Virulence and phylogenetic analysis of enteric pathogenic Escherichia coli isolated from children with diarrhoea in South Africa

•Diarrhoeagenic Escherichia coli pathotypes were identified using multiplex polymerase chain reaction (PCR).•The enterotoxigenic (ETEC) pathotype was predominant, followed by the enteroaggregative (EAEC), enteropathogenic (EPEC) and enterohaemorrhagic (EHEC) pathotypes.•EAEC/ETEC was the predominant hybrid pathotype detected.•The phylogenetic groups of pathotypes were determined using Clermont quadruplex PCR.•Phylogroup B2 was predominant, followed by phylogroups B1, C and E, and A and D.