Antimicrobial resistance, genomic, and public health insights into Enterococcus spp. from Australian cattle

Enterococci are opportunistic, sometimes life-threatening pathogens with increasing antimicrobial resistance, particularly among clinical human isolates in Australia. While recent studies have ruled out pigs and chickens as major reservoirs of resistant enterococci, the role of cattle remains unclear. This study examines the antimicrobial resistance (AMR) profiles of enterococci from Australian cattle and explores the phylogenetic relationship of bovine E. faecium with isolates from other livestock and human sepsis cases.

A total of 1001 bovine faecal samples were tested, yielding E. faecium (n = 343), E. faecalis (n = 92), and E. hirae (n = 284). Minimum inhibitory concentration assays were conducted against 15 antimicrobials. A subset of 67 isolates underwent whole genome sequencing (WGS).

Most isolates were wild-type to all tested antimicrobials. Resistance was most common to erythromycin in E. faecium (18.7 %), daptomycin in E. faecalis (12.1 %), and tetracycline in E. hirae (13.3 %). A single E. faecalis isolate was non-wild-type to vancomycin, and nine isolates (E. faecium n = 4, E. faecalis n = 2, E. hirae n = 3) showed linezolid resistance. However, WGS did not detect known resistance genes or mutations for vancomycin or linezolid. Phylogenetic analysis revealed that bovine E. faecium clustered with other livestock isolates and vancomycin-negative human isolates.

Antimicrobial resistance among enterococci from Australian cattle is low. These strains are genetically distinct from vancomycin-resistant E. faecium circulating in hospitals, suggesting that cattle are not a significant source of clinically relevant AMR enterococci in Australia.