Distinct population structure and genomic context of NarAB between broiler and human clinical Enterococcus isolates

Abstract Background In recent years, reports have emerged linking the NarAB genes with elevated MICs to non-medically important ionophore coccidiostat class (specifically narasin, salinomycin and maduramycin) and potential co-selection of clinically relevant antibiotic resistance genes in Enterococcus faecalis and Enterococcus faecium. Methods We analysed all publicly accessible E. faecalis (n = 7731) and E. faecium (n = 20 594) genomes, focusing specifically on the genomes from broiler-chicken, turkeys, dogs and human clinical infections. Results The NarAB gene was more prevalent in broiler isolates (26% E. faecalis, 39.2% E. faecium) compared with human clinical isolates (2.8% E. faecalis, 2.0% E. faecium). In addition, genes associated with resistance to medically important antibiotics of clinical importance for E. faecalis and E. faecium infections were not found in the vicinity of the NarAB gene in isolates from broiler-chicken, and this refutes claims of the presence of co-selection between NarAB and medically important antibiotics. In addition, the pattern of genes near NarAB differed between broiler-chicken and human clinical isolates, as did the genomic sequence types isolated from each species. Conclusions These findings indicate that E. faecalis and E. faecium from broiler-chicken are unlikely to contribute resistance genes to human clinical isolates, and this should continue to inform any policy that might limit poultry farmers’ and veterinarians’ access to ionophore coccidiostats in broiler-chicken.