Genomic, Antimicrobial Resistance, and Public Health Insights into Enterococcus spp. from Australian Chickens

Abstract

Due to Australia’s management of antimicrobial use in poultry, particularly the discontinued use of avoparcin for nearly 20 years, it is hypothesized that vancomycin-resistant enterococci associated with human disease are not derived from poultry isolates. This study evaluated antimicrobial resistance (AMR) of five enterococcal species isolated from Australian meat chickens, genomic features of Enterococcus faecium and Enterococcus faecalis, and the phylogenetic relationship of the poultry-derived E. faecium with isolates from human sepsis cases. All enterococcal isolates from chicken ceca were subjected to antimicrobial susceptibility testing. E. faecium and E. faecalis underwent whole-genome sequencing. E. faecium was compared at the core genome level to a collection of human isolates (n = 677) obtained from cases of sepsis over a 2-year period spanning 2015 to 2016. Overall, 205 enterococci were isolated consisting of five different species. E. faecium was the most frequently isolated species (37.6%), followed by E. durans (29.7%), E. faecalis (20%), E. hirae (12.2%), and E. gallinarum (0.5%). All isolates were susceptible to vancomycin and gentamicin, while one isolate was linezolid resistant (MIC 16 mg/liter). Core genome analysis of the E. faecium demonstrated two clades consisting predominantly of human or chicken isolates in each clade, with minimal overlap. Principal component analysis for total gene content revealed three clusters comprised of vanA-positive, vanB-positive, and both vanA- and vanB-negative E. faecium populations. The results of this study provide strong evidence that Australian chicken E. faecium isolates are unlikely to be precursor strains to the currently circulating vancomycin-resistant strains being isolated in Australian hospitals.

Antimicrobial Resistance in Porcine Enterococci in Australia and the Ramifications for Human Health

“…E. faecium in pigs did not harbor the vanA or vanB operons, which are commonly found in the major hospital-adapted strains. As hypothesized in a recent study by O'Dea et al, it appears that the genetic makeup of this subset of enterococci found in chickens, humans, and now pigs does not favor the uptake of vanA or vanB operon-containing genetic elements (22). Moreover, MLST, PCA, and SNPbased phylogenetic analysis indicate some similarities within the populations of E. faecium in pigs and humans.…”

“…A recent study performed on enterococci from Australian meat chickens found clinical resistance to a number of antimicrobials. The study, however, did not identify any resistance to vancomycin (22), providing evidence of success in antimicrobial stewardship measures. Moreover, E. faecium from meat chickens was found to be genetically distinct from hospital-adapted strains.…”

Antimicrobial Resistance of Campylobacter jejuni, Escherichia coli and Enterococcus faecalis Commensal Isolates from Laying Hen Farms in Spain

“…The value of resistance to vancomycin in E. faecalis found in laying hens was higher than in other animal productions and should be further investigated, as this could represent a source of AMR to this antibiotic. The highest percentage of resistance obtained was for quinupristin-dalfopristin (93.33%), which was expected considering that E. faecalis are intrinsically resistant to this antibiotic [ 44 ]. This antibiotic is very important in hospital intensive care units to treat vancomycin-resistant E. faecium infections [ 45 , 46 ].…”

Country Income Is Only One of the Tiles: The Global Journey of Antimicrobial Resistance among Humans, Animals, and Environment

“…This means that animal bacteria may become resistant under selective pressure; then, bacteria travel from farms to stores, and then they may cause hard-to-treat infections in the final consumer as a consequence [ 48 , 49 , 50 , 51 ]. The relationship between massive use of antibiotics to treat or prevent illnesses or for growth purposes and the consequent emergence of several AMR mechanisms in food animals followed by spread into the environment has been clearly highlighted in several reports [ 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 ]. Very recently, the first cases of linezolid-resistant coagulase-negative staphylococci recovered in healthy turkeys in Egypt have been reported, as did the massive use of antibiotics in African countries in food-producing animals [ 62 , 63 ].…”