Widespread occurrence of Enteropathogenic Escherichia coli and novel bfpA variants in Australian fruit bats

Enteropathogenic Escherichia coli (EPEC) is an important cause of diarrhoeal disease in human infants. EPEC is characterised by specific virulence factors including intimin (encoded by the eae gene) and bundle forming pili (Bfp; encoded by the bfp operon, including the bfpA gene for the major pilus subunit). By definition, Bfp are only present in typical EPEC (tEPEC). Humans are the only known natural host of tEPEC. Here we investigated the occurrence and genetic characteristics of EPEC from an Australian fruit bat species, the grey-headed flying-fox. Whole genome sequencing of 61 E. coli isolates from fruit bat faeces revealed that 13 were tEPEC, 11 of which had novel bfpA variants. HEp-2 cell adhesion assays indicated that every tEPEC strain carried a functional bfp operon that encoded localised adherence to human-derived epithelial cells in vitro. Additional analysis of faecal samples using an EPEC-specific multiplex PCR, identified tEPEC in fruit bats from three geographic areas in eastern Australia, with sampling conducted on six occasions over a four-year period (mean occurrence 19.1%, range 1.3–87.0%). This is the first report of the widespread occurrence of tEPEC in a non-human host over extensive geographical and temporal scales. Our findings suggest that fruit bats are a natural host of tEPEC and that host-specific lineages may have evolved in bats to comprise part of their commensal microbiome.