Antibiotic Resistance to Critically Important Antimicrobials and Virulence Genes in Enterococcus faecalis Strains Isolated from Eurasian Griffon Vultures (Gyps fulvus) and Their Association with Mobile Genetic Elements

Abstract

Simple Summary The purpose of this study was to investigate whether Eurasian griffon vultures could act as reservoirs of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) that determine the phenotypic resistance of Enterococcus faecalis isolates from these birds to various antimicrobials used in veterinary and human medicine. Additionally, the study aimed to characterize the ARGs, MGEs and virulence genes in the genome of a subset of isolates showing phenotypic resistance to the critically important antimicrobials linezolid, chloramphenicol, ciprofloxacin and gentamicin. Vultures were chosen because of their wide geographical distribution, their scavenging habits and their close proximity to humans. Most E. faecalis isolates (82.1%) exhibited resistance to six antimicrobials, indicating the widespread presence of resistant bacteria within this vulture population. Of particular concern was the detection of isolates resistant to linezolid, chloramphenicol, ciprofloxacin and gentamicin, considered clinically important in human medicine. Overall, a significant proportion of E. faecalis strains recovered from vultures were multidrug resistant (34%) harboring MGEs (plasmid replicons, transposons and composite transposons) that carried antimicrobial resistance and virulence-associated genes. These findings are cause for concern, since vultures may act as spreaders of these genes to the environment and even to other hosts. Abstract The phenotypic resistance of 56 Enterococcus faecalis isolates from Eurasian griffon vultures was subjected to surveillance testing with the microdilution method using a standardized panel of antimicrobials. Isolates were also characterized by MLST. Additionally, the genome of 19 isolates with phenotypic resistance to linezolid, ciprofloxacin, chloramphenicol and/or high-level resistance to gentamicin were sequenced to determine their antimicrobial resistance (ARGs) and virulence-associated genes and to identify mobile genetic elements (MGEs). Most isolates (82.1%) exhibited non-wild-type phenotypes to six antimicrobial agents, and multidrug resistance (MDR) was detected in 34% of the isolates. Most MDR isolates (53%) belonged to ST16, ST116 and ST35. ARGs were localized on the chromosome as well as on various MGEs previously reported in human, food and livestock isolates, suggesting that vultures may acquire antibiotic-resistant bacteria (ARBs) and/or ARGs as a consequence of anthropogenic pollution. Overall, 22 virulence-associated genes encoding cell surface and secreted factors were identified, some of which were located on MGEs that also carried ARGs. The significant proportion of E. faecalis isolates recovered from vultures that exhibited MDR phenotypes and harbored MGEs carrying ARGs and virulence-associated genes is cause for concern, since vultures may act as spreaders of these genes to the environment, domestic animals and humans