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<jats:p>Across the water sector, <jats:italic>Escherichia coli</jats:italic> is the preferred microbial water quality indicator and current guidance upholds that it indicates recent faecal contamination. This has been challenged, however, by research demonstrating growth of <jats:italic>E</jats:italic>. <jats:italic>coli</jats:italic> in the environment. In this study, we used whole genome sequencing to investigate the links between <jats:italic>E</jats:italic>. <jats:italic>coli</jats:italic> and recent faecal contamination in drinking water. We sequenced 103 <jats:italic>E</jats:italic>. <jats:italic>coli</jats:italic> isolates sampled from 9 water supplies in rural Kitui County, Kenya, including points of collection (n = 14) and use (n = 30). Biomarkers for definitive source tracking remain elusive, so we analysed the phylogenetic grouping, multi-locus sequence types (MLSTs), allelic diversity, and virulence and antimicrobial resistance (AMR) genes of the isolates for insight into their likely source. Phylogroup B1, which is generally better adapted to water environments, is dominant in our samples (n = 69) and allelic diversity differences (z = 2.12, p = 0.03) suggest that naturalised populations may be particularly relevant at collection points with lower <jats:italic>E</jats:italic>. <jats:italic>coli</jats:italic> concentrations (&lt;50 / 100mL). The strains that are more likely to have originated from human and/or recent faecal contamination (n = 50), were found at poorly protected collection points (4 sites) or at points of use (12 sites). We discuss the difficulty of interpreting health risk from <jats:italic>E</jats:italic>. <jats:italic>coli</jats:italic> grab samples, especially at household level, and our findings support the use of <jats:italic>E</jats:italic>. <jats:italic>coli</jats:italic> risk categories and encourage monitoring that accounts for sanitary conditions and temporal variability.</jats:p>

Original publication




Journal article




Public Library of Science (PLoS)

Publication Date





e0245910 - e0245910