Antimicrobial resistance in porcine enterococci in Australia and ramifications for human health.

Enterococci are ubiquitous opportunistic pathogens that have become a major public health issue globally. The increasing prevalence of antimicrobial resistance in hospital-adapted enterococci have been thought to originate from livestock. However, this association between livestock and hospital-adapted enterococci is currently unclear. This study investigates the antimicrobial susceptibilities of enterococci isolated from pig caecal samples and compares the genomic characteristics of Enterococcus faecium from pigs to those isolated from meat chickens and from human sepsis cases. From 200 caecal samples, antimicrobial susceptibility testing was performed for E. faecium (n=84), E. hirae (n= 36) and E. faecalis (n=17). Whole genome sequencing was performed for all E. faecium isolates which were compared to previously studied isolates from meat chickens and human sepsis cases through bioinformatics analysis.Resistance to erythromycin, gentamicin, tetracycline, ampicillin, daptomycin, virginiamycin and quinupristin-dalfopristin was identified. More importantly, except for a single isolate harbouring the vanC operon, no resistance was observed in all three species to vancomycin, teicoplanin and linezolid which are critically important antimicrobials used for treating enterococcal infections in humans. E. faecium from chickens were genetically distinct from human and pig isolates which were more closely related. Human strains which were closely related to pig strains were not typical "hospital-adapted strains" as previously identified. The results of this study show that enterococci from Australian finisher pigs are not a source of resistance to critically important antimicrobials and E. faecium from pigs are not part of the current human hospital-adapted population. Importance Resistance to the critically important antimicrobials vancomycin, teicoplanin and linezolid were not found in enterococci collected from Australian finisher pigs. However, some antimicrobial resistance was observed. In particular, resistance to quinupristin-dalfopristin, a combination of two streptogramin class antimicrobials, was identified despite the absence of streptogramin use Australia-wide since 2005. Other observed resistance amongst enterococci from pigs include chloramphenicol, erythromycin and tetracycline resistance.Genomic comparison of E. faecium from Australian pigs to isolates collected from previous studies on chickens and humans indicate that E. faecium from pigs are genetically more similar to those of humans than those from chickens. Despite the increased genetic similarities, E. faecium strains from pigs are phylogenetically distinct and did not belong to the dominant sequence types found in hospital-adapted strains causing sepsis in humans. Therefore, the results indicate that Australian finisher pigs are not a source of hospital-adapted E. faecium in Australia.