THE ROLE OF GENUS ENTEROCOCCUS IN THE SPREAD OF ANTIMICROBIAL RESISTANCE IN HUMAN THROUGH FOOD CHAIN

The bacteria belonging to genus Enterococcus are commensals of human and animal gastrointestinal tract but, thanks to their ability to survive under harsh conditions, they are able to colonize different ecological niches, including soil, water and food matrices. Their high genomic plasticity, together with their capacity to act as reservoirs and vectors of antimicrobial resistance (AMR) genes, makes them a major concern within a One Health framework. This PhD project aimed to investigate the role of Enterococcus spp. in the dissemination of AMR along the food chain, with a focus on isolates obtained from intensive swine farming and ready-to-eat (RTE) foods. A special focus was dedicated to resistance against linezolid, a last resort antibiotic for infections caused by vancomycin-resistant enterococci (VRE) and multidrug-resistant (MDR) Gram-positive bacteria. The detection of linezolid resistance determinants (cfr, optrA and poxtA) in both E. faecium and E. faecalis, as well as in non-faecalis/faecium (NFF) species, highlights the risk of resistance development and dissemination outside clinical settings. The results obtained in this research highlighted the presence of different MDR enterococcal species in both animal farming and RTE foods. The first chapter investigates E. faecalis and E. faecium strains isolated from different stages of swine farming, assessing their phenotypic and genotypic resistance, survival rate after gastro-duodenal digestion in vitro and its effect on the bacterial ability to transfer resistance genes. Whole-genome sequencing and plasmidome analysis of tested strains provided further insights into the contribution of mobile genetic elements (MGEs) to resistance spread. The second chapter addresses the underestimated role of NFF species as reservoirs and vectors of resistance genes, with particular emphasis on their potential to transfer determinants to the clinically relevant species E. faecium. The third chapter focuses on RTE food isolates, characterizing their AMR and virulence profiles, focusing on biofilm-forming ability, and their ability to transfer resistance genes after a gastro-duodenal digestion in vitro, supported by genomic analysis. Overall, this study provides a comprehensive overview of the contribution of Enterococcus spp. to the circulation of AMR within the food chain. Combining phenotypic, genotypic and genomic approaches, it underlines the importance of rational antibiotic use in both human and veterinary medicine, the need for strict hygiene measures in food production and the implementation of preventive strategies to reduce the microbiological risk posed by AMR enterococci.