Genomic Analysis of Emerging Florfenicol-Resistant Campylobacter coli Isolated from the Intestinal Cecal Contents of Cattle in the United States

Objective: Genomic analyses were performed on florfenicol resistant (FFNR) Campylobacter coli (C. coli) isolated from cattle and the cfr(C) gene-associated multi-drug resistance (MDR) plasmid was characterized. Methods: Sixteen FFNR C. coli isolates recovered between 2013-2018 from beef cattle were sequenced. SNPs across the genome and the structures of MDR plasmids were investigated. Conjugation was performed to determine the transferability of cfr(C) associated MDR plasmids. The spectrum of resistance encoded by the cfr(C) gene was further investigated by agar dilution. Results: All 16 FFNR isolates were MDR and exhibited co-resistance to ciprofloxacin, nalidixic acid, clindamycin and tetracycline. All isolates carried aph(3′)-III, hph, ΔaadE (truncated), blaOXA-61, cfr(C), and tet(O) genes plus a mutation of GyrA T86I. The cfr(C), aph(3′)-III, hph ΔaadE, and tet(O) genes were co-located on transferable MDR plasmids with size 48-50 kb. These plasmids showed high sequence homology with the pTet plasmid, and carried several Campylobacter virulence genes. The cfr(C) gene conferred resistance to florfenicol (8-32 µg/ml), clindamycin (512-1,024 µg/ml), linezolid (128-512 µg/ml), and tiamulin (1,024 µg/ml). Phylogenetic analysis showed SNP differences ranging from 11-2,248 among the 16 isolates. Conclusions: The results showed that the cfr(C) gene located in the conjugative pTet MDR/virulence plasmid is present in diverse strains, where it confers high levels of resistance to several antimicrobials, including linezolid, a critical drug for treating Gram positive bacterial infections in humans. This study highlights the power of genomic antimicrobial resistance and provides information that is needed for accurate risk assessment and mitigation strategies.