Human fecal contamination of water, soil, and surfaces in households sharing poor-quality sanitation facilities in Maputo, Mozambique

Sanitation in urban areas may limit the spread of antimicrobial resistance via flies

Synanthropic filth flies are common where sanitation is poor and fecal wastes are accessible to them. These flies have been proposed as mechanical vectors for the localized transport of fecal microbes including antimicrobial resistant (AMR) organisms and associated antimicrobial resistance genes (ARGs), increasing exposure risks. We evaluated whether an onsite sanitation intervention in Maputo, Mozambique reduced the concentration of enteric bacteria and the frequency of detection of ARGs carried by flies collected in household compounds of low-income neighborhoods. Additionally, we assessed the phenotypic resistance profile of Enterobacteriaceae isolates recovered from flies during the pre-intervention phase. After fly enumeration at study compounds, quantitative polymerase chain reaction was used to quantify an enteric 16S rRNA gene (i.e., specific to a cluster of phylotypes corresponding to 5% of the human fecal microflora), 28 ARGs, and Kirby Bauer Disk Diffusion of Enterobacteriaceae isolates was utilized to assess resistance to eleven clinically relevant antibiotics. The intervention was associated with a 1.5 log10 reduction (95% confidence interval: -0.73, -2.3) in the concentration of the enteric 16S gene and a 31% reduction (adjusted prevalence ratio = 0.69, [0.52, 0.92]) in the mean number of ARGs per fly compared to a control group with poor sanitation. This protective effect was consistent across the six ARG classes that we detected. Enterobacteriaceae isolates-only from the pre-intervention phase-were resistant to a mean of 3.4 antibiotics out of the eleven assessed. Improving onsite sanitation infrastructure in low-income informal settlements may help reduce fly-mediated transmission of enteric bacteria and the ARGs carried by them.

Multiscalar Evaluation of the Water Distribution System and Diarrheal Disease Risk in Addis Ababa, Ethiopia

Despite growing urbanization, our understanding of the impacts of water and sanitation on human health has largely come from studies in rural sectors. To this end, we collected data at both regional (water quality measures from water treatment systems) and community (cross-sectional surveys) scales to examine determinants of enteric pathogen infection and diarrheal disease among infants in Addis Ababa, Ethiopia. Regionally, the Legedadi water treatment plant had significantly lower heterotrophic plate counts, total coliform counts, and fecal coliform counts compared with the Gefersa water treatment plant. The number of pathogen types in infant stool also differed by plant. Decreases in chlorine levels and increases in the relative abundance of Gammaproteobacteria with distance from treatment plants suggest a compromised water distribution system. In communities, infants in households that obtained water from yard pipes or public taps had significantly lower odds of diarrhea compared to households that had water piped into their dwellings (OR = 0.35, 95% CI 0.16, 0.76, and OR = 0.39, 95% CI 0.15, 1.00, respectively). Similarly, infants in households that boiled or filtered water had significantly lower odds of diarrhea compared to households that did not treat water (OR = 0.40, 95% CI 0.19, 0.86 and OR = 0.23, 95% CI 0.06, 0.84, respectively). Integrating multiscalar data better informs the health impacts of water in urban settings.

Influence of sanitation facilities on diarrhea prevalence among children aged below 5 years in flood-prone areas of Bangladesh: a multilevel analysis

Although the improvement of sanitation facilities has been a major contributor to improving public health, it is not guaranteed to prevent negative health outcomes. This is especially true in areas affected by severe natural disasters, such as flooding or extreme rainfall. Previous studies have examined the association between catastrophic natural disasters and negative health outcomes. However, studies on disaster-prone areas are limited. This study focused on the impact of flood risks and examined whether the improvement of sanitation facilities would be sufficient to suppress the prevalence of diarrhea in flood-prone areas. Two secondary datasets including geodata on flood-prone areas were used for the analysis: one each was obtained from the Bangladesh Demographic and Health Survey and Bangladesh Agricultural Research Council. Two models with categorizations of sanitation facilities based on containment type and excreta flow were applied for analysis. Results showed that the severe flood-prone areas and "diffused" type of sanitation, where the feces are diffused without any containment, had significant positive associations with diarrhea prevalence; however, the interaction between them was negative. Moderate flood-prone areas had a significant positive association with diarrhea prevalence; however, the interaction with unimproved sanitation, which includes containment without clear partition from feces, was significantly negative. These findings indicate that improved sanitation or containment type of sanitation may not positively contribute to the prevention of diarrhea in these severe- and moderate-flood prone areas. The urgent need for alternative sanitation technologies should be addressed in flood-prone regions.

A review of latrine front-end characteristics associated with microbial infection risk; reveals a lack of pathogen density data

Unsafe sanitation accounts for an estimated 898,000 global deaths annually. The faecal pathogen transmission pathway is complex with several possible routes. Latrine front-end characteristics and usage behaviours are one key transmission pathway for microbial pathogens, however, there has not yet been a synthesis of the available research. This review aims to compare the microbial infection risks with latrine front-end components including any quantified microbial densities within the household latrines. This review was conducted with no restriction on the geographical location of the research. Of 118 studies reviewed, only ten (8%) have quantified the microbial density inside the household latrines compared to 109 (92%) measuring the infection risks. The reported risks were most frequent for specific bacterial (n = 34), and helminths infections (n = 32) compared to diarrhoea (n = 23), combined (n = 15), protozoan (n = 4), and viral (n = 4) infections. The infections risk decreased for using latrines lying at a higher position on the sanitation ladder (for example flush latrines) compared to those lying lower (for example pit latrines). The trend was similar for using floor materials that were easier to clean and less favourable for pathogen survival inside the latrines (for example, concrete as opposed to earth). Faecal coliforms were reported highest on the surface of the squat pan (743 CFU/cm2) of pour-flush latrines and helminths on earth floors of pit latrines (1.5 eggs and larvae per gram of soil). Irrespective of latrine type and its position on the sanitation ladder, a dirty latrine, evidenced by a visible lack of cleanliness, significantly increased the risk for all infections. This study recommends that effective microbial infection risk reduction in latrines can be gained efficiently by ensuring washable surfaces and consistent cleaning practices. Future studies should include more rigorous measurements of microbial densities in various latrine types incorporating the different front-end components and usage behaviours.

Long-term impacts of an urban sanitation intervention on enteric pathogens in children in Maputo city, Mozambique: study protocol for a cross-sectional follow-up to the Maputo Sanitation (MapSan) trial 5 years postintervention

INTRODUCTION

We previously assessed the effect of an onsite sanitation intervention in informal neighbourhoods of urban Maputo, Mozambique on enteric pathogen detection in children after 2 years of follow-up (Maputo Sanitation (MapSan) trial, ClinicalTrials.gov: NCT02362932). We found significant reductions in Shigella and Trichuris prevalence but only among children born after the intervention was delivered. In this study, we assess the health impacts of the sanitation intervention after 5 years among children born into study households postintervention.

METHODS AND ANALYSIS

We are conducting a cross-sectional household study of enteric pathogen detection in child stool and the environment at compounds (household clusters sharing sanitation and outdoor living space) that received the pour-flush toilet and septic tank intervention at least 5 years prior or meet the original criteria for trial control sites. We are enrolling at least 400 children (ages 29 days to 60 months) in each treatment arm. Our primary outcome is the prevalence of 22 bacterial, protozoan, and soil transmitted helminth enteric pathogens in child stool using the pooled prevalence ratio across the outcome set to assess the overall intervention effect. Secondary outcomes include the individual pathogen detection prevalence and gene copy density of 27 enteric pathogens (including viruses); mean height-for-age, weight-for-age, and weight-for-height z-scores; prevalence of stunting, underweight, and wasting; and the 7-day period prevalence of caregiver-reported diarrhoea. All analyses are adjusted for prespecified covariates and examined for effect measure modification by age. Environmental samples from study households and the public domain are assessed for pathogens and faecal indicators to explore environmental exposures and monitor disease transmission.

ETHICS AND DISSEMINATION

Study protocols have been reviewed and approved by human subjects review boards at the Ministry of Health, Republic of Mozambique and the University of North Carolina at Chapel Hill. Deidentified study data will be deposited at https://osf.io/e7pvk/.

TRIAL REGISTRATION NUMBER

ISRCTN86084138.

Measurement in the study of human exposure to animal feces: A systematic review and audit

BACKGROUND

Human exposure to animal feces is increasingly recognized as an important transmission route of enteric pathogens. Yet, there are no consistent or standardized approaches to measurement of this exposure, limiting assessment of the human health effects and scope of the issue.

OBJECTIVE

To inform and improve approaches to the measurement of human exposure to animal feces, we audited existing measurement in low- and middle-income countries.

METHODS

We systematically searched peer-reviewed and gray literature databases for studies with quantitative measures of human exposure to animal feces and we classified measures in two ways. First, using a novel conceptual model, we categorized measures into three 'Exposure Components' identified a priori (i.e., Animal, Environmental, Human Behavioral); one additional Component (Evidence of Exposure) inductively emerged. Second, using the exposure science conceptual framework, we determined where measures fell along the source-to-outcome continuum.

RESULTS

We identified 1,428 measures across 184 included studies. Although studies overwhelmingly included more than one single-item measure, the majority only captured one Exposure Component. For example, many studies used several single-item measures to capture the same attribute for different animals, all of which were classified as the same Component. Most measures captured information about the source (e.g. animal presence) and contaminant (e.g. animal-sourced pathogens), which are most distal from exposure on the source-to-outcome continuum.

DISCUSSION

We found that measurement of human exposure to animal feces is diverse and largely distal from exposure. To facilitate better assessment of the human health effects of exposure and scope of the issue, rigorous and consistent measures are needed. We recommend a list of key factors from the Animal, Environmental, and Human Behavioral Exposure Components to measure. We also propose using the exposure science conceptual framework to identify proximal measurement approaches.

Study design and rationale for the PAASIM project: a matched cohort study on urban water supply improvements and infant enteric pathogen infection, gut microbiome development and health in Mozambique

INTRODUCTION

Despite clear linkages between provision of clean water and improvements in child health, limited information exists about the health impacts of large water infrastructure improvements in low-income settings. Billions of dollars are spent annually to improve urban water supply, and rigorous evaluation of these improvements, especially targeting informal settlements, is critical to guide policy and investment strategies. Objective measures of infection and exposure to pathogens, and measures of gut function, are needed to understand the effectiveness and impact of water supply improvements.

METHODS AND ANALYSIS

In the PAASIM study, we examine the impact of water system improvements on acute and chronic health outcomes in children in a low-income urban area of Beira, Mozambique, comprising 62 sub-neighbourhoods and ~26 300 households. This prospective matched cohort study follows 548 mother-child dyads from late pregnancy through 12 months of age. Primary outcomes include measures of enteric pathogen infections, gut microbiome composition and source drinking water microbiological quality, measured at the child's 12-month visit. Additional outcomes include diarrhoea prevalence, child growth, previous enteric pathogen exposure, child mortality and various measures of water access and quality. Our analyses will compare (1) subjects living in sub-neighbourhoods with the improved water to those living in sub-neighbourhoods without these improvements; and (2) subjects with household water connections on their premises to those without such a connection. This study will provide critical information to understand how to optimise investments for improving child health, filling the information gap about the impact of piped water provision to low-income urban households, using novel gastrointestinal disease outcomes.

ETHICS AND DISSEMINATION

This study was approved by the Emory University Institutional Review Board and the National Bio-Ethics Committee for Health in Mozambique. The pre-analysis plan is published on the Open Science Framework platform (https://osf.io/4rkn6/). Results will be shared with relevant stakeholders locally, and through publications.

Urban Onsite Sanitation Upgrades and Synanthropic Flies in Maputo, Mozambique: Effects on Enteric Pathogen Infection Risks

Synanthropic filth flies transport enteric pathogens from feces to food, which upon consumption poses an infection risk. We evaluated the effect of an onsite sanitation intervention─including fly control measures─in Maputo, Mozambique, on the risk of infection from consuming fly-contaminated food. After enumerating flies at intervention and control sites, we cultured fecal indicator bacteria, quantified gene copies for 22 enteric pathogens via reverse transcription quantitative polymerase chain reaction (RT-qPCR), and developed quantitative microbial risk assessment (QMRA) models to estimate annual risks of infection attributable to fly-contaminated foods. We found that the intervention reduced fly counts at latrine entrances by 69% (aRR = 0.31, [0.13, 0.75]) but not at food preparation areas (aRR = 0.92, [0.33, 2.6]). Half of (23/46) of individual flies were positive for culturable Escherichia coli, and we detected ≥1 pathogen gene from 45% (79/176) of flies, including enteropathogenic E. coli (37/176), adenovirus (25/176), Giardia spp. (13/176), and Trichuris trichiura (12/176). We detected ≥1 pathogen gene from half the flies caught in control (54%, 30/56) and intervention compounds (50%, 17/34) at baseline, which decreased 12 months post-intervention to 43% (23/53) at control compounds and 27% (9/33) for intervention compounds. These data indicate flies as a potentially important mechanical vector for enteric pathogen transmission in this setting. The intervention may have reduced the risk of fly-mediated enteric infection for some pathogens, but infrequent detection resulted in wide confidence intervals; we observed no apparent difference in infection risk between groups in a pooled estimate of all pathogens assessed (aRR = 0.84, [0.61, 1.2]). The infection risks posed by flies suggest that the design of sanitation systems and service delivery should include fly control measures to prevent enteric pathogen transmission.

Attenuation of bacterial hazard indicators in the subsurface of an informal settlement and their application in quantitative microbial risk assessment

Pit latrines provide essential onsite sanitation services to over a billion people, but there are concerns about their role in infectious disease transmission, and impacts on groundwater resources. We conducted fieldwork in an informal settlement in Dar es Salaam, where cholera is endemic. We combined plate counting with portable MinION sequencing and quantitative polymerase chain reaction (qPCR) methods for characterization of bacteria in pit latrine sludge, leachate, shallow and deep groundwater resources. Pit latrine sludge was characterized by log₁₀ marker gene concentrations per 100 mL of 11.2 ± 0.2, 9.9 ± 0.9, 6.0 ± 0.3, and 4.4 ± 0.8, for total bacteria (16S rRNA), E. coli (rodA), human-host-associated Bacteroides (HF183), and Vibrio cholerae (ompW), respectively. The ompW gene observations suggested 5 % asymptomatic Vibrio cholerae carriers amongst pit latrine users. Pit leachate percolation through one-meter-thick sand beds attenuated bacterial hazard indicators by 1 to 4 log₁₀ units. But first-order removal rates derived from these data substantially overestimated the longer-range hazard attenuation in the sand aquifers. Cooccurrence of human sewage marker gene HF183 in all shallow groundwater samples testing positive for ompW genes demonstrated the human origin of Vibrio cholerae hazards in the subsurface. All borehole water samples tested negative for ompW and HF183 genes, but 16S rRNA gene sequencing data suggested ingress of faecal pollution into boreholes at the peak of the "long rainy season". Quantitative microbial risk assessment (QMRA) predicted a gastrointestinal disease burden of 0.05 DALY per person per year for the community, well above WHO targets of 10^-4-10^-6 DALY for disease related to drinking water.

Prevalence and determinants of diarrhea among under-five children in five Southeast Asian countries: Evidence from the demographic health survey

PURPOSE

To describe the prevalence and the correlation between individual, environmental and household, health behavior, and source of information factors with diarrhea among under-five children in five Southeast Asian countries based on the National Health Survey.

DESIGN AND METHODS

Cross-sectional design conducted in five countries in Southeast Asia. Datasets from Demographic and Health Surveys and Multiple Indicator Cluster Surveys in five countries were analyzed.

RESULTS

A total of 12,447 children under 5 years of age from five countries in Southeast Asia (Indonesia 1807, Cambodia 2650, Myanmar 1717, the Philippines 3669, and Timor-Leste 2614) were included in this study. Binary logistic regression was performed to analyze the data. A total of 12,447 under-five children were included in the study. Overall, in five Southeast Asian countries, the prevalence of diarrhea is known from 8.39% in the Philippines to 18.21% in Indonesia. Several factors related to diarrhea are individual; environmental and household; health behavior such as stool disposal, breastfeeding mothers, and children's food history; and source of information factors.

CONCLUSION

The findings of this study indicate that diarrhea is a serious public health problem in the Southeast Asian region that must be addressed using preventive and curative approaches.

PRACTICE IMPLICATION

The results indicate the need for cross-collaboration among nurses, medical doctor, and sanitarian is needed to tackle the childhood diarrhea and minimize the severity based on those determinants.

Microbial Source Tracking as a Method of Determination of Beach Sand Contamination

Beach sand may act as a reservoir for numerous microorganisms, including enteric pathogens. Several of these pathogens originate in human or animal feces, which may pose a public health risk. In August 2019, high levels of fecal indicator bacteria (FIB) were detected in the sand of the Azorean beach Prainha, Terceira Island, Portugal. Remediation measures were promptly implemented, including sand removal and the spraying of chlorine to restore the sand quality. To determine the source of the fecal contamination, during the first campaign, supratidal sand samples were collected from several sites along the beach, followed by microbial source tracking (MST) analyses of Bacteroides marker genes for five animal species, including humans. Some of the sampling sites revealed the presence of marker genes from dogs, seagulls, and ruminants. Making use of the information on biological sources originating partially from dogs, the municipality enforced restrictive measures for dog-walking at the beach. Subsequent sampling campaigns detected low FIB contamination due to the mitigation and remediation measures that were undertaken. This is the first case study where the MST approach was used to determine the contamination sources in the supratidal sand of a coastal beach. Our results show that MST can be an essential tool to determine sources of fecal contamination in the sand. This study shows the importance of holistic management of beaches that should go beyond water quality monitoring for FIB, putting forth evidence for beach sand monitoring.

Spatial heterogeneity of neighborhood-level water and sanitation access in informal urban settlements: A cross-sectional case study in Beira, Mozambique

Rapid urbanization, resulting in population growth within informal settlements, has worsened exclusion and inequality in access to water and sanitation (WASH) services in the poorest and most marginalized communities. In this study, we describe the heterogeneity in water service satisfaction and WASH access in low-income, peri-urban neighborhoods of Beira, Mozambique, and examine whether this heterogeneity can be explained by distance to water distribution mains. Using spatial statistics and regression analyses, we identify spatial heterogeneity in household WASH access, as well as consumer-reported satisfaction with water services (services, pressure, quality, and sufficient quantity). We find that as distance from the water main increased, both access to an improved water source at the household and satisfaction with water pressure decreases, and water supply intermittency increases, controlling for household density and socioeconomic status. The odds of a household having access to a water source at the household or on the compound decreases with every 100-meter increase in distance from a water main pipe (odds ratio [OR] 0.87, 95% confidence interval [CI]: 0.82, 0.92). Satisfaction with water services also decreases with every 100-meter increase in distance from a water main pipe (OR: 0.80; 95% CI: 0.69, 0.94). Days of availability in the past week decreases by a factor of 0.22 for every 100-meter increase in distance from the water main (95% CI: −0.29, −0.15). Findings from this study highlight the unequal household access to water and sanitation in urban informal settlements, even within low-income neighborhoods. Describing this heterogeneity of access to water services, sanitation, and satisfaction—and the factors influencing them—can inform stakeholders and guide the development of infrastructural solutions to reduce water access inequities within urban settings.

Climate variability, water supply, sanitation and diarrhea among children under five in Sub-Saharan Africa: a multilevel analysis

Climate variability is expected to increase the risk of diarrhea diseases, a leading cause of child mortality and morbidity in Sub-Saharan Africa (SSA). The risk of diarrhea is more acute when populations have poor access to improved water and sanitation. This study seeks to determine individual and joint effects of climate variation, water supply and sanitation on the occurrence of diarrhea among children under five in SSA using multilevel mixed-effect Poisson regression including cross-level interaction. We merged 57 Demographic and Health Surveys (DHS) from 25 SSA countries covering the period 2000-2019 with climatic data from the DHS geolocation databases. The results of the research indicate that 77.7% of the variation in the occurrence of diarrhea in Sub-Saharan households is due to climatic differences between clusters. Also, a household residing in a cluster with a high incidence of diarrhea is 1.567 times more likely to have diarrhea cases than a household from a cluster with a low incidence. In addition, when average temperature and rainfall increase, households using unimproved sanitation or unimproved water have more cases of diarrhea. For SSA, the results of the multilevel analysis suggest the adoption at both levels; macro (national) and micro (household), of climate change adaption measures in the water sector to reduce the prevalence of diarrhea.

Hygiene in early childhood development centres in low-income areas of Blantyre, Malawi

Diarrhoeal disease remains a leading cause of death in children in sub-Saharan Africa, attributed to environmental health factors such as inadequate water, sanitation and hygiene (WASH) and food hygiene. This formative study in low-income areas of Blantyre focussed on the practices in Early Childhood Development Centre (ECDCs) environments where children spend a significant amount of time. A mixed-methods approach was applied to identify key hygiene behaviours in ECDCs through; checklist and structured observations (n = 849 children; n = 33 caregivers), focus group discussions (n = 25) and microbiological sampling (n = 261) of drinking water, food handler's hands, and eating utensils. ECDCs had inadequate WASH infrastructure; coupled with poor hygiene practices and unhygienic environments increased the risk of faecal-oral disease transmission. Presence of E. coli in drinking water confirmed observed poor water handling habits by staff and children. Addressing undesired hygiene practices in ECDCs has the potential to improve the health outcomes of children in low-income settings.

ENTEROBACTERIACEAE IN SOILS AND ATMOSPHERIC DUST AEROSOL ACCUMULATIONS OF MOSCOW CITY

The topsoils and atmospheric dust aerosols of the various areas of the city of Moscow were studied. Most of the dust samples contained a considerable number of particles enriched in phosphorus - a sign of contamination by feces. A variety of Enterobacteriaceae species, including opportunistic and pathogenic species, were isolated from the topsoil and dust samples and identified using 16S rDNA nucleotide sequences: Enterobacter aerogenes, E. agglomerans, E. cloacae, E. kobei, E. nimipressuralis, Escherichia coli, Citrobacter europaeus, Klebsiella granulomatis, K. grimontii, K. oxytoca, K. quasipneumoniae, K. variicola, Kluyvera ascorbate, Kluyvera intermedia, Leclercia adecarboxylata, Salmonella enterica and Trabulsiella guamensis. The greatest diversity of pathogens was isolated from spring soil and dust samples immediately after spring snowmelt. Antibiotic resistance of the isolated E. coli strains was tested using disks with a wide range of antimicrobial drugs: Amoxicillin, Ampicillin, Meropenem, Pefloxacin, Streptomycin, Ticarcillin+clavulanic acid, Fosfomycin, Ceftibuten, Ciprofloxacin. Resistance was observed in more than 22% of E. coli strains. The traffic area had a significant number of antibiotic-resistant E. coli strains, clearly indicating a high health risk from soil and dust exposure.

Benefits and Risks of Smallholder Livestock Production on Child Nutrition in Low- and Middle-Income Countries

Livestock production may improve nutritional outcomes of pregnant women and children by increasing household income, availability of nutrient-dense foods, and women's empowerment. Nevertheless, the relationship is complex, and the nutritional status of children may be impaired by presence of or proximity to livestock and their pathogens. In this paper, we review the benefits and risks of livestock production on child nutrition. Evidence supports the nutritional benefits of livestock farming through income, production, and women's empowerment. Increasing animal source food consumption requires a combination of efforts, including improved animal management so that herd size is adequate to meet household income needs and consumption and addressing sociocultural and gendered norms. Evidence supports the inclusion of behavior change communication strategies into livestock production interventions to facilitate the sustainability of nutritional benefits over time, particularly interventions that engage women and foster dimensions of women's empowerment. In evaluating the risks of livestock production, evidence indicates that a broad range of enteric pathogens may chronically infect the intestines of children and, in combination with dietary deficits, may cause environmental enteric dysfunction (EED), a chronic inflammation of the gut. Some of the most important pathogens associated with EED are zoonotic in nature with livestock as their main reservoir. Very few studies have aimed to understand which livestock species contribute most to colonization with these pathogens, or how to reduce transmission. Control at the point of exposure has been investigated in a few studies, but much less effort has been spent on improving animal husbandry practices, which may have additional benefits. There is an urgent need for dedicated and long-term research to understand which livestock species contribute most to exposure of young children to zoonotic enteric pathogens, to test the potential of a wide range of intervention methods, to assess their effectiveness in randomized trials, and to assure their broad adaptation and sustainability. This review highlights the benefits and risks of livestock production on child nutrition. In addition to identifying research gaps, findings support inclusion of poor gut health as an immediate determinant of child undernutrition, expanding the established UNICEF framework which includes only inadequate diet and disease.

Contextual Determinants of General Household Hygiene Conditions in Rural Indonesia

Household hygiene is critical to prevent pathogen transmission at the household level. Assessing household hygiene conditions and their determinants are needed to improve hygiene conditions, especially in rural and less developed areas where the housing conditions are relatively worse than they are in urban areas. This study used data from 278 household interviews and observations in rural areas in the district of East Sumba, province East Nusa Tenggara, Indonesia. The data were analyzed using statistical methods. In general, the household hygiene conditions in the study need to be improved. The main potential sources of pathogen transmission were from the surrounding environment, i.e., non-permanent floor and garbage, and personal hygiene, i.e., handwashing facilities with water and soap were only observed in the homes of four out of ten respondents. The presence of livestock roaming freely in the house’s yard was another source of contamination. Easy access to water and wealth significantly influenced the hygiene conditions. Implementing low-cost interventions, i.e., cleaning the house of garbage and animal feces and cleaning nails, should be the priority in immediate intervention, while providing easier access to water supply, especially during the dry season, could be a long-term intervention. This paper also argues that analyzing household hygiene conditions or practices should be complemented by analyzing contextual determinants of the hygiene conditions or practices, so that we can develop more precise intervention by considering the local or household context.

Impacts of an Urban Sanitation Intervention on Fecal Indicators and the Prevalence of Human Fecal Contamination in Mozambique

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.

Impact of an Urban Sanitation Intervention on Enteric Pathogen Detection in Soils

Environmental fecal contamination is common in many low-income cities, contributing to a high burden of enteric infections and associated negative sequelae. To evaluate the impact of a shared onsite sanitation intervention in Maputo, Mozambique on enteric pathogens in the domestic environment, we collected 179 soil samples at shared latrine entrances from intervention (n = 49) and control (n = 51) compounds during baseline (preintervention) and after 24 months (postintervention) as part of the Maputo Sanitation Trial. We tested soils for the presence of nucleic acids associated with 18 enteric pathogens using a multiplex reverse transcription qPCR platform. We detected at least one pathogen-associated gene target in 91% (163/179) of soils and a median of 3 (IQR = 1, 5) pathogens. Using a difference-in-difference analysis and adjusting for compound population, visibly wet soil, sun exposure, wealth, temperature, animal presence, and visible feces, we estimate the intervention reduced the probability of detecting ≥1 pathogen gene by 15% (adjusted prevalence ratio, aPR = 0.85; 95% CI: 0.70, 1.0) and the total number of pathogens by 35% (aPR = 0.65; 0.44, 0.95) in soil 24 months following the intervention. These results suggest that the intervention reduced the presence of some fecal contamination in the domestic environment, but pathogen detection remained prevalent 24 months following the introduction of new latrines.

Attributes of drinking water, sanitation, and hygiene associated with microbiological water quality of stored drinking water in rural schools in Mozambique and Uganda

Contaminated drinking water causes morbidity and mortality worldwide, especially in low- and middle-income countries. Drinking water quality has been studied extensively in household settings, but little research is available on drinking water quality in schools. School settings are of particular importance, because children are more susceptible than adults to a variety of diseases from contaminated drinking water. Many school water, sanitation and hygiene (WaSH) interventions have been studied for their efficacy to reduce diarrheal disease incidence, but few have evaluated drinking water quality, which reflects an important exposure pathway between WaSH services and health outcomes. Using school surveys developed from internationally established WaSH indicators and field microbiological water quality tests, we studied 374 rural schools in Mozambique and Uganda to understand the association between specific WaSH services and drinking water microbiological contamination, specifically testing most probable number (MPN) of Escherichia coli, an indicator of fecal contamination, per 100 mL. In Mozambique and Uganda, 71% and 83% respectively of rural schools had low risk drinking water quality (<1 E. coli/100 mL); thirteen percent and seven percent had very high-risk water quality (≥100 E. coli/100 mL). When accounting for all WaSH services studied, schools that used an improved-type water source had 0.22 times less E. coli in stored drinking water in Mozambique (95% CI: 0.07, 0.65) and 0.12 times less E. coli in Uganda (95% CI: 0.02, 0.80). In Mozambique, use of a water source within 30 minutes for travel and collection and the presence of water and soap/ash for handwashing were also significantly associated with less E. coli in drinking water. The findings of this study provide public health practitioners with implementable WaSH services to improve school drinking water quality, which has implications for the health, learning environment, and cognitive development of school children in rural Mozambique and Uganda.

Longitudinal Effects of a Sanitation Intervention on Environmental Fecal Contamination in a Cluster-Randomized Controlled Trial in Rural Bangladesh

Household latrine access generally is not associated with reduced fecal contamination in the environment, but its long-term effectiveness has not been measured. We conducted an environmental assessment nested within the WASH Benefits Bangladesh randomized controlled trial (NCT01590095). We quantified E. coli and fecal coliforms in samples of stored drinking water, child hands, mother hands, soil, and food among a random sample of households from the sanitation and control arms of the trial. Samples were collected during eight quarterly visits approximately 1-3.5 years after intervention initiation. Overall, there were no substantial differences in environmental fecal contamination between households enrolled in the sanitation and control arms. Statistically significant reductions were found in stored water and child hands after pooling across sampling rounds, but the effects were small and not consistent across rounds. In addition, we assessed potential effect modification of intervention effects by follow-up time, season, wealth, community-level latrine density and coverage, population density, and domestic animal ownership. While the intervention had statistically significant effects within some subgroups, there were no consistent patterns of effect modification. Our findings support a growing consensus that on-site latrines are insufficient to prevent fecal contamination in the rural household environment.

Evaluation of Low-Cost Phage-Based Microbial Source Tracking Tools for Elucidating Human Fecal Contamination Pathways in Kolkata, India

Phages, such as those infecting Bacteroides spp., have been proven to be reliable indicators of human fecal contamination in microbial source tracking (MST) studies, and the efficacy of these MST markers found to vary geographically. This study reports the application and evaluation of candidate MST methods (phages infecting previously isolated B. fragilis strain GB-124, newly isolated Bacteroides strains (K10, K29, and K33) and recently isolated Kluyvera intermedia strain ASH-08), along with non-source specific somatic coliphages (SOMCPH infecting strain WG-5) and indicator bacteria (Escherichia coli) for identifying fecal contamination pathways in Kolkata, India. Source specificity of the phage-based methods was first tested using 60 known non-human fecal samples from common animals, before being evaluated with 56 known human samples (municipal sewage) collected during both the rainy and dry season. SOMCPH were present in 40-90% of samples from different animal species and in 100% of sewage samples. Phages infecting Bacteroides strain GB-124 were not detected from the majority (95%) of animal samples (except in three porcine samples) and were present in 93 and 71% of the sewage samples in the rainy and dry season (Mean = 1.42 and 1.83 log10PFU/100mL, respectively), though at lower levels than SOMCPH (Mean = 3.27 and 3.02 log10PFU/100mL, respectively). Phages infecting strain ASH-08 were detected in 89 and 96% of the sewage samples in the rainy and dry season, respectively, but were also present in all animal samples tested (except goats). Strains K10, K29, and K30 were not found to be useful MST markers due to low levels of phages and/or co-presence in non-human sources. GB-124 and SOMCPH were subsequently deployed within two low-income neighborhoods to determine the levels and origin of fecal contamination in 110 environmental samples. E. coli, SOMCPH, and phages of GB-124 were detected in 68, 42, and 28% of the samples, respectively. Analyses of 166 wastewater samples from shared community toilets and 21 samples from sewage pumping stations from the same districts showed that SOMCPH were present in 100% and GB-124 phages in 31% of shared toilet samples (Median = 5.59 and <1 log10 PFU/100 mL, respectively), and both SOMCPH and GB-124 phages were detected in 95% of pumping station samples (Median = 5.82 and 4.04 log10 PFU/100 mL, respectively). Our findings suggest that GB-124 and SOMCPH have utility as low-cost fecal indicator tools which can facilitate environmental surveillance of enteric organisms, elucidate human and non-human fecal exposure pathways, and inform interventions to mitigate exposure to fecal contamination in the residential environment of Kolkata, India.

Monitoring of diverse enteric pathogens across environmental and host reservoirs with TaqMan array cards and standard qPCR: a methodological comparison study

BACKGROUND

Multiple bacteria, viruses, protists, and helminths cause enteric infections that greatly impact human health and wellbeing. These enteropathogens are transmited via several pathways through human, animal, and environmental reservoirs. Individual qPCR assays have been extensively used to detect enteropathogens within these types of samples, whereas the TaqMan array card (TAC), which allows simultaneous detection of multiple enteropathogens, has only previously been validated in human clinical samples.

METHODS

In this methodological comparison study, we compared the performance of a custom 48-singleplex TAC relative to standard qPCR. We established the sensitivity and specificity of each method for the detection of eight enteric targets, by using spiked samples with varying levels of PCR inhibition. We then tested the prevalence and abundance of pathogens in wastewater from Melbourne (Australia), and human, animal, and environmental samples from informal settlements in Suva, Fiji using both TAC and qPCR.

FINDINGS

Both methods exhibited similarly h specificity (TAC 100%, qPCR 94%), sensitivity (TAC 92%, qPCR 100%), and quantitation accuracy (TAC 91%, qPCR 99%) in non-inhibited sample matrices with spiked gene fragments. PCR inhibitors substantially affected detection via TAC, though this issue was alleviated by ten-fold sample dilution. Among samples from informal settlements, the two techniques performed similarly for detection (89% agreement) and quantitation (R² 0·82) for the eight enteropathogen targets. The TAC additionally included 38 other enteric targets, enabling detection of diverse faecal pathogens and extensive environmental contamination that would be prohibitively labour intensive to assay by standard qPCR.

INTERPRETATION

The two techniques produced similar results across diverse sample types, with qPCR prioritising greater sensitivity and quantitation accuracy, and TAC trading small reductions in these for a cost-effective larger enteropathogen panel enabling a greater number of enteric pathogens to be analysed concurrently, which is beneficial given the abundance and variety of enteric pathogens in environments such as urban informal settlements. The ability to monitor multiple enteric pathogens across diverse reservoirs could allow better resolution of pathogen exposure pathways, and the design and monitoring of interventions to reduce pathogen load.

FUNDING

Wellcome Trust Our Planet, Our Health programme.

Effects of an urban sanitation intervention on childhood enteric infection and diarrhea in Maputo, Mozambique: A controlled before-and-after trial

We conducted a controlled before-and-after trial to evaluate the impact of an onsite urban sanitation intervention on the prevalence of enteric infection, soil transmitted helminth re-infection, and diarrhea among children in Maputo, Mozambique. A non-governmental organization replaced existing poor-quality latrines with pour-flush toilets with septic tanks serving household clusters. We enrolled children aged 1-48 months at baseline and measured outcomes before and 12 and 24 months after the intervention, with concurrent measurement among children in a comparable control arm. Despite nearly exclusive use, we found no evidence that intervention affected the prevalence of any measured outcome after 12 or 24 months of exposure. Among children born into study sites after intervention, we observed a reduced prevalence of Trichuris and Shigella infection relative to the same age group at baseline (<2 years old). Protection from birth may be important to reduce exposure to and infection with enteric pathogens in this setting.

Quantitative Microbial Risk Assessment of Pediatric Infections Attributable to Ingestion of Fecally Contaminated Domestic Soils in Low-Income Urban Maputo, Mozambique

Rigorous studies of water, sanitation, and hygiene interventions in low- and middle-income countries (LMICs) suggest that children are exposed to enteric pathogens via multiple interacting pathways, including soil ingestion. In 30 compounds (household clusters) in low-income urban Maputo, Mozambique, we cultured Escherichia coli and quantified gene targets from soils (E. coli: ybbW, Shigella/enteroinvasive E. coli (EIEC): ipaH, Giardia duodenalis: β-giardin) using droplet digital PCR at three compound locations (latrine entrance, solid waste area, dishwashing area). We found that 88% of samples were positive for culturable E. coli (mean = 3.2 log10 CFUs per gram of dry soil), 100% for molecular E. coli (mean = 5.9 log10 gene copies per gram of dry soil), 44% for ipaH (mean = 2.5 log10), and 41% for β-giardin (mean = 2.1 log10). Performing stochastic quantitative microbial risk assessment using soil ingestion parameters from an LMIC setting for children 12-23 months old, we estimated that the median annual infection risk by G. duodenalis was 7100-fold (71% annual infection risk) and by Shigella/EIEC was 4000-fold (40% annual infection risk) greater than the EPA's standard for drinking water. Compounds in Maputo, and similar settings, require contact and source control strategies to reduce the ingestion of contaminated soil and achieve acceptable levels of risk.

Associations among Household Animal Ownership, Infrastructure, and Hygiene Characteristics with Source Attribution of Household Fecal Contamination in Peri-Urban Communities of Iquitos, Peru

Using previously validated microbial source tracking markers, we detected and quantified fecal contamination from avian species and avian exposure, dogs, and humans on household cooking tables and floors. The association among contamination, infrastructure, and socioeconomic covariates was assessed using simple and multiple ordinal logistic regressions. The presence of Campylobacter spp. in surface samples was linked to avian markers. Using molecular methods, animal feces were detected in 75.0% and human feces in 20.2% of 104 households. Floors were more contaminated than tables as detected by the avian marker Av4143, dog marker Bactcan, and human marker Bachum. Wood tables were consistently more contaminated than non-wood surfaces, specifically with the mitochondrial avian markers ND5 and CytB, fecal marker Av4143, and canine marker Bactcan. Final multivariable models with socioeconomic and infrastructure characteristics included as covariates indicate that detection of avian feces and avian exposure was associated with the presence of chickens, maternal age, and length of tenancy, whereas detection of human markers was associated with unimproved water source. Detection of Campylobacter in surface samples was associated with the avian fecal marker Av4143. We highlight the critical need to detect and measure the burden of animal fecal waste when evaluating household water, hygiene, and sanitation interventions, and the possibility of decreasing risk of exposure through the modification of surfaces to permit more effective household disinfection practices. Animals may be a more important source of household fecal contamination than humans in many low-resource settings, although interventions have historically focused almost exclusively on managing human waste.

Assessing the faecal source sensitivity and specificity of ruminant and human genetic microbial source tracking markers in the central Ethiopian highlands

This study tested genetic microbial source tracking (MST) methods for identifying ruminant‐ (BacR) and human‐associated (HF183/BacR287, BacHum) bacterial faecal contaminants in Ethiopia in a newly created regional faecal sample bank (n = 173). BacR performed well, and its marker abundance was high (100% sensitivity (Sens), 95% specificity (Spec), median log₁₀ 8·1 marker equivalents (ME) g⁻¹ ruminant faeces). Human‐associated markers tested were less abundant in individual human samples (median: log₁₀ 5·4 and 4·2 (ME + 1) g⁻¹) and were not continuously detected (81% Sens, 91% Spec for BacHum; 77% Sens, 91% Spec for HF183/BacR287). Furthermore, the pig‐associated Pig2Bac assay was included and performed excellent (100% Sens, 100% Spec). To evaluate the presence of MST targets in the soil microbiome, representative soil samples were tested during a whole seasonal cycle (n = 60). Only BacR could be detected, but was limited to the dry season and to sites of higher anthropogenic influence (log₁₀ 3·0 to 4·9 (ME + 1) g⁻¹ soil). In conclusion, the large differences in marker abundances between target and non‐target faecal samples (median distances between distributions ≥log₁₀ 3 to ≥log₁₀ 7) and their absence in pristine soil indicate that all tested assays are suitable candidates for diverse MST applications in the Ethiopian area.

Where Shared Sanitation is the Only Immediate Option: A Research Agenda for Shared Sanitation in Densely Populated Low-Income Urban Settings

Shared sanitation is not currently accepted within the international normative definitions of "basic" or "safely managed" sanitation. We argue that pro-poor government strategies and investment plans must include high-quality shared sanitation as an intermediate step in some densely populated urban areas. User experience must be considered in establishing the definition of high quality. We call for additional research on effective interventions to reach these quality standards and for the development of rigorous measures applicable to global monitoring.

Validation of microbial source tracking markers for the attribution of fecal contamination in indoor-household environments of the Peruvian Amazon

The performance of eight microbial source tracking (MST) markers was evaluated in a low-resource, tropical community located in Iquitos, Peru. Fecal samples from humans, dogs, cats, rats, goats, buffalos, guinea-pigs, chickens, ducks, pigeons, and parrots were collected (n = 117). All samples were tested with human (BacHum, HF183-Taqman), dog (BactCan), pig (Pig-2-Bac), and avian (LA35, Av4143, ND5, cytB) markers using quantitative PCR (qPCR). Internal validity metrics were calculated using all animal fecal samples, as well as animal fecal samples contextually relevant for the Peruvian Amazon. Overall, Pig-2-Bac performed best, with 100% sensitivity and 88.5% specificity to detect the correct fecal source. Human-associated markers showed a sensitivity of 80.0% and 76.7%, and specificity of 66.2% and 67.6%. When limiting the analysis to contextually relevant animal fecal samples for the Peruvian Amazon, Av143 surpassed cytB with 95.7% sensitivity and 81.8% specificity. BactCan demonstrated 100% sensitivity and 47.4% specificity. The gene copy number detected by BacHum and HF183-Taqman were positively correlated (Pearson's correlation coefficient: 0.785), as well as avian markers cytB with Av4143 (Pearson's correlation coefficient: 0.508) and nd5 (Pearson's correlation coefficient: 0.949). These findings suggest that markers such as Av4143, Pig2Bac, cytb and BacHum have acceptable performance to be impactful in source attribution studies for zoonotic enteric disease transmission in this and similar low-resource communities.

A New Hypothesis on Informal Land Supply, Livelihood, and Urban Form in Sub-Saharan African Cities

In sub-Saharan Africa, the urban majorities are financially excluded from the formal housing markets and reside in informal settlements. Limited knowledge on the development of informal settlements compromises the efficacy of urban planning and policies targeting such areas. This study presents an analysis of informal urban land use in four major cities in East Africa, as well as an analysis of urban form and household conditions in a case study area in each city. The study found more compact urban form, higher levels of tenants and overcrowding, and lower levels of access to water and sanitation in the examined cities with limited informal urban land use. The study argues that government repression of informal urban development decreases informal land supply and leads to increased competition in the informal land market, causing higher costs of accommodation and consequent fewer household resources for investments in infrastructure and thereby more compromised livelihood. The study argues that governments should accept some modes of informal development, simplify the urban development administration processes, and use technological innovation in land surveys and management, in order to lower costs of accommodation and improve livelihoods for the urban majority financially excluded from the formal housing market in East Africa.

Water, sanitation, and hygiene (WASH) factors associated with growth between birth and 1 year of age in children in Soweto, South Africa: results from the Soweto Baby WASH study

Interventions to reduce undernutrition and improve child growth have incorporated improved water, sanitation, and hygiene (WASH) as part of disease transmission prevention strategies. Knowledge gaps still exist, namely, when and which WASH factors are determinants for growth faltering, and when WASH interventions are most effective at improving growth. This study drew cross-sectional data from a longitudinal cohort study and used hierarchical regression analyses to assess associations between WASH factors: water index, sanitation, hygiene index, and growth: height-for-age (HAZ), weight-for-age (WAZ), weight-for-height (WHZ) at 1, 6, and 12 months postpartum among infants a priori born healthy in Soweto, Johannesburg. Household access to sanitation facilities that were not safely managed was associated with a decrease in HAZ scores at 1 month (β = -2.24) and 6 months (β = -0.96); a decrease in WAZ at 1 month (β = -1.21), 6 months (β = -1.57), and 12 months (β = -1.92); and finally, with WHZ scores at 12 months (β = -1.94). Counterintuitively, poorer scores on the hygiene index were associated with an increase at 1 month for both HAZ (β = 0.53) and WAZ (β = 0.44). Provision of safely managed sanitation at household and community levels may be required before improvements in growth-related outcomes are obtained.

Microbial Indicators of Fecal Pollution: Recent Progress and Challenges in Assessing Water Quality

PURPOSE OF REVIEW

Fecal contamination of water is a major public health concern. This review summarizes recent developments and advancements in water quality indicators of fecal contamination.

RECENT FINDINGS

This review highlights a number of trends. First, fecal indicators continue to be a valuable tool to assess water quality and have expanded to include indicators able to detect sources of fecal contamination in water. Second, molecular methods, particularly PCR-based methods, have advanced considerably in their selected targets and rigor, but have added complexity that may prohibit adoption for routine monitoring activities at this time. Third, risk modeling is beginning to better connect indicators and human health risks, with the accuracy of assessments currently tied to the timing and conditions where risk is measured. Research has advanced although challenges remain for the effective use of both traditional and alternative fecal indicators for risk characterization, source attribution and apportionment, and impact evaluation.

Self-Reported Versus Observed Measures: Validation of Child Caregiver Food Hygiene Practices in Rural Malawi

Few studies have attempted to measure the differences between self-reported and observed food hygiene practices in a household setting. We conducted a study to measure the level of agreement between self-reported and observed food hygiene practices among child caregivers with children under the age of five years in rural Malawi. Fifty-eight child caregivers from an intervention and 29 from a control group were recruited into the study. At the end of a nine-month food hygiene intervention, household observations were conducted followed by self-reported surveys. Overall, practices were found to be more frequently reported than observed in both groups. However, the difference between self-reports and observed practices was minimal in the intervention compared to the control group. The odds ratio results confirm that more desirable practices were observed in the intervention group compared to the control group. Despite the effects of reactivity during observations, the study results imply that the intervention group did not just improve their knowledge, but also translated the messaging into better practice. Researchers and implementing agencies in water, sanitation and hygiene and food hygiene sector should ensure that interventions are context-appropriate, and that effective methods of observation are used to confirm any reported effects of an intervention.