Whole genome analysis identified a cefotaxime-resistant Empedobacter brevis GBW-1 isolate from ground beef encoding a novel metallo-beta-lactamase variant, blaEBR-6

Abstract

While investigating foodstuffs for ESBL-producing Aeromonas species on ampicillin dextrin agar with vancomycin and cefotaxime, a multidrug-resistant Empedobacter brevis strain GBW-1 was identified from ground beef. Phylogenetic analysis supports the interconnectedness of environment, humans and food driving this species evolutionary development. Antimicrobial susceptibility testing demonstrated resistance to gentamicin, carbapenems and third-generation cephalosporins. Whole genome sequencing of this strain detected a 3.74 Mb genome with 32.8% GC content containing 3,780 coding genes. Among these genes, at least three known antimicrobial resistance (AMR) genes were identified with qacG, vanT gene within the vanG cluster, and a novel variant of the metallo-{beta}-lactamase blaEBR-6. This novel homologue, EBR-6, was compared against previously known EBR variants and was found to be closest to EBR-3 with an 84.98% amino acid identity match. Docking software predicted these mutations vary the binding to meropenem. Furthermore, nearly 100 annotated regions associated with mobile genetic elements, including the presence of three, separate tra operons were identified on the genome. Together, these findings implicate the importance of horizontal gene transfer in the acquisition of AMR among the emerging pathogen Empedobacter brevis and further stress its One Health nature. ImportanceAs global trade and commerce continues to create a more interconnected world, the increasing frequency and spread of antimicrobial resistance amongst foodborne bacteria poses a significant challenge to public health. Here, we report the isolation of the multi-drug resistant Empedobacter brevis GBW-1, a bacterial strain harboring resistance against meropenem, third-generation cephalosporins, and gentamicin. Of particular note, this strain displays a novel variant of a metallo-{beta}-lactamase (MBL) gene, blaEBR-6, as well as three distinct tra operons, suggesting enhanced capacity of horizontal gene transfer. These findings highlight how foodborne bacteria may serve as reservoirs and vectors for the further spread of resistance genes, reinforcing the necessity of utilizing a collaborative One Health approach to combat AMR across sectors.