Characterization of antimicrobial resistance in Enterococcus spp. recovered from a commercial beef processing plant

The objective of this study was to characterize antimicrobial resistance in Enterococcus spp. recovered from a commercial beef processing plant. Samples were obtained from conveyers used for moving carcasses before the start of operation (CC), 2 h after operation has started (DC), and from ground beef (GB). Randomly selected isolates from each positive sample (13 from CC; 28 from DC; 26 from GB) were confirmed to genus and species levels using PCR and the API 20 Strep kit (BioMérieux Canada, Inc., St. Laurent, Canada). A total of 199 isolates comprising 39, 84, and 76 from CC, DC, and GB, respectively, were used for antimicrobial resistance testing, major resistance genes detection, and genetic analysis. Enterococcus faecalis (87%) was the most common species found followed by Enterococcus faecium (10%). The majority of enterococci were highly associated with DC samples. About 42% of E. faecium from DC samples were resistant to quinupristin-dalfopristin. Resistance to lincomycin was observed in >90% of E. faecalis from all the three sample sources. The tetracycline-resistant enterococci (52%) were significantly higher in DC samples. Intermediate resistance to erythromycin was significantly higher in enterococci from CC and DC samples. The tetracycline and quinupristin-dalfopristin resistance in enterococci was highly correlated with the presence of tet(M) and vat(E) genes. The erm(B) gene was found in about 50% of the E. faecium isolates from GB samples and was also present in >12% of the E. faecalis isolates from all the three sample sources. Enterococci from individual sample sources were genetically similar. A number of E. faecalis from CC, DC, and GB were clustered together at >85% similarity level. These findings suggest that antimicrobial-resistant Enterococcus spp. are prevalent during commercial beef processing and can transfer between various locations in the plant and that a pool of resistance genes can be found in these enterococci.