Genomic Characterization of Enterococcus casseliflavus Isolated from Beef Cows and Calves

<i>Enterococcus</i> species are used as One Health indicators of antimicrobial resistance (AMR) in humans, animals, and the environment. A surveillance study in beef cows and calves isolated <i>Enterococcus casseliflavus</i> along with <i>E. faecium</i>, <i>E. faecalis</i>, and <i>E. hirae</i>. Given the high prevalence of <i>E. casseliflavus</i>, we elected to characterize this species to better understand its role in the antimicrobial resistance of enterococci in cows and calves. Almost 12% of <i>E. casseliflavus</i> isolates exhibited multidrug resistance with the majority being resistant to lincomycin (99%), followed by quinupristin-dalfopristin (34%), ciprofloxacin (9.6%), tylosin (4.5%), erythromycin (2.7%), tetracycline (1.8%), tigecycline (1.5%), daptomycin (0.6%), streptomycin (0.3%), and kanamycin (0.3%). All <i>E. casseliflavus</i> were susceptible to chloramphenicol, penicillin, streptomycin, nitrofurantoin, gentamicin, and linezolid. Whole genome antimicrobial resistance gene profiling identified <i>vanC</i>-type intrinsic vancomycin resistance genes in all <i>E. casseliflavus</i>, with the <i>vanC4XYT</i> gene cluster being dominant (67%) followed by <i>vanC2XYT</i> (31%) and <i>vanC3XYT</i> (1.5%). Resistance genes for erythromycin (<i>ermB</i>) and tetracycline (<i>tetM</i>) were rarely identified (2.1% and 1.2%, respectively) within <i>E. casseliflavus</i> genomes. No resistance genes were identified to explain either the quinupristin-dalfopristin or ciprofloxacin resistance in these isolates. A core genome phylogenetic tree revealed two clades that exhibited no distinct association with the age of the host, time of sample collection, or the farm sampled. The open nature of the <i>E. casseliflavus</i> pan-genome highlighted its intraspecies diversity. These findings suggest that <i>E. casseliflavus</i> is likely a low-risk species in terms of contributing to antimicrobial resistance in the cow-calf sector.