Environmental exposures associated with the gut microbiome and resistome of pregnant women and children in Northwest Ecuador

Inadequate water, sanitation, and hygiene (WASH) infrastructure may increase exposure to antimicrobial resistance (AMR). In addition, close human-animal interactions and unregulated antibiotic use in livestock facilitate the spread of resistant bacteria. We use metagenomic sequence data and multivariate models to assess how animal exposure and WASH conditions affect the gut resistome and microbiome in 53 pregnant women and 84 children in Ecuador. Here we show improving WASH infrastructure and managing animal exposure may be important in reducing AMR but could also reduce taxonomic diversity in the gut. Escherichia coli, Klebsiella pneumoniae, and clinically relevant antimicrobial resistance genes (ARGs) are detected across all age groups, but the highest abundance is found in children compared to mothers. In mothers, higher animal exposure trends towards a higher number of unique ARGs compared to low animal exposure and is significantly associated with greater taxonomic diversity. In addition, mothers with sewer systems or septic tanks and piped drinking water have fewer unique ARGs compared to those without, and mothers with longer duration of drinking water access have lower total ARG abundance. In contrast, few associations are observed in children, likely due to the dynamic nature of the gut microbiome during early childhood.