Appl Environ Microbiol. 2021 Mar 12:AEM.03037-20. doi: 10.1128/AEM.03037-20. Online ahead of print.
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.