Pathogens and Antimicrobial Resistance Genes in Household Environments: A Study of Soil Floors and Cow Dung in Rural Bangladesh

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Abstract
In low- and middle-income countries, living in homes with soil floors and animal cohabitation may expose children to fecal organisms, increasing risk of enteric and antimicrobial-resistant infections. Our objective was to understand whether cow cohabitation in homes with soil floors in rural Bangladesh contributed to the presence and diversity of potential pathogens and antimicrobial resistance genes (ARGs) in the home. In 10 randomly selected households in rural Sirajganj District, we sampled floor soil and cow dung, which is commonly used as sealant in soil floors. We extracted DNA and performed shotgun metagenomic sequencing to explore potential pathogens and ARGs in each sample type. We detected 6 potential pathogens in soil only, 49 pathogens in cow dung only, and 167 pathogens in both soil and cow dung. Pathogen species with relative abundances >5% in both soil floors and cow dung from the same households included E. coli (N=8 households), Salmonella enterica (N=6), Klebsiella pneumoniae (N=2), and Pseudomonas aeruginosa (N=1). Cow dung exhibited modestly higher pathogen genus richness compared to soil floors (Wilcoxon signed-rank test p=0.002). Using Bray-Curtis dissimilarity, pathogen species community composition differed between floors and cow dung (PERMANOVA pE. coli , Salmonella enterica , Klebsiella pneumoniae, and Pseudomonas aeruginosa . Antibiotic resistance genes were found in all samples. In cow dung, the most common genes conferred resistance to the antibiotics lincosamide, rifamycin, cephamycin, and tetracycline. In soil floors, the most common genes conferred resistance to rifamycin, sulfonamides, and aminoglycosides. Household soil and cow dung may be important reservoirs of pathogens and antimicrobial resistance in low-income countries.

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