Animal husbandry and environmental conditions are associated with cefotaxime-resistant Escherichia coli in yard soil in peri-urban Malawi

Abstract

Soil is an important reservoir for antimicrobial resistance (AMR) and increasingly recognized as a pathogen transmission pathway, especially for young children. However, drivers of domestic AMR soil contamination in low-income countries remain unidentified. We conducted a cross-sectional study with 237 peri-urban households in southern Malawi to identify household and environmental factors associated with cefotaxime-resistant E. coli in yard soil. Enumerators employed structured surveys and sampled 900 cm2 of yard soil per household. We enumerated cefotaxime-resistant E. coli in soil using IDEXX Quanti-Tray/2000 with Colilert-18 and cefotaxime supplement, and assessed associations with household sanitation, animal ownership and management, child health and antibiotic use, and weather. Among children <5 years, 25-90% played, ate, slept, or crawled on the ground outside. Of 233 soil samples, 69% harbored cefotaxime-resistant E. coli at a mean of 0.90 log10 most probable number (MPN) per dry gram. Compared to households without animals, household soil had approximately 0.50-log lower mean cefotaxime-resistant E. coli concentration if animals were enclosed at night and 0.40-log higher concentration if they were not (p-values<0.05). Mean cefotaxime-resistant E. coli concentrations were approximately 0.90-log lower if soil was dry at the time of collection, 0.70-log lower if the household was in the top wealth quintile (p-values<0.005), and 0.30-log lower if any child in the household used antibiotics in the last four weeks (p-value = 0.05). There were no associations with daytime animal confinement, household sanitation, temperature, and ambient humidity. Findings suggest that animal husbandry and soil moisture had stronger associations with cefotaxime-resistant E. coli in soil compared to sanitation or antibiotic use, underscoring the importance of a One Health approach to AMR that incorporates domestic animals and environmental factors. Given children's frequent soil contact, our findings also highlight potential AMR acquisition from soilborne pathways. Studies should quantify soilborne AMR exposure and evaluate associations with animal management/enclosure practices.