Abstract
<jats:p>In low-resource settings, drinking water is susceptible to faecal contamination, but the epidemiological link between extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in humans and in drinking water is poorly understood. This study characterised E. coli from household drinking water and human clinical samples in a closed setting with the aim of investigating the directionality of ESBL-positive E. coli spread. Sixty E. coli isolates from 38 human clinical and 22 drinking water samples were assessed for resistance to 17 antibiotics and genome-sequenced using Oxford Nanopore long-read technology (ONT). An additional 255 E. coli genomes associated with human infections in the setting were retrieved from public sequence read archives and included in the study. Core-genome alignments were used to build maximum-likelihood phylogenetic trees. To identify transmission events, pairwise single-nucleotide polymorphism (SNP) distances were computed for all strains with a maximum inter-isolate distance of 25 SNPs, defining a transmission network. Escherichia coli strains obtained from human and drinking water sources bore similar resistance genes encoding resistance to tetracycline, aminoglycosides, ciprofloxacin, and β-lactams, including carbapenems, often encoded on plasmids. Screening all 316 isolates for resistance genes reveals that human-derived isolates bore the greatest burden of resistance genes. Evidence of recent E. coli transmission between drinking water sources and of strain sharing among human hosts was observed. Core genome analysis revealed that at least one pair of human and environmental isolates was within the SNP cutoff, implying that some E. coli causing human infection could be traced to drinking water sources.</jats:p>