Exploring the genetic diversity, virulence and antimicrobial resistance of diarrhoeagenic Escherichia coli from Southern Africa using whole-genome data

Abstract

INTRODUCTION : Previous studies, including our research, provide critical insights on the contamination of food, water and environment in the Southern African Development Community (SADC) with diarrhoeagenic Escherichia coli (DEC). This study used whole‐genome sequencing to investigate the genetic diversity, virulence‐associated factors and antimicrobial resistance (AMR) patterns of DEC isolated from children under 5 years old and food sources in Maputo and compared these findings with publicly available DEC genome assemblies from the Southern Africa region. METHODS : Whole‐genome sequence data from 11 DEC isolates from food, children under 5 and water sources in Maputo, Mozambique, were analysed alongside 125 publicly available DEC genomic assemblies from the SADC region. The latter were retrieved from the EnteroBase database (http://enterobase.warwick.ac.uk) and included isolates previously collected from food, animals and environmental sources. Genomic analyses were performed using the online pipelines provided by the Centre for Genomic Epidemiology (CGE), Denmark. Unsupervised hierarchical clustering was applied to visualize patterns in genetic diversity, AMR, virulence‐associated genes and plasmid content using the R software. RESULTS: Clustering based on single nucleotide polymorphism (SNP) and core genome multilocus sequence typing (cgMLST) alleles revealed associations based on geographic locations, sample niche, pathovar and O:H antigen, pointing to evolutionary relatedness between the clades with principal coordinate analysis uncovering this accounted for 27.55% of the genetic diversity. Virulence‐associated genes encoding for attaching and effacing (eae) (63.97%), heat‐labile toxin (LT) (25.00%) and Shiga toxin 1 (Stx1) (15.44%) were most abundant, with an inverse association between genes encoding for the presence of LT and eae. Resistance to folate pathway antagonists (sulfamethoxazole—55.9%), β‐lactamases (amoxicillin, ampicillin and piperacillin—all 54.4%) and aminoglycoside (streptomycin—55.1%) was most abundant. CONCLUSIONS : The study revealed region‐specific lineages, evidence of horizontal gene transfer and the clustering patterns suggest both localized and cross‐border transmission. The study provides insightful evidence on DEC transmission patterns associated with antimicrobial and disinfectant resistance and associated virulence factors.