Oxazolidinone resistance genes in florfenicol-resistant enterococci from beef cattle and veal calves at slaughter.

Background: Linezolid is a critically important oxazolidinone antibiotic used in human medicine. Although linezolid is not licensed for use in food-producing animals, the use of florfenicol in veterinary medicine co-selects for oxazolidinone resistance genes.
Objective: This study aimed to assess the occurrence of cfr, optrA , and poxtA in florfenicol-resistant isolates from beef cattle and veal calves from different herds in Switzerland.
Methods: A total of 618 cecal samples taken from beef cattle and veal calves at slaughter originating from 199 herds were cultured after an enrichment step on a selective medium containing 10 mg/L florfenicol. Isolates were screened by PCR for cfr, optrA , and poxtA which are genes known to confer resistance to oxazolidinones and phenicols. One isolate per PCR-positive species and herd was selected for antimicrobial susceptibility testing (AST) and whole-genome sequencing (WGS).
Results: Overall, 105 florfenicol-resistant isolates were obtained from 99 (16%) of the samples, corresponding to 4% of the beef cattle herds and 24% of the veal calf herds. Screening by PCR revealed the presence of optrA in 95 (90%) and poxtA in 22 (21%) of the isolates. None of the isolates contained cfr . Isolates included for AST and WGS analysis were Enterococcus ( E .) faecalis ( n = 14), E. faecium ( n = 12), E. dispar ( n = 1), E. durans ( n = 2), E. gallinarum ( n = 1), Vagococcus ( V .) lutrae ( n = 2), Aerococcus ( A .) urinaeequi ( n = 1), and Companilactobacillus ( C .) farciminis ( n = 1). Thirteen isolates exhibited phenotypic linezolid resistance. Three novel OptrA variants were identified. Multilocus sequence typing identified four E. faecium ST18 belonging to hospital-associated clade A1. There was a difference in the replicon profile among optrA- and poxtA -harboring plasmids, with rep9 (RepA_ N ) plasmids dominating in optrA -harboring E. faecalis and rep2 (Inc18) and rep29 (Rep_3) plasmids in poxtA -carrying E. faecium .
Conclusion: Beef cattle and veal calves are reservoirs for enterococci with acquired linezolid resistance genes optrA and poxtA . The presence of E. faecium ST18 highlights the zoonotic potential of some bovine isolates. The dispersal of clinically relevant oxazolidinone resistance genes throughout a wide variety of species including Enterococcus spp., V. lutrae, A. urinaeequi , and the probiotic C. farciminis in food-producing animals is a public health concern.
Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
(Copyright © 2023 Nüesch-Inderbinen, Biggel, Haussmann, Treier, Heyvaert, Cernela and Stephan.)