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Fecal source tracking (FST) may be useful to assess pathways of fecal contamination in domestic environments and to estimate the impacts of water, sanitation, and hygiene (WASH) interventions in low-income settings. We measured two nonspecific and two human-associated fecal indicators in water, soil, and surfaces before and after a shared latrine intervention from low-income households in Maputo, Mozambique, participating in the Maputo Sanitation (MapSan) trial. Up to a quarter of households were impacted by human fecal contamination, but trends were unaffected by improvements to shared sanitation facilities. The intervention reduced Escherichia coli gene concentrations in soil but did not impact culturable E. coli or the prevalence of human FST markers in a difference-in-differences analysis. Using a novel Bayesian hierarchical modeling approach to account for human marker diagnostic sensitivity and specificity, we revealed a high amount of uncertainty associated with human FST measurements and intervention effect estimates. The field of microbial source tracking would benefit from adding measures of diagnostic accuracy to better interpret findings, particularly when FST analyses convey insufficient information for robust inference. With improved measures, FST could help identify dominant pathways of human and animal fecal contamination in communities and guide the implementation of effective interventions to safeguard health.

Pit latrines are the most common sanitation option in the developing world. They are simple to build but require periodic emptying which results in widespread dispersion of fecal pathogens in the environment. While much is known about the health risks of fecal-oral exposure, little is known about those resulting from the aerosolization of pathogens from fecal material. Bioaerosols were sampled around seven pit latrines before, after, and during emptying in Blantyre, Malawi. Bioaerosols were collected directly onto nutrient and selective medium agar plates using an impact sampler. DNA was extracted from some plates and analyzed for selected enteric pathogens. Total heterotrophic bacteria in the air during active emptying ranged from 198 to >13,000 colony forming units (CFU) per m3, and generally increased above background levels during pit emptying. At about one meter from the pit latrine emptying, E. coli and total coliforms concentrations in air reached up to 350 and 790 CFU m−3, respectively. Additionally, at four out of the seven pit latrines sites sampled, enterotoxigenic E. coli (ETEC) LT/ST was confirmed to be present in bioaerosols. This work demonstrates the potential for airborne dispersion of enteric pathogens during pit latrine emptying operations., Graphical abstract Unlabelled Image, Highlights • Bioaerosols were sampled during pit latrines emptying in Blantyre, Malawi. • E. coli, coliforms and enterotoxigenic E. coli (ETEC) were detected. • High bioaerosols concentrations correlated with certain emptying practices • The results highlight aerosolization of enteric pathogens during pit emptying. • Further studies are needed to quantify exposure and health risks.

Additional file 1: Text A1. Details of MapSan intervention facilities. Text A2. Sampling procedures. Text A3. Further details on intervention reach.

Additional file 2. Process evaluation domains, subdomains and indicators. Process indicators used, with details of dichotomisation and role of variables in path models (exogenous / endogenous, intermediary outcome / potential mediator).

Additional file 4. Generalised structural equation model with probit link using data from small compounds (≤ 20 members). Abbreviations: HWF, handwashing facility; HWWS, handwashing with soap.

Additional file 6. Linear probability path analysis of data from small compounds (≤ 20 members) – standardised coefficients and covariances between exogenous variables. Abbreviations: HWF, handwashing facility; HWWS, handwashing with soap.

Additional file 5. Generalised structural equation model with probit link using data from large compounds (> 20 members). Abbreviations: ‘chefe’, chefe de composto (informal compound leader); HWF, handwashing facility; HWWS, handwashing with soap.

Additional file 7. Linear probability path analysis of data from large compounds (> 20 members) – standardised coefficients and covariances between exogenous variables. Abbreviations: ‘chefe’, chefe de composto (informal compound leader); HWF, handwashing facility; HWWS, handwashing with soap.

Sewage surveillance is increasingly used in public health applications; metabolites, biomarkers, and pathogens are detectable in wastewater and can provide useful information about community health. Work on this topic has been limited to wastewaters in mainly high-income settings, however. In low-income countries, where the burden of enteric infection is high, nonsewered sanitation predominates. In order to assess the utility of fecal sludge surveillance as a tool to identify the most prevalent enteric pathogens circulating among at-risk children, we collected 95 matched child stool and fecal sludge samples from household clusters sharing latrines in urban Maputo, Mozambique. We analyzed samples for 20 common enteric pathogens via multiplex real-time quantitative PCR. Among the 95 stools matched to fecal sludges, we detected the six most prevalent bacterial pathogens (Enteroaggregative E. coli, Shigella/Enteroinvasive E. coli, Enterotoxigenic E. coli, Enteropathogenic E. coli, shiga-toxin producing E. coli, Salmonella), and all three protozoan pathogens (Giardia duodenalis, Cryptosporidium parvum, Entamoeba histolytica) in the same rank order in both matrices. We did not observe the same trend for viral pathogens or soil-transmitted helminths, however. Our results suggest that sampling fecal sludges from onsite sanitation offers potential for localized pathogen surveillance in low-income settings where enteric pathogen prevalence is high.

Background Enteric infections are common where public health infrastructure is lacking. This study assesses risk factors for a range of enteric infections among children living in low-income, unplanned communities of urban Maputo, Mozambique. Methods & findings We conducted a cross-sectional survey in 17 neighborhoods of Maputo to assess the prevalence of reported diarrheal illness and laboratory-confirmed enteric infections in children. We collected stool from children aged 1–48 months, independent of reported symptoms, for molecular detection of 15 common enteric pathogens by multiplex RT-PCR. We also collected survey and observational data related to water, sanitation, and hygiene (WASH) characteristics; other environmental factors; and social, economic, and demographic covariates. We analyzed stool from 759 children living in 425 household clusters (compounds) representing a range of environmental conditions. We detected ≥1 enteric pathogens in stool from most children (86%, 95% confidence interval (CI): 84–89%) though diarrheal symptoms were only reported for 16% (95% CI: 13–19%) of children with enteric infections and 13% (95% CI: 11–15%) of all children. Prevalence of any enteric infection was positively associated with age and ranged from 71% (95% CI: 64–77%) in children 1–11 months to 96% (95% CI: 93–98%) in children 24–48 months. We found poor sanitary conditions, such as presence of feces or soiled diapers around the compound, to be associated with higher risk of protozoan infections. Certain latrine features, including drop-hole covers and latrine walls, and presence of a water tap on the compound grounds were associated with a lower risk of bacterial and protozoan infections. Any breastfeeding was also associated with reduced risk of infection. Conclusions We found a high prevalence of enteric infections, primarily among children without diarrhea, and weak associations between bacterial and protozoan infections and environmental risk factors including WASH. Findings suggest that environmental health interventions to limit infections would need to be transformative given the high prevalence of enteric pathogen shedding and poor sanitary conditions observed. Trial registration ClinicalTrials.gov NCT02362932, Author summary Enteric pathogens such as bacteria, protozoa, and viruses can cause diarrhea and other longer-term health problems. Poor sanitary conditions, including inadequate sanitation facilities, can lead to contamination of the living environment and higher risk of exposure to and transmission of enteric pathogens. Young children, who are vulnerable to both the short- and long-term health effects of enteric infections, interact with their environment in different ways than older children or adults. In order to limit enteric pathogen transmission among this vulnerable group, we must understand the infection burden and the environmental or sanitation-related factors that are associated with infection. Among a group of children younger than four years old living in low-income neighborhoods of Maputo, Mozambique, we found over 85% tested had ≥1 enteric infection. Children living in environments visibly contaminated with feces were more likely to have an infection than children whose living environments were not visibly contaminated. In contrast, children living in compounds with certain latrine features, including walls and pit covers (potential indicators of build quality), had reduced infection risk. Understanding that these risk factors may play important roles in exposure and transmission in this setting is key to planning effective interventions.