Animal husbandry and environmental conditions are associated with cefotaxime-resistant <i>Escherichia coli</i> 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. While studies have detected AMR in soil in various settings, dominant contributors to domestic soil contamination with antimicrobial-resistant organisms in low-income countries remain unidentified. We conducted a cross-sectional study with 237 households in southern Malawi, specifically peri-urban Bangwe near Blantyre, to identify factors associated with the abundance of cefotaxime<i>-</i>resistant <i>E. coli</i> in yard soil. Enumerators employed structured surveys and sampled 30 cm² of yard soil per household. We used IDEXX Quanti-Tray/2000 with Colilert-18 and cefotaxime supplement to enumerate the most probable number (MPN) of cefotaxime-resistant <i>E. coli</i> per dry gram of soil. We conducted multivariable regression to assess associations between the abundance of cefotaxime-resistant <i>E. coli</i> and household sanitation, animal ownership and management, child health and antibiotic use, and weather. Of 228 soil samples, 68% harbored cefotaxime-resistant <i>E. coli</i> at a mean of 0.90 log₁₀-MPN/dry gram<i>.</i> Compared to households without animals, households had approximately 0.50-log lower mean cefotaxime-resistant <i>E. coli</i> abundance in soil if animals were enclosed at night and 0.50-log higher abundance if they were not (p-values<0.005). Additionally, samples had approximately 0.70-log lower mean cefotaxime-resistant <i>E. coli</i> abundance if soil was dry at the time of collection and if it came from a household in the top wealth quintile (p-values<0.005). Daytime animal confinement, household sanitation, child health, antibiotic use, rainfall, temperature and ambient humidity were not associated with cefotaxime-resistant <i>E. coli</i> abundance. Findings suggest that animal husbandry and soil moisture had stronger associations with cefotaxime-resistant <i>E. coli</i> in soil compared to sanitation or antibiotic use. These results underscore the importance of a One Health approach and the relevance of domestic animals and environmental factors to AMR in soil. Studies should quantify soilborne AMR exposure and evaluate associations with specific animal management/enclosure practices.