Characterization of antimicrobial resistant Empedobacter from fresh meat and meat preparations

Empedobacter has been identified as an opportunistic pathogen that frequently exhibits resistance to multiple antibiotics, including some of those known as of last-resort. This study describes the phenotypic and genotypic characterization of carbapenem-resistant Empedobacter isolates obtained from retail fresh meat and meat preparations. The antimicrobial susceptibility of 62 isolates to 15 common antibiotics was assessed using the broth microdilution method. Additionally, whole genome sequencing (WGS) was performed on 24 of these isolates to determine their taxonomic classification and to identify antimicrobial resistance genes (ARGs), as well as their chromosomal or plasmid-borne location. Resistance to meropenem, ciprofloxacin, amikacin, gentamicin, chloramphenicol, tetracycline, and/or colistin was frequently detected, with 61.3 % of the Empedobacter strains being classified as multi-drug resistant (MDR) despite the absence of breakpoints for some of the antibiotics tested. WGS revealed the presence of blaEBR-1 genes in all Empedobacter falsenii isolates and the single Empedobacter tilapiae isolate, of a chromosomic ere(D) gene in one E. falsenii isolate, and of tet(X2) genes in eight E. falsenii isolates, seven of them harboured in plasmids. These findings underscore the need for further research to determine the role of neglected non-ESKAPE bacteria, such as Empedobacter, in the spread of antimicrobial resistance in meat production systems.