Genomic analysis of Campylobacter animal clinical isolates illustrates clonal expansion of antimicrobial-resistant lineages and genomic proximity to human isolates

ABSTRACT Whole-genome sequencing of 114 Campylobacter animal clinical isolates identified tet (O) in 49% and the fluoroquinolone resistance-associated gyrA (T86I) mutation in 32% of isolates. Two Campylobacter coli isolates carried the macrolide resistance mutation 23S(A2075G), including one with concurrent gyrA (T86I). Single-nucleotide polymorphism (SNP) analysis identified host- and geographically associated resistant lineages. Forty-eight isolates (42.1%) were within ≤10 SNPs of a human clinical isolate. These findings illustrate clonal expansion of AMR-associated lineages and genomic overlap between animal and human Campylobacter populations. IMPORTANCE Antimicrobial-resistant Campylobacter in animals may contribute to the population of strains associated with human disease. Genomic analysis of animal clinical isolates identified resistant lineages associated with particular hosts and geographic regions and showed that many isolates were closely related to human clinical isolates. These findings demonstrate the value of integrating veterinary genomic data with public health surveillance to identify circulating Campylobacter lineages of potential animal and human health importance.