Abstract Description

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 recognized as critical sources of enteric pathogens. This study used whole-genome sequencing (WGS) to characterize Escherichia coli isolates from the Jukskei rivers in Johannesburg South Africa. Twenty-seven E. coli isolates were subjected to pathotype-specific polymerase chain reaction (PCR) and WGS for characterization. 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 we 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.