Novel strains of typical enteropathogenic Escherichia coli (tEPEC) in Pteropus bats, including the first report of a phylogroup G tEPEC

Typical enteropathogenic <i>Escherichia coli</i> (tEPEC) is an important cause of prolonged diarrhoea in human infants. Humans are considered the primary reservoir and the only natural host of human-associated tEPEC. Recently, bat-specific tEPEC lineages were consistently detected in an Australian fruit bat species (<i>Pteropus poliocephalus</i>; grey-headed flying fox), indicating that <i>P. poliocephalus</i> is also a natural tEPEC host. tEPEC are differentiated from other pathogenic <i>E. coli</i> by the presence of the bundle-forming pilus (<i>bfp</i>) operon. In this study, we characterize two additional bat-associated tEPEC strains, the first (FF593) from <i>P. poliocephalus</i> and the second (FF618) from another Australian <i>Pteropus</i> species, <i>Pteropus conspicillatus</i> (spectacled flying fox). Whole-genome sequencing of the two bat tEPEC isolates revealed that both strains belonged to novel bat tEPEC lineages (FF593 to Clade F and FF618 to Clade E) and both carried novel <i>bfp</i> operons. FF593 is the first report of a phylogroup G tEPEC strain, and FF618 was phylogenetically related to a human aEPEC lineage (ST1041). Phylogenetic analysis of 11 bat and 11 human <i>bfp</i> operons determined that bat and human variants belong to separate lineages but share an evolutionary origin. This study provides further evidence that diverse bat-specific tEPEC lineages and <i>bfp</i> operons have evolved in Australian <i>Pteropus</i> bats and suggests that multiple species of Australian <i>Pteropus</i> bats are natural hosts for bat-specific tEPEC strains.