Faecal Pathogen Survival and Risks of Use of Ecological Sanitation By-Products in Burera District, Rwanda: A Quantitative Microbial Risks Assessment

Reuse of human excreta and derivatives is becoming a common practice in areas with agricultural predominance. While in situ treated faeces through ecological sanitation (Ecosan), known as “faecal by-products” are being used to sustain soil nutrients and improve on-site sanitation, the concern remains about the health risks related to the survival of pathogens in these by-products in the community of farmers. This study assessed the survival of faecal pathogens and estimated microbial risks associated with the use of Ecosan faecal by-products in agriculture. The quantitative microbial risks assessment (QMRA) framework was used to estimate the risks posed by each faecal pathogen in solid and semi-solid faecal by-products under the probabilistic model of Monte Carlo simulation. Ascaris lumbricoides (6.5 eggs/gr), Taenia species (0.3 egg/gr), Schistosoma species (9.3 cercariae/gr), Entamoeba species (4.4 cysts/gr), and Escherichia coli (451 Cfu/gr) were detected in semi-solid faecal products. Exposure scenarios were observed throughout four critical points: vault faecal by-products removal/unloading, transport, collection, and application of faecal by-products in the gardens. Due to the presence of eggs and cysts, an estimated annual risk of infections was found in semi-solid faecal by-products with Schistosoma species (88%) and Ascaris lumbricoides (90%). Both concentrations were above World Health organisation (WHO) standards of associated infective risks of 0–10% of helminths in faecal sludge applied in the gardens. The users of faecal by-products, particularly farmers are exposed not only to high concentrations of helminth eggs but also to protozoa and bacteria with infective risks of Entamoeba species (99%) and E. coli species (62%). A stepwise implementation of faecal pathogens die-off during treatment of faecal by-products in compliance with the WHO’s 2018 guidelines can prevent the use of unsanitary faecal by-products. According to these findings, the proper control of intestinal protozoa and soil-transmitted helminths (STHs) should be enforced through personal protective measures in Burera district, Rwanda.