Molecular Characterisation of Escherichia coli Collected From an Urban River in Johannesburg, South Africa

Abstract

Diarrheal diseases remain a significant public health concern worldwide, particularly among children under five. Surveillance is primarily focused on clinical samples. However, environmental reservoirs, particularly rivers, are increasingly recognised as critical sources of enteric pathogens. This study used whole-genome sequencing (WGS) to characterise Escherichia coli isolates from the Jukskei River in Johannesburg, South Africa. Twenty-seven E. coli isolates were subjected to pathotype-specific PCR and WGS for characterisation. Diarrheagenic E. coli accounted for 44% (12/27) of the isolates, including enterotoxigenic, atypical enteropathogenic and a hybrid enterotoxigenic-enteroinvasive E. coli. Most isolates (63%, 17/27) were O16:H48, and fimbrial typing revealed nine Fimtypes, with fimH27 being the most prevalent at 56% (15/27). Resistance to ciprofloxacin, sulfamethoxazole and azithromycin was noted in 11% (3/27) of the isolates. The most prevalent virulence-associated genes were fimH, csgA, gad, terC, ompT, iss and yehA-D, associated with adhesion, invasion and stress response. Phylogroup A dominated the collection (70%, 19/27), and phylogenetic analysis revealed diversity among the river isolates. Some genetic links between human and livestock strains were noted, suggesting cross-environmental transmission. These findings highlight the Jukskei River as a potential vehicle for E. coli transmission and underscore the importance of integrated surveillance across the environmental, human and animal sectors.

Keywords: Escherichia coli; Jukskei River; enteropathogenic E. coli; enterotoxigenic E. coli; polymerase chain reaction; whole‐genome sequencing.

FIGURE 1

A 2% (w/v) agarose gel showing the amplification of the uidA gene (556 bp). A 1 kb DNA molecular weight marker was used to size the PCR products of isolates. Lanes 1, 2, 3, 4, 5 and 6 are the isolates ECBR0223, ECGI0523, ECMA0423, ECBU0523, ECBU0723 and ECDA1023, respectively. Lane 7 is the positive control ( Escherichia coli ATCC 35218), and Lane 8 is the NTC (nuclease‐free water).

FIGURE 2

Frequency of VAGs in the 27 Escherichia coli isolates from the Jukskei River.

FIGURE 3

An SNP‐based maximum likelihood Phylogenetic Tree. The tree represents the phylogenetic relationships among the different isolates based on the SNP data obtained from the genomes using Escherichia coli K‐12 MG1655 as a reference genome. The annotations on the tips of the tree provide information about each isolate, including the isolate source (river, human and livestock), phylogroups, MLST, serotypes and FimH types. The tree is presented with branch lengths to emphasise relationships. Cluster I, II and III, are highlighted using light colours (green, blue and purple).