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

Abstract

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 log 10 CFUs per gram of dry soil), 100% for molecular E. coli (mean = 5.9 log 10 gene copies per gram of dry soil), 44% for ipaH (mean = 2.5 log 10 ), and 41% for β-giardin (mean = 2.1 log 10 ). 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.

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

“…The Sanitation, Hygiene, Infant Nutrition Efficacy Project (SHINE) trial in rural Zimbabwe has not yet published the results from a substudy on environmental fecal contamination. In separate analyses of environmental samples collected during MapSan baseline and the 24 month phase, ,, we found widespread fecal contamination in soils and other environmental compartments. At the 12-month MapSan trial phase, Holcomb et al 2021 found the intervention reduced E.…”

“…24,58 Sample Processing. At the Georgia Institute of Technology in Atlanta, GA, USA, we incubated 250 mg of each soil sample at 105 °C for 1 h to determine moisture content 13,59 and then discarded the dry soil. We then extracted total nucleic acids from a separate 1 g (calculated for dry weight) portion of each sample and spiked samples with approximately 10 7 plaque-forming units MS2 (Luminex Corporation, Austin, TX) as an extraction control.…”

“…There is a growing body of literature that indicates soils contaminated by feces in public and domestic environments pose infection risks. − In health impact trials that assess improved onsite sanitation systems, soils are assessed to measure how effectively the intervention sequestered human feces. − Latrines and septic tanks are useful barriers against the transport of human feces into the environment. However, enteric pathogens may still move into soils through open defecation, unhygienic pit emptying, , fecally contaminated greywater, , improper disposal of children’s feces or anal cleansing materials, , latrine flooding, ,, animal feces, − or subsurface transport from unlined pits. − Domestic soils contaminated by enteric pathogens can pose infection risks beyond incidental and direct soil ingestion: contaminated soil may be transported to hands, food, fomites, or household stored water .…”

Microfluidic hotspots in bacteria research: A review of soil and related advances

“…Droplet digital PCR can be combined with fluorescent probes to improve the detection of microbial strains. Recently, ddPCR was used to culture E. coli and quantify gene targets from soils (Capone et al, 2021). Moreover, ddPCR has also been optimized to quantify soil total bacteria and archaea as well as the nitrification (bacterial and archaeal amoA) and denitrification (nirS, nirK, nosZI, nosZII) genes involved in the generation or reduction of the greenhouse gas nitrous oxide (Voegel et al, 2021).…”

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

“…Such data may help explain why some WASH interventions observed improved health outcomes and others did not. 8 There is a growing body of literature that soils contaminated by feces in public and domestic environments pose infection risks. [9][10][11][12][13] In health impact trials that assess improved onsite sanitation systems, soils are assessed to measure how effectively the intervention sequestered human feces.…”