictive definition as the lowest concentration at which there is 95% likelihood of detection, detection was 1% (5 of 365). The liberal definition shows high specificity (90%) and accuracy (78%), but moderate sensitivity (64%) when benchmarked against available clinical case reporting, which contrasts with higher specificity (98%) but lower sensitivity (10%) and accuracy (56%) of the 95% likelihood definition. Wastewater-based epidemiology applied to an emergent pathogen will require optimizing public health trade-offs between reporting data with high degrees of uncertainty and delaying communication and associated action. Information sharing with relevant public health stakeholders could couple early results with clear descriptions of uncertainty.Impact Statement: When a novel pathogen threatens to enter a community, wastewater-based epidemiology offers an opportunity to track its emergence and spread. However, rapid deployment of methods for to detect a novel pathogen may rely on assays with uncertain sensitivity and specificity. Benchmarking the detection of mpox DNA in Swiss wastewaters with reported clinical cases in 2022, we demonstrate how definitions of detection of a qPCR assay influence epidemiological insights from wastewater. The results highlight the need for information sharing between public health stakeholders that couple early insights from wastewater with descriptions of methodological uncertainty to optimize public health actions.

  View details for DOI 10.1007/s12560-024-09603-5

  View details for PubMedID 38780822

  View details for PubMedCentralID PMC11422434

• Potential crypticity within two decapod (Crustacea) genera: <i>Galathea</i> Fabricius, 1793 and <i>Eualus</i> Thallwitz, 1891 suggested by integrative taxonomic approach MEDITERRANEAN MARINE SCIENCE conforti, S., Costantini, F. 2022; 23 (3): 499-+

  View details for DOI 10.12681/mms.27733

  View details for Web of Science ID 000814243200004

• Comparative effects of the parasiticide ivermectin on survival and reproduction of adult sepsid flies. Ecotoxicology and environmental safety Conforti, S., Dietrich, J., Kuhn, T., Koppenhagen, N. v., Baur, J., Rohner, P. T., Blanckenhorn, W. U., Schäfer, M. A. 2018; 163: 215-222

  Abstract

  Ivermectin is a veterinary pharmaceutical widely applied against parasites of livestock. Being effective against pests, it is also known to have lethal and sublethal effects on non-target organisms. While considerable research demonstrates the impact of ivermectin residues in livestock dung on the development and survival of dung feeding insect larvae, surprisingly little is known about its fitness effects on adults. We tested the impact of ivermectin on the survival of adult sepsid dung fly species (Diptera: Sepsidae) in the laboratory, using an ecologically relevant and realistic range of 69-1978 µg ivermectin/kg wet dung, and compared the sensitivities of larvae and adults in a phylogenetic framework. For one representative, relatively insensitive species, Sepsis punctum, we further investigated effects of ivermectin on female fecundity and male fertility. Moreover, we tested whether females can differentiate between ivermectin-spiked and non-contaminated dung in the wild. Adult sepsid flies exposed to ivermectin suffered increased mortality, whereby closely related species varied strongly in their sensitivity. Adult susceptibility to the drug correlated with larval susceptibility, showing a phylogenetic signal and demonstrating systemic variation in ivermectin sensitivity. Exposure of S. punctum females to even low concentrations of ivermectin lowered the number of eggs laid, while treatment of males reduced egg-to-adult offspring survival, presumably via impairment of sperm quality or quantity. The fitness impact was amplified when both parents were exposed. Lastly, sepsid flies did not discriminate against ivermectin-spiked dung in the field. Treatment of livestock with avermectins may thus have even more far-reaching sublethal ecological consequences than currently assumed via effects on adult dung-feeding insects.

  View details for DOI 10.1016/j.ecoenv.2018.07.029

  View details for PubMedID 30055386