Genomic characterization of resistant Escherichia coli isolated from household water in municipal Ibadan, Nigeria

Escherichia coli in water indicates recent faecal contamination and possible presence of enteric pathogens. Strains harbouring virulence and/or antimicrobial resistance genes (ARGs) heighten the public health risk. Although, E. coli contamination of water sources is frequently documented in Nigeria, isolates are typically not characterized. This study whole genome sequenced (WGS) previously isolated E. coli from household water in Ibadan, Nigeria to understand community transmission of this fecal indicator, its role as a resistance gene reservoir and the extent to which household water isolates carry virulence genes. The recent E. coli isolates were antimicrobial susceptibility tested and Illumina sequenced. Multi-Locus Sequence Types (MLST), virulence genes and plasmid replicons were determined using ABRicate. ARGs were detected using AMRFinderplus, while phylogroups and serotypes determined using ClermonTyper and ECTyper, respectively. Phylogenetic relatedness was assessed with RAxML. Of the 97 isolates, most arising from wells across all Ibadan metropolitan Local Government Areas, 39(40.2%) were multidrug resistant (MDR) and 13(15.9%) possessed virulence genes associated with enteroaggregative and enterotoxigenic pathotypes. Thirty-seven ARGs spanning nine antibiotic classes were detected. Most isolates belonged to phylogroup A and B1, comprising 35 unique STs and there were seven expanded clones of four or more isolates. Frequent recovery of MDR and potentially pathogenic E. coli from household water in Ibadan highlights a serious public health threat, particularly as phylogenetic evidence suggests that clonal expansion may be driving AMR transmission. Strengthening household water safety practices and implementing routine genomic surveillance are essential to mitigate waterborne diseases risks and limit AMR dissemination.