Occurrence of oxazolidinone resistance genes in enterococci, staphylococci, and Mammaliicoccus sciuri from swine slaughterhouse wastewater, Italy

Unlabelled: Oxazolidinones (linezolid and tedizolid) are last-resort antibiotics used to treat severe infections caused by multidrug-resistant Gram-positive bacteria. Although linezolid is not approved for veterinary use, resistant bacteria—particularly enterococci—have increasingly been reported in food-producing animals worldwide. Slaughterhouses represent potential hotspots for the transmission of antimicrobial-resistant pathogens along the food chain. This study investigated the presence of oxazolidinone resistance genes and relevant genetic elements in florfenicol-resistant enterococci and staphylococci isolated from wastewater collected from an Italian swine slaughterhouse. In total, five enterococci, six staphylococci, and one Mammaliicoccus sciuri (previously known as Staphylococcus sciuri) isolate were recovered. PCR screening revealed that all staphylococci and M. sciuri carried the cfr gene, while enterococci were positive for either optrA or poxtA. Nine isolates were selected for whole genome sequencing. Enterococcus hirae EM2 carried poxtA on the novel pEhEM2-poxtA plasmid. In E. faecium ED1 and EF1, optrA was located on the novel pEfmED1-optrA plasmid. E. durans EF2 carried poxtA within a Tn6657 transposon integrated into a pEgFS4-2-like plasmid also containing tet(M), tet(L), and genes related to transposition and plasmid replication. In Staphylococcus simulans SN1 and SF3, cfr was found on the novel pSsSN1-cfr plasmid and on p12-02300 plasmid, respectively. In Staphylococcus cohnii SD1, cfr was located on the previously described plasmid unnamed1, while in S. cohnii SF2 it was inserted into a chromosomal Tn558-like transposon along with fexA. M. sciuri SN4 harboured cfr on a small plasmid showing high similarity to the pK8D55P-cfr plasmid previously found in an M. sciuri isolate from ducks. These results highlight the role of slaughterhouse wastewater as a potential reservoir of oxazolidinone resistance genes and emphasize the need for continued monitoring to limit the environmental spread of antimicrobial resistance from animal production systems. Graphical abstract: [Image: see text] Supplementary information: The online version contains supplementary material available at 10.1007/s11274-026-04968-0.