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

Abstract

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 pathogenassociated 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.

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

“…As the diagnostic accuracy framework is currently limited to binary outcomes, analysis of such high-prevalence indicators would benefit from the development of analogous approaches for continuous outcomes. Given the intermingling in low-income settings of humans and animals, and their gut microbiomes, alternative FST targets such as mitochondrial DNA could prove more accurate. , Recent technological advances also present opportunities for new approaches that might bypass the limitations of the current FST paradigm, including portable, long-read sequencing platforms for metagenomic-based source tracking and parallel PCR platforms that render simultaneous analysis of multiple FST markers and comprehensive direct pathogen detection increasingly feasible. ,− These technologies will also need to overcome the substantial variability, limited analytical sensitivity, and matrix interference characteristic of environmental microbial assessments …”

Applying a WASH Risk Assessment Tool in a Rural South African Setting to Identify Risks and Opportunities for Climate Resilient Communities

“…The pit latrines are not often well constructed and are not designed to be resilient to seasonal variation or seasonal shocks, such as high rainfall events. Flooding of these latrines increases possible exposure to disease-causing pathogens leading to a rise in illnesses [ 38 , 39 ]. Individuals using such facilities are at a disproportionately high risk of sanitation-related diseases including diarrhea, gastroenteritis, and hookworm, compared to those who use piped sewerage facilities [ 40 ].…”

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 five years post-intervention

“…We are sampling environmental compartments at a randomly selected subset of 100 intervention and 100 control compounds to represent compound-and household-level exposures [37]. At the entrance to the compound latrine we collect soil, flies, and a large volume air sample, as well as fecal sludge from the latrine or septic tank and any animal feces observed in the shared outdoor space [49,50,56,57]. One household is selected at random among the households in the compound with children enrolled in the child health study, from which we collect swabs of flooring at the household entrance, flies in cooking area, prepared child's food, stored drinking water, and water from the household's primary source [52,58,59].…”

“…Molecular detection of selected enteric and non-enteric pathogens and fecal source tracking (FST) markers is performed for environmental samples from both the private (compound & household) and public domains using a second custom TAC [49,56,73,74] [53,75,76], other human pathogens detectable in feces (SARS-CoV-2, Zika virus, HIV proviral DNA; Plasmodium spp. ; Mycobacterium tuberculosis) [77][78][79][80], FST markers (human, poultry, and canine mitochondrial DNA; avian 16S rRNA) [81,82], and general bacterial and anthropogenic pollution/antimicrobial resistance markers (bacterial 16S rRNA; class 1 integron-integrase gene intl1) [83,84].…”