The unravelled Enterococcus faecalis zoonotic superbugs: Emerging multiple resistant and virulent lineages isolated from poultry environment

Abstract This study aimed to investigate the zoonotic potential by virtue of phylogenetic analysis, virulence and resistance gene profiles of Enterococcus faecalis originating from poultry environment. The ERIC, BOX and RAPD PCR analysis showed the clustering of E. faecalis strains ( n = 74) into five groups (G1‐G5) and fifteen sub‐clusters (B1‐B15), which share 50%–80% similarities with ATCC E. faecalis and clinical strains of human infection. E. faecalis strains harboured seven enterocins genes including ent1097 (85%), entB (84%), enterolysinA (51%), entSEK4 (51%), entL50 (31%), entA (25.7%) and ent1071 (14.9%). The highest prevalence of gelE‐sprE (90%), lip‐fl (90%) followed by cylL (62%), hyl (60%), katA (16%) and cylA (5.4%) was observed in poultry isolates. The fsr operon and gelE ‐ sprE was co‐associated in 66.2% strains. E. faecalis also harboured biofilm and endocarditis‐associated genes, including efaAfs (97%), ebp‐ pilli ( ebpABC and srtC 69.9%–80%), asa1 (71%), agg (55%), ace (54%) and esp‐Tim (3%). Despite all found sensitive to vancomycin, 98.6% strains were multi‐drug resistant to five to twelve tested antimicrobials. An increased‐level of resistance (≥32 μg/ml) was observed to ampicillin (8.1%), meropenem (21.6%), chloramphenicol (73.4%), erythromycin (90.5%), tetracycline (100%) and high‐level resistance to kanamycin (79.7%) and gentamicin (52.7%). The multi‐drug resistant E. faecalis (MDR e.f ) were carried pbp4 (90%), tetL (90%), tetM (70%), ermB (81%), cat (52.7%), acc6‐aph2 (58.1%), aaph(3)‐III (49.9%), gyrA (97%) and parC (98%) genes. Moreover, these MDR e.f were also harboured, hospital‐associated marker IS 16 (58%) and pheromone responsive genes, that is ccf (88%), cpd (74%), cob (62%) and eep (66%). Thus, regardless of the distinct phylogenetic background of E. faecalis of poultry origin, ATCC E. faecalis and clinical strains of human origin, we found major similarities in virulence, resistance gene profiles and mobile genetic elements (IS 16 and pheromone responsive plasmids), supporting the zoonotic/reverse zoonotic risk associated with this organism.