Rabbit carcasses as important vectors of multidrug-resistant Enterococcus faecalis, but not E. faecium: prevalence and molecular characterization from a study in Poland

Abstract Background Numerous studies indicate that multidrug-resistant Enterococcus bacteria are widely present on the carcasses of various food-producing animal species as well as in facilities used for their production. However, in the global literature, there is no information available regarding the prevalence, species composition or antibiotic resistance of enterococci contaminating rabbit carcasses. Therefore, the aim of this study was to determine the prevalence of Enterococcus bacteria on the surface of carcasses of rabbits slaughtered in an EU-approved abattoir with particular emphasis on two species, i.e., Enterococcus faecalis (E. faecalis) and Enterococcus faecium (E. faecium). In addition, the phenotypic and genotypic resistance to antibiotics of rabbit-origin E. faecalis isolates and the relatedness of multi-drug resistance strains has been evaluated. Results The study revealed that 425 out of 496 examined rabbit carcasses were contaminated with Enterococcus spp., with a prevalence of 85.69% (95% CI: 82.60–88.77%). E. faecalis was confirmed on the surface of 237 carcasses, which constituted 55.8% of the Enterococcus-positive swabs and 47.8% of all carcasses examined. E. faecium was not detected on the surface of any of the rabbit carcasses tested. Phenotypically, 97.5% of isolates were classified as resistant to tetracycline, 92.4% to erythromycin, 65% to kanamycin, 54% to streptomycin, 40.4% to ciprofloxacin, 30% to enrofloxacin, and 0.4% to penicillin and ampicillin. Moreover, 66.40% of E. faecalis isolates showed multidrug resistance to at least three classes of antibiotics. The presence of genes determining the resistance to tetracycline (tetM and tetL), erythromycin (ermB), aminoglycosides (aac(6’)-Ie-aph(2”)-Ia), and streptomycin (ant(6)-Ia), was consistent with the phenotypic resistance pattern observed in E. faecalis isolates. Using ADSRRS fingerprinting analysis, four main clusters were visualized, with almost every branch containing multi-drug resistant isolates from rabbits bred on farms in different locations. Conclusion The high prevalence of enterococci on rabbit carcass surfaces indicates poor hygiene during the production process at rabbit abattoirs. Compared to E. faecium, E. faecalis appears better adapted to persist on the surface of rabbit carcasses and/or meat cuts in the slaughterhouse environment. This may be attributed to its stronger biofilm-forming ability, as E. faecalis was the only species detected in all Enterococcus-positive samples tested. Rabbit carcasses are also an important vector of multidrug-resistant E. faecalis. The high genetic similarity of multidrug-resistant E. faecalis isolates from rabbit carcasses raised on different farms suggests a common source of these bacteria or cross-contamination at slaughter. Our results supported E. faecalis as an indicator bacterium for antibiotic resistance under Commission Implementing Decision (EU) 2020/1729 and highlighted the need to extend monitoring to rabbit meat production at the national level.