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Antimicrobial resistance (AMR) represents a growing global threat with significant implications for both human and veterinary health. Among the microorganisms commonly associated with AMR, Enterococcus spp. play a relevant role. As commensals of the gastrointestinal tract in humans and animals, they are known for their ability to acquire and transfer resistance genes, thus contributing to the spread of AMR along the agri-food chain. In addition to intrinsic resistance to several antibiotic classes (e.g., cephalosporins, sulfonamides, lincosamides), enterococci can acquire resistance to vancomycin, macrolides, glycopeptides, and aminoglycosides, making them important indicators in AMR surveillance programmes.
This study aimed to compare the AMR profiles of enterococci isolated from three dairy farms selected based on their antibiotic use: high, low, and no use (organic). Sampling was conducted between 2023 and 2024 on environmental matrices (milking parlour, manure pit, bedding) and bulk milk. Identification by MALDI-TOF MS revealed multiple Enterococcus species. E. faecalis and E. hirae were most prevalent in the low-use (37.5%, 18.5%) and organic farm (29.7%, 24%). E. malodoratus was more frequently isolated from the farms using antibiotics (22% and 18%), while E. canintestini (20%) appeared exclusively in the high-use farm, suggesting a link between antibiotic pressure and microbial community composition.
E. hirae, the most widespread in environmental samples across all farms, was selected for whole-genome sequencing using the Oxford Nanopore GridION platform to identify AMR genes and mobile genetic elements (plasmids, transposons, integrons). Preliminary results revealed the aac(6')-Iid gene in 90% of isolates, encoding an aminoglycoside N-acetyltransferase conferring resistance to some aminoglycosides (streptomycin, tobramycin).
These findings highlight the potential role of E. hirae as an environmental AMR reservoir. A complete AMR profile analysis of dominant species will help clarify their contribution to AMR gene dissemination along the dairy chain.
