Distinct population structure and genomic context of narAB between broiler and human clinical Enterococcus isolates—authors’ response

We thank Professor Wong for his commentary on our article ‘Distinct population structure and genomic context of narAB between broiler and human clinical Enterococcus isolates’. He raises two concerns: firstly, the hypothesized linkage between narAB and clinically relevant resistance genes; and secondly, the enterococcal genetic structure between human and broiler host species. For ionophore use in broilers to drive antimicrobial resistance (AMR) to clinically relevant antibiotics in human isolates through co-selection, narAB and MIA resistance genes must be co-inherited specifically within the broiler population experiencing ionophore selection pressure. The statistical associations that Wong references, observed across all populations from multiple host species, cannot distinguish between (i) ionophore use in broilers co-selecting for resistance to medically important antibiotic (MIA) genes versus (ii) hospital antibiotic use co-selecting for multiple resistance genes including narAB in human isolates. Our study addresses this by examining the genomic context separately in broiler and human populations. In broiler isolates where ionophore selection occurs: