Flies from meat processing facilities are carriers of multidrug-resistant Escherichia coli and diverse Staphylococcaceae species

Flies are important vectors of antimicrobial resistance (AMR) in food production, but their role in meat processing environments remains poorly characterized. This study isolated Enterobacteriaceae and Staphylococcaceae (including Mammaliicoccus sciuri) from flies collected in bovine and swine slaughterhouses and meat processing industries. Phenotypic AMR was assessed, and the presence of selected antimicrobial resistance and virulence genes (mecA, sea, see, sec, stx1, stx2, and eae) was verified. Out of 60 flies collected, a total of 34 isolates were identified using MALDI-TOF with 13 different bacterial species, including Escherichia coli, Citrobacter braakii, C. freundii, Klebsiella pneumoniae, Hafnia alvei, Enterobacter kobei, S. aureus, S. epidermidis, S. saprophyticus, S. simulans, S. warneri, S. xylosus, and M. sciuri. Among Staphylococcaceae isolates, 17.6% were resistant to oxacillin and 23.5% to gentamicin. Regarding the Enterobacteriaceae isolates, 41.2% were resistant to streptomycin. Ten isolates (two E. coli, one S. epidermidis, two S. saprophyticus, one S. simulans, one S. warneri and three M. sciuri) were considered multidrug-resistant (MDR). Notably, none of the targeted genes (mecA, sea, see, sec, stx1, stx2, eae) were detected by PCR. These findings suggest that flies can disseminate important resistant opportunistic bacteria in meat processing environments, posing concerns due to the capacity of flies to transmit these bacteria across food, processing facilities, animals and humans. These results underscore the need for continuous AMR surveillance and effective vector control to reduce the risks posed by flies in meat processing environments.