Genomic characterisation of Escherichia coli isolates from drinking water systems in rural Kenya

Across the water sector, Escherichia coli is the preferred microbial water quality indicator and current guidance upholds that it indicates recent faecal contamination. Use of Escherichia coli as an indicator of faecal contamination has been challenged, however, by research that demonstrates growth of E. coli in the environment. In this study, we used whole genome sequencing to investigate the links between E. coli and health risk from faecal contamination in water supplies and household stored water. We sequenced 108 E. coli isolates sampled from 9 water systems in rural Kitui County, Kenya, including collection (14) and storage (30) sites. We analysed the pan-genome, phylogenetic grouping, multi-locus sequence types (MLSTs), and virulence and antimicrobial resistance (AMR) genes of the isolates.