PLOS Water

Background Bacteriological contamination of drinking water remains a major public health burden in sub-Saharan Africa, yet the full contamination chain from source to household has rarely been quantified at national scale. This study analyses water quality at both levels using the 2021 Cote d'Ivoire Demographic and Health Survey (DHS-CI 2021). Methods Cross-sectional secondary analysis of DHS-CI 2021 data. Households with paired bacteriological tests at the source (SH3227) and at the household (SH3225) were included (n = 2,541 for determinants; n = 2,528 for chain analysis). Contamination was defined as >0 CFU/100 ml. Determinants of source contamination were assessed by weighted logistic regression accounting for complex survey design. The contamination chain was described across four categories: safe throughout, recontaminated during transport/storage, decontaminated at home, and contaminated throughout. Results Weighted prevalence of source contamination was 63.6% [95% CI: 60.7-66.5%] and 77.0% [74.1-79.9%] at the household. Only 15.0% of households had safe water throughout the chain; 21.2% showed domestic recontamination and 60.8% consumed water contaminated at both levels. Key determinants of source contamination were use of an unimproved source (aOR = 8.15; 95% CI: 4.54-14.66), administrative region, travel time [≤]30 minutes (aOR = 1.92; 95% CI: 1.41-2.62), and higher wealth quintiles (protective; aOR = 0.25 for richest). Model discrimination was good (AUC = 0.809). Conclusions The vast majority of Ivorian households consume bacteriologically unsafe water, with domestic recontamination representing a distinct and significant degradation pathway even among users of improved sources. Dual interventions targeting source protection and safe household water storage are urgently needed to advance progress toward SDG 6 in Cote d'Ivoire.

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

Fresh produce encounters pathogens at various stages of production and supply, with the harvesting process serving as one of these stages. To evaluate contamination associated with harvesting, we systematically swabbed zone 1 harvester surfaces and quantified Bacteroidales as a fecal biomarker using quantitative polymerase chain reaction (qPCR). Baseline contamination was dominated by non-detects, with occasional low-level detections (<25 copies/cm2) near the assay limit of detection (LoD). Detection occurred more frequently post-harvest (overall [~]4% pre-harvest and 10% post-harvest), while microbial loads remained low, indicating that harvesting primarily affected the likelihood of low-level contamination rather than increasing contamination abundance. Additionally, we developed and field-deployed a portable loop- mediated isothermal amplification (LAMP) assay for rapid harvester hygiene assessment and benchmarked its field performance against qPCR. Together, these results support a practical molecular tool for monitoring fecal contamination and informing cleaning and sanitization decisions.

Traditionally, studies have explored the impacts of individual water chemistry parameters on the persistence of Mycobacterium spp. and Legionella spp. in isolation with the underlying assumption that these associations are likely monotonic in nature. Yet chemical and microbiological changes are complex, and associations are likely highly combinatorial. In this study, we use interpretable machine learning models to disentangle the integrative and nonlinear associations between water chemistry and occurrence/abundance of Mycobacterium spp. and Legionella spp. Seasonal data from source water, point-of-entry and distribution systems of eight full-scale drinking water systems demonstrated that shifts in overall water chemistry were associated with the changes in microbial abundance during treatment and distribution. Machine learning models indicated moderate predictive ability of integrated water chemistry towards Legionella spp. abundance and towards the occurrence of both Legionella spp. and Mycobacterium spp., whereas predictive performance for Mycobacterium spp. abundance was limited. The association between nitrate and Legionella spp. abundance was disinfectant regimes dependent, while dissolved organic carbon exhibited a concentration dependent response type (i.e., positive and negative association). In chloraminated systems, Legionella spp. abundance was positively associated with ammonia and nitrate, highlighting the critical role of nitrification. Here, it appears that pH likely influences the initial colonization of Legionella spp. while ammonia governs its abundance in drinking water. Overall, this study demonstrates that integrated water chemistry and parameter-specific nonlinear effects collectively explain persistence of Mycobacterium spp. and Legionella spp. in drinking water systems. SynopsisThis study elucidates the integrative impact of water chemistry and the nonlinear responses of individual water chemistry parameters on the occurrence and abundance of Mycobacterium spp. and Legionella spp. in drinking water using interpretable machine learning. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/26351579v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@12334e4org.highwire.dtl.DTLVardef@65696borg.highwire.dtl.DTLVardef@1ec2452org.highwire.dtl.DTLVardef@44899b_HPS_FORMAT_FIGEXP M_FIG C_FIG

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.

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.

Background: Wastewater and environmental surveillance (WES) expanded rapidly during the COVID-19 pandemic and is increasingly proposed for routine public health use across a broader range of pathogens. Yet empirical evidence on how decision-makers judge when WES is actionable, how it integrates with existing surveillance, and how its role varies across resource and epidemiological contexts remains limited. Methods: We conducted three structured tabletop exercises (TTXs) at regional Global Wastewater Surveillance Consortium (GLOWACON) meetings in Singapore, Ethiopia, and Panama between March 2024 and May 2025, engaging more than 1,100 participants from over 60 countries spanning public health, government, research, industry, and international organisations. Standardised scenarios and decision prompts, covering respiratory, contact-transmitted, and vector-borne pathogens across multiple outbreak phases, elicited how participants prioritised, implemented, and responded to WES. Data from structured observation notes, participant worksheets, and post-exercise surveys were systematically analysed using a thematic qualitative approach to identify cross-cutting decision patterns and context-specific considerations across regions. This working paper has not been peer reviewed. Findings: Four cross-cutting decision patterns emerged. First, WES was most actionable when it addressed defined surveillance gaps, particularly during early outbreak phases when clinical testing was limited or delayed. Second, decisions to initiate, scale, or de-escalate WES depended on disease severity, the availability of actionable interventions, and the completeness of existing surveillance, not on pathogen type. Third, participants consistently treated WES as complementary to, not a substitute for, clinical and epidemiological surveillance, with its role evolving over the course of an outbreak. Fourth, implementation considerations, including sewer infrastructure, resource constraints, tourism, and mass gatherings varied substantially by setting, while governance, data-sharing, and trust concerns recurred across all three regions. Interpretation: The value of WES is determined less by pathogen-specific characteristics than by how it is embedded within decision-making frameworks in public health systems. These findings provide empirical evidence on how WES is operationalised across diverse global contexts and underscore an urgent need for clearer governance, integration, and prioritisation frameworks without which WES risks remaining an underutilised or inconsistently applied tool despite its demonstrated potential to strengthen pandemic preparedness and response. Funding: This working paper was independently initiated and conducted within the Center on AI, Security, and Technology using income from operations and gifts and grants from philanthropic supporters. A complete list of donors and funders is available at www.rand.org/CAST. RAND clients, donors, and grantors have no influence over research findings or recommendations.

BackgroundChildhood lead exposure is prevalent worldwide including low- and middle-income countries (LMICs). Structured screening and prevention programs to address pediatric lead exposure are largely absent in these settings. Adapted interventions are needed to close this implementation gap in an urban African context. This paper describes the protocol for the Lead Exposure Intervention Program (LEIP), which aims to adapt, pilot, and evaluate a pediatric lead exposure screening and risk-reduction protocol in Nairobi, Kenya. MethodsLEIP is a multi-phase, hybrid type 3 implementation-effectiveness study. Phase 1 is a formative one-arm study leveraging an existing mother-child cohort and stakeholder-led tools adaptation to pilot a program comprising blood lead level (BLL) screening with a lead risk survey and tailored caregiver risk reduction messaging. Phase 2 is a randomized trial in public sector clinics. In this phase, approximately 1,500 children will be screened to identify 100 with elevated BLL ([&ge;]5 {micro}g/dL) for enrollment, who will then be randomized 1:1 to receive either clinic-only risk-reduction messaging or the same clinic-based messaging plus a home visit for environmental assessment and additional tailored messaging. Follow-up at 3 and 9 months will assess caregiver recall of key messages and adoption of recommended exposure-reduction behaviors, as well as changes in child BLL. Phase 3 involves qualitative interviews with caregivers and key stakeholders to identify multi-level barriers and facilitators to intervention uptake. Quantitative and qualitative findings will be integrated to inform refinements for scale-up. DiscussionThis study represents a critical opportunity to develop and evaluate an adaptive, screening-based lead exposure intervention tailored to the urban LMIC context. By incorporating implementation science principles and stakeholder-driven design, LEIP is well-positioned to inform scalable national and regional approaches. The inclusion of both quantitative and qualitative components enhances the protocols ability to capture multilevel dynamics of uptake, fidelity, and sustainability, and generate actionable insights for future large-scale implementations. Trial RegistrationRegistered on ClinicalTrials.gov (NCT07401251)

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.

IntroductionAccess 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 ResultsA 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. Conclusionstrengthening 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.

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.

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.

BackgroundIn September 2021, the U.S. Centers for Disease Control and Prevention (CDC) implemented the Traveler-based Genomic Surveillance (TGS) program, a surveillance system that leverages genomic sequencing of samples from international air travelers and aviation wastewater for early detection of infectious threats. MethodsDuring September 2021-August 2024, nasal samples were collected anonymously from volunteer international travelers arriving at eight U.S. airports. During February 2023- August 2024, aviation wastewater samples were collected from arriving flights. Nasal samples were pooled and sent to a laboratory for RT-PCR testing. Genomic sequencing was conducted for SARS-CoV-2 and respiratory, gastrointestinal (wastewater), and other pathogens of public health importance. FindingsNasal samples from 694,798 travelers were grouped into 67,308 pools and tested; 13,990 (20.8%) were positive for SARS-CoV-2. Over 80% (400/495) of airplane and 96{middle dot}6% (422/437) triturator (a wastewater collection point from multiple airplanes) samples were positive for SARS-CoV-2. Sequence results were made publicly available a median of 11 days (IQR 10- 13 days) after sample collection. Predominant SARS-CoV-2 variants changed over time. Positive tests for influenza virus and respiratory syncytial virus were high in December/January, and gastrointestinal viruses were detected in wastewater during all months. Monitoring was scaled in response to reported outbreaks of COVID-19 and Mycoplasma pneumoniae in China and clade 1 monkeypox virus in central Africa. InterpretationTraveler nasal and aviation wastewater sampling can provide critical early detection of infectious pathogens before widespread U.S. community transmission. The TGS program provides a model for integrated traveler-based genomic surveillance. FundingCDC Research in ContextO_ST_ABSEvidence before this projectC_ST_ABSWe searched PubMed for relevant studies published during December 1, 2020-August 31, 2024, using the terms "traveler surveillance", "wastewater monitoring", "SARS-CoV-2 genomics", and "airport-based surveillance", without language restrictions. Previous reports have shown the feasibility of using travelers as sentinel populations for disease surveillance. Modeling studies have proposed integrating genomic data into international travel surveillance systems to enhance early pathogen detection, and evidence from Australia, Canada, and the UK suggests such programs could be scalable and effective. Early pandemic-era wastewater surveillance, particularly aviation wastewater, demonstrated that air travel hubs can be used to monitor pathogen importation. Prior efforts largely focused on SARS-CoV-2, with limited integration of multi-pathogen surveillance or side-by-side comparisons of nasal and wastewater surveillance modalities. A limited number of public health reviews have examined the broader implications of airport-based surveillance, including novel methods like airplane wastewater testing. However, empirical data on sustained, large-scale implementation of these models especially outside of regulatory or mandatory testing frameworks have been sparse. Added value of this projectThis is the first real-world implementation and scale-up of an anonymized, multi-pathogen traveler-based surveillance system across multiple U.S. international airports. We developed a scalable framework that integrated nasal swab testing, airplane and airport wastewater sampling, with genomic sequencing into a unified pathogen surveillance platform. Unlike prior efforts which primarily focused on SARS-CoV-2, this program captured respiratory and gastrointestinal viruses simultaneously and tracked genomic variation in near-real time. The program transitioned from a pilot to a multi-modality national surveillance system in under four years, engaging nearly 700,000 international travelers, and nearly 1000 aviation wastewater samples. Our findings demonstrate the feasibility of rapidly adapting this infrastructure for emerging threats and underscores the importance of sentinel surveillance in addressing global sequencing blind spots. Implications of all the available evidenceThe successful scale-up and real-time application of the TGS program illustrates that traveler-based surveillance can serve as a critical global early warning tool. Data generated from this program have filled gaps in global pathogen tracking, informed public health responses to outbreaks, and demonstrated that surveillance of international travelers can be achieved without mandatory testing. The scalability, speed, and adaptability of the program offer a viable model for global replication, especially as routine surveillance capacities decline. Our findings suggest that integration of multi-modal, voluntary traveler surveillance including sequencing and wastewater-based epidemiology should be considered a core component of pandemic preparedness and response frameworks worldwide.

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.

Reducing the cost and environmental impact of cell culture media is an important goal for cultivated meat, the process of generating meat in vitro using proliferating animal cells. While prior approaches have demonstrated the use of microbial lysates to replace expensive animal-based fetal bovine serum (FBS) in media, these formulations still rely on large quantities of growth factors such as fibroblast-like growth factor 2 (FGF2). Here, we demonstrate the use of FGF2-expressing Vibrio natriegens to create whole-cell lysates that replace both FBS and FGF2 in cell culture media for cultivated meat applications. This medium, named "VN40FGF", supports rapid proliferation of immortalized bovine muscle satellite cells (iBSCs) in the absence of supplemented FGF2. Cells grown in VN40FGF maintain phenotype and differentiation capacity. We also demonstrate that engineered V. natriegens can grow in spent cell culture media, further improving sustainability and economics, and reducing potential eutrophication concerns associated with waste disposal. Our approach combines multiple strategies for reducing the total number of media inputs, demonstrating opportunities for more economical and sustainable cell culture, especially for cultivated meats.

Ballast water (BW) is an important vector for the global translocation of bacterial taxa, including pathogens. Legal frameworks establishing limits on the discharge of live organisms into recipient environments have been designed to reduce risks of microbial invasions, and understanding the impacts of BW management on bacterial communities is critical for assessing the effectiveness of these practices. Here we evaluate changes in bacterial communities associated with both BW treatment (BWT) and a combined management approach of BWT plus BW exchange (BWT+E). Samples were collected on two experimental voyages designed specifically to compare BW-associated biota before and after management. Microbial community structure and inferred function were assessed based on high throughput sequencing of 16S rRNA amplicons, and bacterial indicator taxa E. coli and enterococci were analyzed using targeted qPCR. As expected, both BWT alone and BWT+E dramatically changed bacterial communities, with the latter resulting in the largest overall decreases in bacterial diversity. Increases in Gammaproteobacteria, especially in the genus Pseudomonas, were particularly notable, with concomitant decreases in Alphaproteobacteria and Bacteroidia. Shifts in predicted bacterial function associated with BWT were similar for both voyages, despite significant differences in community structure, and may represent selection for r-strategists capable of active regrowth after BWT. qPCR estimates of indicator taxa were similar to those obtained through standard culture methods but may offer increased sensitivity for detecting changes associated with management. Our results indicate that BW management is effective at reducing bacterial communities but suggest that further research is needed to understand risks associated with taxa that may survive BWT.

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 [&ge;]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.

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.

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.

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.