PLOS Water
● Public Library of Science (PLoS)
Preprints posted in the last 90 days, ranked by how well they match PLOS Water's content profile, based on 11 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit.
DeJonge, P. M.; Pray, I.; Poretsky, R.; Shafer, M.; McLellan, S. L.; Kittner, A.; Korban, C.; Sanchez Gonzalez, D.; Horton, A.; Lamin Jarju, M.; Lin, C.-Y.; Newcomer, E. P.; Barbian, H. J.; Green, S.; Burbano Abril, B.; Kloczko, N.; Rasmussen, M.; Antkiewicz, D.; Roguet, A.; Everett, D.; Schussman, M. K.; McSorley, V.; Ruestow, P.
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IntroductionWastewater-based epidemiology (WBE) was implemented at the 2024 Republican and Democratic National Conventions (RNC and DNC, respectively)--two prominent large-scale events, each with estimated attendances of >50,000 persons. In preparation for event monitoring, the Wisconsin and Chicago WBE programs (associated with the RNC and DNC public health response, respectively) developed site-specific monitoring strategies and response plans, prioritized additional pathogens for event surveillance, and further optimized laboratory workflows to ensure rapid daily data reporting to public health. The Chicago program expanded the sewer sampling network to include new locations closer to event venues than previously available. Sampling was also conducted before the events, to establish baselines for endemic pathogens, as well as after each event to monitor for residual community transmission. MethodsSurveillance was expanded from the four respiratory pathogens regularly assessed by both WBE programs (SARS-CoV-2, influenza A, influenza B, respiratory syncytial virus) to include 3 gastrointestinal pathogens (norovirus, Salmonella enterica, Shiga toxin-producing E. coli). The Wisconsin program also conducted monitoring for the measles, mumps, rubella, and hepatitis A viruses. Wastewater sampling for the RNC was conducted at the community water reclamation facility level, while at the DNC samples were collected from manholes located downstream of the event venues. For both events, WBE data were summarized and contextualized alongside traditional public health surveillance data in daily situation reports. ResultsBetween the RNC and DNC response, a total of 112 wastewater samples were collected and assayed to provide concentration data on as many as 11 distinct pathogens of interest. Concentration results for the suite of pathogens were available within 12 to 36 hours of sample collection. In each instance when wastewater concentrations exceeded pre-established thresholds for action and flagged as an alert, other sources of contemporaneous public health surveillance information (e.g., clinical data) did not corroborate the WBE findings. ConclusionExisting WBE infrastructure in two U.S. cities was readily adapted for public health surveillance at two high-profile, large-scale events. Assays for additional event-relevant pathogens were quickly incorporated into routine laboratory workflows and data from wastewater samples were generated and reported with rapid turnaround-time. In considering the unique benefits of wastewater data, WBE results were a valuable supplement to other public health surveillance data in monitoring potential public health threats during these two large-scale events.
Teshome, W. F.; Edao, B. Y.
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BACKGROUND: Integrated WASH interventions are essential for improving public health by increasing access to safe water, sanitation, and hygiene services. This study evaluates their impact on water access and household knowledge, attitudes, and practices (KAP) in rural communities by comparing intervention and non-intervention areas. METHODS: A cross-sectional survey was conducted in May 2025 across six kebele administrations (three intervention and three control). Data were collected from 396 households with children under five using structured questionnaires, with equal representation from both groups. Descriptive analysis was applied to compare outcomes. RESULTS: Children in intervention areas experienced significantly lower diarrhea rates (2.5% vs. 34.9%). Households also showed improved health behaviors, including higher rates of facility births (88.9% vs. 63.6%), breastfeeding (98% vs. 89.9%), and vaccination (78.8% vs. 59.1%). Access to safe water improved markedly: all intervention households used protected sources, spent less time collecting water (13.9 vs. 55.8 minutes), and consumed more water daily (20.6 vs. 10.5 liters). Safely managed water services reached 59.6% compared to just 1% in control areas. Sanitation and hygiene practices were also better, with higher latrine access (95% vs. 78.3%), reduced open defecation (23.2% vs. 52%), and increased handwashing with soap (48.5% vs. 12.1%). Knowledge, attitudes, and practices were significantly stronger in intervention communities. CONCLUSION: Integrated WASH interventions significantly improve water access, hygiene practices, and child health outcomes. Sustaining these benefits requires continued investment in infrastructure, community awareness, and behavior change programs. KEY WORDS: Water, sanitation and hygiene, KAP, rural Ethiopia
Dalton, J.; Rao, G.; Chiluvane, M.; Cumbane, V.; Holcomb, D.; Kowalsky, E.; Lai, A.; Mataveia, E.; Monteiro, V.; Viegas, E.; Brown, J.; Capone, D.
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Wastewater surveillance has been widely adopted since the COVID-19 pandemic, but non-sewered or onsite sanitation is a common form of sanitation in cities of low- and middle-income countries. Environmental surveillance in these settings requires expanding analyses beyond wastewater. We collected 81 soil samples adjacent to public waste bins inside the sewered and non-sewered areas of Maputo and a 150-meter-wide buffer zone between the two areas, as well as from subsistence farms near the wastewater treatment plant for comparison. We cultured Escherichia coli (E. coli) using the IDEXX Quanti-Tray/2000 system and determined the prevalence of 29 unique enteric pathogens via RT-qPCR on TaqMan array cards. E. coli concentrations were significantly higher (p<.001) in soils adjacent to public waste bins (mean = 5.05x105 per gram) compared to soils from farms (mean = 8.70x101 per gram). The mean number of unique pathogens was higher in soils from the non-sewered area (mean = 7.9, n=32) and the 150-meter buffer area (mean = 10.5, n=10) compared to the sewered area (mean = 4.6, n=20) and soils from farms (mean=3.8, n=19). Findings demonstrate that the presence of enteric pathogens in soils adjacent to public waste bins were associated with neighborhood sanitation infrastructure and may be a useful matrix for surveillance. In high-burden settings with poor sanitation, direct examination of soils and other environmental matrices are potentially scalable means of environmental pathogen surveillance to consider beyond conventional sampling matrices.
Young, I.; Jardine, R.; Desta, B. D.; Edge, T. A.; Saleem, F.; Pearl, D. L.; Majowicz, S. E.; Brooks, T.; Nesbitt, A.; Sanchez, J. J.; Schellhorn, H. E.; Elton, S.; Schwandt, M.; Lyng, D.; Krupa, B.; Montgomery, E.; Patel, M.; Tustin, J.
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Background: Beaches are popular summertime destinations in Canada. However, they can be affected by specific fecal pollution sources, increasing the risk of recreational water illness. Objectives: This study was conducted to determine the risks of acute gastrointestinal illness (AGI) among Canadian beachgoers and to evaluate the influence of different fecal indicator bacteria (FIB) and other water quality measures on assessing these risks. Methods: In a prospective cohort design, beachgoers were recruited at sites across Canada from 2023 to 2025. Sociodemographic characteristics and exposures were determined through an on-site survey, with a 7-day follow-up survey to determine risks of AGI. Bayesian mixed-effects logistic regression models were fitted to evaluate the effects of an ordinal water contact variable (no contact, minimal contact, body immersion, and swallowed water) on the incident risk of AGI, with an interaction included for water quality indicators. The levels of six FIB and water quality measures were assessed: Escherichia coli, enterococci DNA, three microbial source tracking DNA markers (human HF183/BacR287, human mitochondria, seagull Gull4), and turbidity. Results: A total of 4085 participants were recruited, with 67.6% completing the follow-up survey. The overall incident risk of AGI was 2.6%. Both swallowing water and body immersion increased AGI risks compared to no water contact: median of 20 excess cases (95% Credible Interval [CrI]: 4, 64) and 5 excess cases (95% CrI: 1, 19) of AGI predicted per 1000 beachgoers, respectively. Escherichia coli and seagull DNA marker levels were associated with AGI among those who had water contact, particularly among those who reported swallowing water. Discussion: While the overall burden of AGI due to beach water contact in Canada was low, increased risks are associated with E. coli levels particularly among those who swallow water. This could be related to fecal contamination from seagulls. However, there is substantial uncertainty in the predicted effect sizes.
Budden, E.; Niven, C. G.; Clark, B.; Floess, E.; Chirwa, B.; Matekenya, M.; Cadono, S.; Chavula, J.; Chisamanga, V.; Dzinkambani, A.; Kaponda, C.; Ngondo, N.; Patterson, N.; Symon, S.; Chunga, B. A.; Holm, R. H.; Chigwechokha, P.; de los Reyes, F. L.; Workman, C. L.; Harris, A. R.; Ercumen, A.
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Soil is an important reservoir for antimicrobial resistance (AMR) and increasingly recognized as a pathogen transmission pathway. While studies have detected AMR in soil in various settings, dominant contributors to domestic soil contamination with antimicrobial-resistant organisms in low-income countries remain unidentified. We conducted a cross-sectional study with 237 households in southern Malawi, specifically peri-urban Bangwe near Blantyre, to identify factors associated with the abundance of cefotaxime-resistant E. coli in yard soil. Enumerators employed structured surveys and sampled 30 cm2 of yard soil per household. We used IDEXX Quanti-Tray/2000 with Colilert-18 and cefotaxime supplement to enumerate the most probable number (MPN) of cefotaxime-resistant E. coli per dry gram of soil. We conducted multivariable regression to assess associations between the abundance of cefotaxime-resistant E. coli and household sanitation, animal ownership and management, child health and antibiotic use, and weather. Of 228 soil samples, 68% harbored cefotaxime-resistant E. coli at a mean of 0.90 log10-MPN/dry gram. Compared to households without animals, households had approximately 0.50-log lower mean cefotaxime-resistant E. coli abundance in soil if animals were enclosed at night and 0.50-log higher abundance if they were not (p-values<0.005). Additionally, samples had approximately 0.70-log lower mean cefotaxime-resistant E. coli abundance if soil was dry at the time of collection and if it came from a household in the top wealth quintile (p-values<0.005). Daytime animal confinement, household sanitation, child health, antibiotic use, rainfall, temperature and ambient humidity were not associated with cefotaxime-resistant E. coli abundance. Findings suggest that animal husbandry and soil moisture had stronger associations with cefotaxime-resistant E. coli in soil compared to sanitation or antibiotic use. These results underscore the importance of a One Health approach and the relevance of domestic animals and environmental factors to AMR in soil. Studies should quantify soilborne AMR exposure and evaluate associations with specific animal management/enclosure practices.
Clerkin, T.; Smith, S.; Zhu, K.; Blackwood, D.; Gallard-Gongora, J.; Capone, D.; Brown, J.; Noble, R. T.
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Digital PCR (dPCR) is increasingly used for SARS-CoV-2 wastewater surveillance due to its precision, absolute quantification, and reduced sensitivity to inhibition compared to quantitative PCR. Although the Bio-Rad ddPCR and QIAGEN QIAcuity dPCR platforms are widely adopted, their performance has not been directly compared for wastewater applications. We conducted a blinded comparison of these platforms using 95 archived wastewater influent samples from North Carolina collected in 2021-2022, spanning three orders of magnitude in SARS-CoV-2 concentration (1x103 to 5x105 copies L-1). Samples were stratified into low, medium, and high concentration bins and analyzed in triplicate for N1 and N2 gene targets and a bovine coronavirus processing control. Both platforms demonstrated statistically equivalent quantification across all targets, with mean differences [≤]0.12 log copies L-1 (R2 > 0.93). Coefficients of variation were similar (3.96 - 7.61%), with no significant differences across concentration bins except for N2 in the low bin (difference: 0.87 percentage points). Measurement variability correlated strongly with wastewater treatment plant site (R2 = 0.89) rather than platform, indicating that sample matrix characteristics drive precision more than analytical platform. Process limits of detection ranged from 2,160-2,680 copies L-1 for Bio-Rad and 5,650-9,700 copies L-1 for QIAcuity for N1 and N2, respectively. The Bio-Rad platform processed samples 32% faster (305 vs. 435 minutes per 96 wells), while QIAcuity offered 29% lower consumables cost ($4.68 vs. $6.11 per well). These findings support the interchangeable use of both platforms for wastewater surveillance, with platform selection based on laboratory-specific operational needs. ImportanceAs wastewater-based epidemiology transitions from emergency response to sustained public health infrastructure, standardized molecular methods are essential for reliable data integration across surveillance networks. This study provides the first blinded comparison of two digital PCR platforms widely deployed for wastewater pathogen surveillance in the United States. We demonstrate quantitative equivalence between Bio-Rad ddPCR and QIAGEN QIAcuity platforms across three orders of magnitude in viral concentration, establishing that data from both platforms can be interpreted interchangeably for public health decision-making. This platform equivalence is critical as national surveillance systems aggregate data from diverse laboratories and as monitoring expands beyond SARS-CoV-2 to encompass additional respiratory viruses, antimicrobial resistance genes, and emerging pathogens. Our findings provide a methodological foundation for multi-platform surveillance networks and demonstrate that measurement variability is driven primarily by sample matrix characteristics rather than analytical platform choice.
Mulungu, C.; Zimba, N.; Nambeye, L.; Samu, D.; Muyembe, G.; Kaluah, C.; Musonda, C.; Maseka, A. K. Y.
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Research background. Foodborne diseases (FBDs) remain a pressing global public health issue, with courier-based food delivery systems increasingly recognized as potential contamination pathways. In Zambia, despite the Food Safety Act No. 7 of 2019, limited evidence exists on microbial risks in courier-mediated food transport. This study was conducted to assess pathogenic contamination in food carriers used by courier bikers in Lusaka during the 2025/2026 cholera outbreak response. Experimental approach. An analytical cross sectional design was employed. Ninety three food carriers (bags, cooler boxes, and metal containers) were randomly sampled from courier bikers. Swabs from internal surfaces were processed within 24 hours using standard microbiological culture and biochemical identification methods. Statistical analyses (Chi square tests, Pearson correlations, and logistic regression) were applied to determine associations between contamination and operational factors. Results and conclusions. Microbial contamination was detected in 69% of carriers. The most common pathogens were Escherichia coli (30%), coagulase negative Staphylococcus (24%), and Staphylococcus aureus (18%), with additional isolates including Gram-positive bacilli (11%) and Klebsiella pneumoniae (8%). Logistic regression identified cleaning frequency as the strongest predictor of contamination, with infrequent cleaning associated with significantly higher odds ratios (26.5 to 94.7, p < .05). Carrier type also influenced contamination risk, while years in service and certification status were not significant. The findings highlight that inadequate cleaning practices and carrier design are primary drivers of microbiological risks in courier based food delivery systems. Novelty and scientific contribution. This study provides the first empirical evidence of microbial contamination in courier food carriers in Lusaka, Zambia. It underscores the urgent need for strengthened hygiene protocols and routine sanitation enforcement to protect consumers from foodborne pathogens and antimicrobial resistance. The work contributes novel insights into food safety risks in emerging delivery systems, with implications for policy, public health interventions, and consumer protection in Zambia and beyond.
Vaz, A. B. M.; Murad, B.; Lopes, B. C.; Castro, M. L. P.; Fernandes, G. R.; Oliveira, W. K.; Fonseca, P. L. C.; Aguiar, E. R. G. R.; Mota Filho, C. R.; Santos, A. B.; Starling, C. E. F.
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Antimicrobial resistance (AMR) in ESKAPE pathogens represents a major global health threat. Although these organisms are well established as causes of healthcare-associated infections, aquatic environments may function as reservoirs and transmission pathways for resistance. This systematic review aimed to estimate the prevalence of AMR in ESKAPE pathogens isolated from water and wastewater and to compare resistance patterns with those observed in human clinical isolates. The review followed PRISMA guidelines and was registered in PROSPERO (CRD420251020930). PubMed, Embase, and the Cochrane Library were searched to January 14, 2025. Eligible studies were original research reporting antimicrobial susceptibility data for ESKAPE pathogens isolated from both aquatic environmental matrices and clinical samples. Pooled resistance prevalence was estimated using generalized linear mixed models, with heterogeneity assessed using {tau}{superscript 2} and I{superscript 2} statistics and small-study effects evaluated by funnel plots and Eggers test. Of 304 records identified, 18 studies met the inclusion criteria. The pooled overall resistance prevalence was 0.46 (95% CI: 0.36-0.57), with heterogeneity (I{superscript 2} = 98.8%). Resistance was higher in clinical isolates (0.67; 95% CI: 0.55-0.77) than in environmental isolates (0.24; 95% CI: 0.14-0.39), and environmental resistance was greater in effluent-impacted waters than in non-effluent sources. Interpretation is limited by methodological heterogeneity, selective isolation approaches in environmental studies, and imprecision due to small and unevenly distributed samples. Overall, AMR in ESKAPE pathogens remains more prevalent in clinical settings, but aquatic environments, particularly wastewater, represent resistance reservoirs, underscoring the need for standardized methodologies within a One Health framework. Systematic review registrationhttps://www.crd.york.ac.uk/PROSPERO/view/CRD420251020930, CRD420251020930 HighlightsAntimicrobial resistance was higher in clinical isolates than in aquatic isolates. Resistance patterns showed extreme heterogeneity across studies. Effluent-impacted waters showed higher resistance than non-effluent sources. Higher environmental resistance in some classes reflected methodological artifacts.
Palma, F. A. G.; Cuenca, P. R.; de Oliveira, D. S.; Silva, A. M. N.; Lopez, Y. A. A.; Santiago, D. C. d. C.; das Virgens, M. N. R.; do Carmo, A. S.; dos Reis, A.; do Carmo, G. d. J.; Lima, A. M.; Almeida, R. S.; Oliva, L.; Santana, J. O.; Maciel, P.; Bourouphael, T.; Giorgi, E.; Lustosa, R.; Eyre, M. T.; Zeppelini, C. G.; Cremonese, C.; Costa, F.
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Despite the relevance of spatial mapping in analyzing the health situation and understanding the risk factors and determinants of leptospirosis, peripheral urban communities often remain invisible on maps, which tend to use data and methods that do not express community contribution nor promote local participation. Furthermore, in the implementation of sanitation interventions, the same happens: there is limited user participation, and a lack of identification of intervention needs based on the perception of community residents, failing the interventions. We conducted a cross-sectional study through collaborative mapping from February to October 2022 with 213 residents and self-declared heads-of-household in two peripheral urban communities. We analyzed the perception of sanitation needs indicated by residents and their relationship with the risk of leptospirosis in these communities. Based on community perception, sewage (NS: 87.1%; JSI/ME: 84.9%) and urban cleaning and solid waste management (NS: 25.9%; JSI/ME: 32.6%) were the sanitation needs. In NS, most participants indicated that the necessary interventions for sewage improvement were actions of sewer cleaning and sealing (26.5%), sewer cleaning and piping (23.5%), and implementation/installation/construction of a sanitary sewage network (41.4%). In JSI/ME, interventions included sewage sealing (48.7%) and piping (25.6%), in addition to actions to maintain sewage cleaning (93.3%). The removal of solid waste (trash) in the square (NS: 22.2%) and on the streets (JSI/ME: 69.2%), as well as community awareness (JSI/ME: 15.4%), were indicated as interventions to meet the needs of urban cleaning and solid waste management. Respondents agreed on where interventions should occur, which congregated around the local river. We found a negative correlation between the predicted leptospirosis seropositivity and perceived intervention needs in both study areas. The prevention of diseases such as leptospirosis in peripheral urban communities requires integrated basic sanitation interventions, encompassing different components and aligned with the local needs perceived by residents.
SERONEY, G. C.; Magak, N. A. G.; Mchunu, G. G.
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Introduction Access to safe water, sanitation, and hygiene (WASH) in schools is critical for child health, learning, and gender equity. In Kenya, the Kenya School Health Policy and the Basic Education Act outline standards for school WASH; however, implementation remains uneven due to inadequate infrastructure, weak inter-sectoral coordination, and limited financing. This study aimed to identify priority components for strengthening school WASH implementation and generate policy-relevant recommendations based on expert consensus in Uasin Gishu County, Kenya. Methods and Results A Delphi technique consisting of two iterative rounds was used to reach expert consensus. In Round 1, 20 purposively selected experts including head teachers, county education officials, public health officers, water and public works officers, and NGO representatives participated in key informant interviews. Emergent themes informed development of a structured Round 2 questionnaire administered through CommCare online app. Quantitative data were analyzed using descriptive statistics (means, standard deviations, percentage agreement), while qualitative responses underwent thematic coding using NVivo 12. Experts reached strong consensus on essential components required for strengthening school WASH implementation. Key priorities included clear governance structures, designated budget lines, inclusive infrastructure, menstrual hygiene management (MHM), curriculum integration, sustained capacity building, and systematic monitoring. Multi-sectoral collaboration and recognition of best-performing schools were also emphasized as important motivators for compliance and sustainability. Equity considerations particularly the need for disability-friendly facilities and school-community outreach were highlighted as critical. Agreement levels ranged from 74% to 100%, with most items scoring mean values between 4.5 and 4.8 on a 5-point Likert scale, indicating strong consensus among experts. Conclusion strengthening implementation of school WASH in Kenya requires coordinated governance, predictable funding, reliable water systems, inclusive sanitation, strengthened MHM, and consistent monitoring beyond infrastructure investment alone. Integrating these expert-validated priorities within existing national policies offers a practical pathway to improving learner health, reducing absenteeism especially among girls and promoting equitable educational outcomes.
Hoidal, N.; Bugeja, S.; Grossman, J.; Fernandez, A.; Cates, A. M.; LaBine, K. M.; Khokhani, D.; Pagliari, P.
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Small-scale vegetable farms are increasingly important to local food systems, but the soils on these farms are not well understood, particularly in high tunnel production environments. Therefore, this study aimed to 1. Compare soil nutrients and soil health metrics in high tunnels and nearby open fields. 2. Document soil nutrient accumulation on diversified vegetable farms and assess loss potential. 3. Explore the impacts of specific management practices (input use, cover crops, tillage, and soil testing) and farm demographics on a variety of soil health and soil nutrient metrics. Just under half of the high tunnels in this study had soluble salt accumulation, which was associated with higher soil nitrate concentrations. The pH of many high tunnel soils was above the optimal range for crop production, which was correlated with irrigation water alkalinity. Some high tunnel soils had rapid water infiltration rates, with implications for irrigation water management. Both high tunnel and open field soil were rich in nutrients compared with other Minnesota farms. Preliminary assessments suggested risks to surface and groundwater from nutrient runoff and leaching. While farmer experience and more years in vegetable production were negatively associated with soil health metrics, management practices including reduced tillage, organic management, and application of plant-based compost were positively associated with soil health. Cation exchange capacity and permanganate oxidizable carbon did not provide significantly more insight than simply measuring organic matter. Arbuscular mycorrhizal fungal spore counts were inconclusive, but aggregate stability and bulk density were responsive to farmer reported soil management activities. Core ideasO_LIHigh tunnel soil tends to be rich in nutrients and organic matter. They also accumulate soluble salts, likely from excess inputs C_LIO_LIIrrigation water routinely tested high in pH and alkalinity. These factors may explain high soil pH in high tunnels. C_LIO_LISmall-scale vegetable farms often have high concentrations of soil nutrients in both high tunnels and open fields, with potential to cause environmental contamination through leaching and runoff C_LIO_LIVegetable production may be inherently hard on soil health, but conservation practices including reduced tillage, organic management, and use of plant-based composts can improve soil health in these production systems C_LI
Paulos, A. P.; Zulli, A.; Duong, D.; Shelden, B.; White, B. J.; North, D.; Boehm, A. B.; Wolfe, M. K.
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Respiratory infections caused by bacterial pathogens like Mycobacterium tuberculosis and Bordetella pertussis have increased since the COVID 19 pandemic, yet clinical surveillance of both suffers from underreporting and delayed diagnoses. Wastewater monitoring is a valuable public health surveillance tool that can help fill gaps in clinical data yet has rarely been applied to respiratory bacterial pathogens despite evidence of bacterial shedding via excretion types that enter wastewater. In this study, we investigated the possibility for wastewater monitoring of two bacterial respiratory diseases, tuberculosis and pertussis, using two case studies of wastewater monitoring for M. tuberculosis and B. pertussis. We retrospectively measured concentrations of these pathogens in wastewater samples collected longitudinally from communities with and without known outbreaks of these diseases. We designed and validated a novel B. pertussis specific assay for the NAD(P) gene; B. pertussis nucleic acids were detected sporadically in wastewater during an identified outbreak. We used a highly specific, established assay for M. tuberculosis nucleic acids, and found low concentrations of the marker in wastewater that were lag-correlated with clinical incidence rates 5 weeks later. Findings support the potential of wastewater monitoring for M. tuberculosis and B. pertussis to enable identification of communities with outbreaks of tuberculosis and pertussis and provide early warning for tuberculosis.
Kingwara, L.; Madada, R. S.; Morangi, V.; Akasa, S.; Kiprutto, V.; Julie, O.; Muthoka, R.; Rombo, C.; Kimonye, K.; Okunga, E.; Masika, M.; Ochieng, E.; Nyaga, R.; Otieno, O.; Cham, F.; Hull, N.; Kimenye, K.
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Background SARS-CoV-2 genomic surveillance data remain limited in most low and middle-income countries (LMICs), resulting in significant gaps in the understanding of variant circulation and evolution. Wastewater-based epidemiology (WBE) presents a non-invasive, cost-effective, and population-representative surveillance approach that can complement clinical testing, particularly in densely populated urban informal settlements with limited healthcare access. This study aimed to pilot wastewater-based genomic surveillance as a multifaceted public health tool in Kenya. Methods A prospective study was conducted using wastewater samples collected from two WHO-validated environmental surveillance sites -- Eastleigh A (Kamukunji sub-county) and Mathare (Starehe sub-county) -- in Nairobi, Kenya, between December 2022 and October 2023. A total of 272 samples were collected using Moore swabs at a frequency of two to three times per week. Samples were concentrated using Nanotrap(R) Magnetic Virus Particles, and nucleic acid was extracted using the Qiagen QIAamp Viral RNA Mini Kit. SARS-CoV-2 was detected using RT-PCR (TaqPath COVID-19 CE-IVD RT-PCR Kit). Library preparation for whole-genome sequencing was performed using the Illumina COVIDSeq kit, and sequencing was conducted on the Illumina MiSeq platform. Bioinformatic analysis was performed using Terra.bio and RStudio, and phylogenetic analysis included sequences abstracted from GISAID. Results Of 272 samples, 238 (87.5%) tested positive with a cycle threshold (Ct) value of less than 36. Genomic analysis of 181 sequences identified Omicron as the predominant circulating variant, detected in 59% of samples. Other variants included XBB (16%), XBB.2.3(10%), XBB.1.9.X (5%), and additional minor variants. These findings were concordant with clinical sequencing data from Kenya over the same period. Conclusions Wastewater-based genomic surveillance reliably reflected SARS-CoV-2 variant trends observed in clinical data. This approach provides early signals of variant emergence and evolution, offering a cost-effective complement to clinical surveillance in resource-limited settings.
Akello, J. O.; Bellekom, B.; Shaw, A. G.; Grassly, N. C.
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Methods to concentrate wastewater samples are essential for sensitive environmental surveillance of infectious diseases. We defined six main principles used to concentrate viral pathogens in wastewater and performed a systematic review and meta-analysis of their performance. PubMed and Web of Science were searched on 31 January 2025 using terms wastewater, sewage, concentration methods and wastewater surveillance. We included all studies comparing [≥]2 concentration methods for virus detection. Our search identified 49 eligible studies published since 2013 across seven continents. We ranked the performance of evaluated methods in each study and generated an overall performance metric for each method principle by virus group (enveloped vs. non-enveloped) using Plackett-Luce analysis. Precipitation and filtration methods were the most studied, while magnetic bead-based and centrifugation were least studied. Magnetic bead-based methods were more effective for concentrating enveloped viruses (63% of pairwise comparisons), whereas flocculation performed better for non-enveloped viruses (60%). However, no single method strongly dominated and method rankings were variable between studies. This study provides evidence-based guidance for selecting wastewater concentration methods to support environmental surveillance of viral pathogens.
McCarthy, W. C.; Crain, C. J.; Olubodun, T.; George, I. A.; Birk, S. L.; Ekpo, U. F.; Mogaji, H.; Leng, H. T.; Kathiresan, R.; Salas, C.; Sekou, M. H.; Soneye, I.; Adeniyi, M. A.; Beaubrun, J.; Nwosu, K. O. S.; Oludolamu, A.; Kafil-Emiola, M.; Okesola, B. B.; Koether, P. J.; Simbassa, S. B.; Shah, N.; Ngai, M. K.; Oluwanifemi, O. B.; Efosa, I.; Hassan, A. E.; Fagbohun, V.; Oladokun, B. D.; Cannon, C.; Oncho, F.; Rehman, M.; Adeola, A.; Stella, A. J.; Abiodun, A.; Naimot, K.; Adeola, S. T.; Adelakun, O.; Copeland, T.; Amao, D.; Shokeen, V.; Kothari, A.; Tebo, K. K.; Lee, J.; Prakash, M.
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BackgroundUrogenital schistosomiasis is a major cause of preventable morbidity, primarily in rural, resource-limited regions. After decades of mass drug administration, changing epidemiologic landscapes, and ongoing resource limitations, test-and-treat models may be necessary to meet elimination goals. However, diagnostic capacity remains centralized and laboratory-dependent, and community-led, contextually adapted implementation strategies remain poorly defined. This study describes the accuracy and feasibility of a low-cost diagnostic toolkit and explores community-integrated implementation models. Methodology/Principal FindingsThis mixed-methods study enrolled 418 participants from five endemic sites near Oyan River Dam, Ogun State, Nigeria in July 2025. Urine samples underwent parallel analysis by community health extension workers utilizing the toolkit and by laboratory technicians using standard microscopy. The toolkit consisted of a reusable urine filtration device paired with a under-$2 paper microscope. Semi-structured interviews with community health extension workers and key informants were analyzed using the Consolidated Framework for Implementation Research. Prevalence was 27.5% (115/418). Community health extension workers demonstrated progressive improvement in diagnostic accuracy across five sequential communities (n=237), rising from 52.5% (95% CI 37.5-67.1) to 92.1% (79.2-97.3) over eight study days (Cochran-Armitage Z=3.08, p=0.002). Specificity improved from 53.6% to 96.3% (Z=3.00, p=0.003), final sensitivity reached 81.8% (52.3-94.9), and final Cohens kappa reached 0.803. In the hands of laboratory scientists, Foldscope microscopy achieved 91.0% sensitivity and 99.3% specificity. Conclusions/SignificanceCommunity-led diagnostic task-shifting for urogenital schistosomiasis control is accurate, feasible, and implementation-ready. Consolidated Framework for Implementation Research-guided analysis demonstrated strong end-user acceptability, with local ownership, collaboration, and trust-building as key implementation facilitators. This approach addresses diagnostic gaps in resource-limited endemic settings with relevance to other community health worker-led strategies. Author SummarySchistosomiasis is a parasitic infection that spreads through contact with freshwater and often goes undetected and untreated for years. Most common in sub-Saharan Africa, the disease damages the bladder and genitourinary tract, increasing risk of infertility, bladder cancer, and HIV transmission. It is most prevalent in rural communities where the snail intermediate host thrives in local water sources used daily for fishing, farming, and bathing. One such area is the Oyan River in Nigeria. Here, we found that barriers to diagnosis and treatment of the illness include distance and transportation. In this study, community health workers diagnosed their neighbors and community members using a low-cost toolkit: a <$2 / 2700 microscope, called the Foldscope paired with a small steel filter card we designed, called the SchistoFilter.. We enrolled 418 people across five villages along the Oyan River in Nigeria and trained eight community health workers to use this toolkit at the point of care. By the fifth community visite, they reached 92.1% accuracy. The study team interviewed community health workers and government officials to contextualize this approach, and they were enthusiastic: The tools can be used with confidence, the training is feasible, and what is most needed is a reliable supply chain and supportive oversight.
Knee, J.; Sumner, T.; Adriano, Z.; Opondo, C.; Holcomb, D.; Viegas, E.; Nala, R.; Brown, J.; Cumming, O.
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BackgroundThe rapid growth of the worlds urban population has contributed to the expansion of informal urban settlements in many cities across the world. In these settings, lack of safe sanitation combined with high population density and poverty contributes to heightened health risks for often vulnerable populations. The aim of this study was to evaluate the effect of a shared, onsite sanitation intervention on the nutritional status of children in Maputo, Mozambique. MethodsThe Maputo Sanitation (MapSan) trial was a controlled before-and-after study to evaluate the effect of a shared, onsite sanitation intervention on child health in Maputo, Mozambique. Here, we report the effects on childhood stunting, wasting and underweight, and height-for-age, weight-for-height and weight-for-age z-scores. Children were enrolled aged 1-48 months at baseline and outcomes were measured before and 12 and 24 months after the intervention, with concurrent measurement among children in a comparable control arm. The primary analysis was intention-to-treat. The trial was registered at ClinicalTrials.gov, number NCT02362932. ResultsWe enrolled 757 and 852 children in the intervention and control groups respectively. There was no evidence for an effect of the intervention on any outcome at 12 or 24 months of follow-up except for wasting where there was very weak evidence for an effect (adjusted prevalence ratio: 0.497; 95% CI: 0.22-1.11; p=0.09). In two exploratory analyses - one including only those children born into compounds post-intervention and a second excluding children in control compounds which had independently improved their sanitation facilities during follow-up - we found that stunting increased in the intervention group whilst wasting decreased. ConclusionsThis study contributes to the growing evidence on the role of sanitation in shaping child health outcomes in informal urban settlements. We found no evidence for an effect on stunting and weak evidence for an effect on wasting. More research is needed to understand how sanitation can reduce childhood undernutrition in complex urban environments.
Wade, M. J.; Ruskey, I.; Perry, E.; Meehan, V.; Rothstein, A. P.; Gratalo, D.; Rush, S.; Simen, B. B.; UKHSA Laboratory Team, ; Friedman, C. R.
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We present findings from the first known pilot study of transatlantic airplane wastewater monitoring, conducted over six months at two connected international airports in the United States and the United Kingdom. This study demonstrates the feasibility of implementing bilateral wastewater-based pathogen surveillance at international travel hubs. We outline the operational and analytical methodologies employed, highlight key challenges encountered in transnational coordination, and provide recommendations for the design and implementation of future surveillance programs at points of entry.
Schaeffer, B. A.; Ferriby, H.; Salls, W.; Reynolds, N.; Hollister, J. W.; Kreakie, B.; Shivers, S. D.; Johnson, B.; Cronin-Golomb, O.; Myers, K.; Beal, M.
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We developed a model to predict surface water temperature across U.S. lakes using satellite remote sensing and in situ observations to enhance cyanobacterial harmful algal bloom (cyanoHAB) forecasting. The study focused on Sentinel-3 Ocean and Land Colour Instrument (OLCI) sensor resolved lakes. We developed random forest models using both Landsat-derived and in-situ-measured surface water temperature. Landsat models offered broad spatial and temporal coverage of all OLCI resolved lakes, but they were sensitive to cloud cover and required filtering to minimize error. In contrast, the in situ model represented fewer OLCI resolved lakes, but yielded lower mean absolute error and bias. The models predicted lake surface temperature across the entire calendar year, with best performance (RMSEapplied=1.11; biasapplied=0.01; MAEapplied=0.77) from the in situ model. This approach allowed for the continuous prediction of lake surface temperatures from 1.1 to 31.6 {degrees}C for unfrozen, open-water conditions critical for improving the accuracy of cyanoHAB forecasting. A key strength of this study was the use of an extensive dataset and model validation against in situ observations, which improved predictive accuracy throughout the year across all seasons. The predictive model offers a water resource tool for management, ecosystem protection, and public health.
Hernandez-Mendez, J. M. E.; Ovando-Ovando, C. I.; Dominguez-Espinosa, M. E.; Del Mazo-Monsalvo, I.; Reyes-Vallejo, O.; Cruz-Salomon, A.; Santiago-Martinez, M. G.
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Natural freshwater streams harbor diverse microbial communities that support ecosystem functioning. Due to their great biodiversity and geomorphological characteristics, these ecosystems are often very attractive ecotourism destinations, which makes them highly vulnerable to anthropogenic disturbances. The Agua Azul Waterfalls (Cascadas de Agua Azul, in Spanish), a major tourist destination located in indigenous territories of southeastern Mexico (Chiapas, Mexico), offer a unique setting to investigate how sustained human activity influences microbial diversity and quality of water and sediments. To determine the ecological sensitivity of this freshwater stream to tourism pressure, we sampled sites spanning gradients of tourist activity and conducted an integrated analysis of water and sediment physicochemistry, elemental composition, and the composition of microbial communities (bacteria, archaea, and fungi). Areas associated with ecotourism activities showed notable changes in physicochemical parameters and microbial community composition, indicating localized impacts on this ecosystem. Furthermore, evidence of effective management by local Indigenous communities suggests a partial mitigation of anthropogenic disturbances through ecotourism activities. Our findings highlight the potential of microbial diversity in combination with physicochemical parameters as a tool to detect early stages of human impacts on freshwater ecosystems and establish a basis for future monitoring and conservation efforts. The distinctive characteristics of this site position it as a promising model for advancing our understanding of microbial diversity and the dynamics of freshwater stream ecosystems. ImportanceThis study shows evidence that ecotourism is already impacting the biodiversity and water quality of Agua Azul Waterfalls, a freshwater stream located within a protected natural area in southeastern Mexico. While the water still meets basic quality standards, areas with higher tourist activity show early signs of nutrient enrichment and measurable changes in the types of microbes present and the roles they play in this ecosystem. As the first analysis of microbial diversity in this ecosystem, our work highlights the value of microbes as early and sensitive indicators of human impact. By directly comparing tourist and non-tourist areas, we provide evidence of how recreational pressure is transforming this freshwater environment. We expect that our findings will help guide local communities and policymakers in creating more sustainable tourism practices to preserve the cultural and economic value of this ecosystem before irreversible damage occurs.
Nahiduzzaman, F.; Zarin, T.; Jhinuk, N. A.; Hasan, H.; Khatun, M. M.; Islam, M. A.
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This cross-sectional study assessed hygienic practices, microbial contamination, and associated factors among street food vendors in Mymensingh City, Bangladesh, from August 2024 to February 2025. Using purposive sampling, 300 vendors were evaluated through structured questionnaires, observational assessments, and laboratory analysis of food samples (n = 300) for bacterial load (log-transformed Total Viable Count, log_TVC). Results revealed that 87.33% (95% CI: 83.6-91.1) of vendors practiced poor hygiene: 90.7% (95% CI: 87.4-94.0) did not cover food, 7% (95% CI: 4.1-9.9) used disinfectants, and 81.00% (95% CI: 76.6-85.4) reused ingredients beyond one day. Knowledge gaps were stark, with 89.7% (95% CI: 86.3-93.1%) demonstrating insufficient basic hygiene knowledge and 90.7% (95% CI: 87.4-94.0%) lacking understanding of hygienic food processing. Education significantly influenced practices; secondary-educated vendors exhibited markedly better hygiene awareness (65.0% vs. 2.89% in uneducated groups). Bacterial loads varied across food types, with Velpuri showing the highest mean log_TVC (8.00, 95% CI: 7.65-8.35) and fast food the lowest (7.69, 95% CI: 7.34-8.03). Significant correlations emerged between hygiene knowledge and practices: vendors aware of foodborne diseases were more likely to use gloves (Spearman's r = 0.199, p = 0.001) and cover food (r = 0.118, p = 0.041). Challenges included financial constraints (62.25% [95% CI: 56.1-68.4] among uneducated vendors), knowledge gaps, and time limitations. The study underscores systemic issues in street food safety, driven by low education and economic barriers. Interventions targeting vendor education, affordable hygiene solutions, and stricter enforcement of ingredient freshness protocols are urgently needed to mitigate foodborne disease risks in urban Bangladesh.