A One Health Genomic Investigation of Gentamicin Resistance in Escherichia coli from Human and Chicken Sources in Canada, 2014 to 2017

We investigated whether gentamicin resistance (Gen(r)) in Escherichia coli isolates from human infections was related to Gen(r) E. coli in chicken and whether resistance may be due to coselection from use of lincomycin-spectinomycin in chickens on farms. Whole-genome sequencing was performed on 483 Gen(r) E. coli isolates isolated between 2014 and 2017. These included 205 human-source isolates collected by the Canadian Ward (CANWARD) program and 278 chicken-source isolates: 167 from live/recently slaughtered chickens (animals) and 111 from retail chicken meat collected by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). The predominant Gen(r) gene was different in human and chicken sources; however, both sources carried aac(3)-11d, aac(3)-Vla, and aac(3)-lVa. Forty-one percent of human clinical isolates of Gen(r) E. coli contained a bla(CTX-M) extended-spectrum beta-lactamase (ESBL) gene (84/205), and 53% of these were sequence type 131 (ST131). Phylogenomic analysis revealed a high diversity of Gen(r) isolates; however, there were three small clusters of closely related isolates from human and chicken sources. Gen(r) and spectinomycin resistance (Spec(r)) genes were colocated in 148/167 (89%) chicken animal isolates, 94/111 (85%) chicken retail meat isolates, and 137/205 (67%) human-source isolates. Long-read sequencing of 23 isolates showed linkage of the Gen(r) and Spec genes on the same plasmid in 14/15 (93%) isolates from chicken(s) and 6/8 (75%) isolates from humans. The use of lincomycin-spectinomycin on farms may be coselecting for gentamicin-resistant plasmids in E. coli in broiler chickens; however, Gen(r) isolates and plasmids were mostly different in chickens and humans.