Detection of amoxicillin-resistant and multidrug-resistant Escherichia coli in young Australian bats (grey-headed flying fox, Pteropus poliocephalus).

Antimicrobial-resistant Escherichia coli have now infiltrated the gut microbiomes of wild animals globally, posing a threat to the health and conservation of endangered species. In previous studies of an Australian fruit bat species, the grey-headed flying fox (GHFF; Pteropus poliocephalus), the prevalence of amoxicillin-resistant E. coli was significantly higher (77.4%) in GHFF pups from South Australia (SA) compared to adult GHFF (3.8%). In rehabilitation settings, amoxicillin is one of the most frequently administered antibiotics to GHFF. Our study aimed to determine the prevalence and genetic characteristics of amoxicillin-resistant E. coli in two additional cohorts of young GHFF: hand-reared pups from New South Wales (NSW) undergoing rehabilitation for release back to wild habitats (n=25) and older juveniles from SA in a pre-release facility (n=30), and compare these with previous findings in GHFF. Amoxicillin-resistant E. coli were cultured from GHFF faecal samples using amoxicillin-supplemented media. Isolates confirmed as E. coli by PCR underwent whole-genome sequencing and antimicrobial susceptibility testing. Amoxicillin-resistant E. coli were identified in 40.0% (10 out of 25) of NSW GHFF pups and 3.3% (1 out of 30) of SA juvenile GHFF. Twelve amoxicillin-resistant E. coli isolates were obtained from 11 bats, with all belonging to anthropogenic-associated lineages. Additional resistance to amoxicillin-clavulanic acid, cephalosporins, tetracyclines, fluoroquinolones and trimethoprim-sulfamethoxazole was detected across the 12 isolates. Overall, 33.3% of GHFF E. coli were multidrug-resistant, and 66.7% had extraintestinal pathogenic traits and were classified as opportunistic pathogens. These findings indicate that the prevalence of amoxicillin-resistant E. coli is significantly higher in GHFF pups than in juvenile and adult GHFF, and carriage may not be long-term. Further research is required to examine the prevalence and dynamics of antibiotic-resistant E. coli in GHFF pups as they mature. The infiltration of antibiotic-resistant E. coli into GHFF microbiomes presents yet another threat to this endangered species and highlights the need for good antimicrobial stewardship when treating wildlife.