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

TL;DR

A new metallo-beta-lactamase variant was found in a multidrug-resistant Empedobacter brevis strain from ground beef, highlighting its potential spread through food and environment.

Contribution

Discovery of a novel metallo-beta-lactamase variant, blaEBR-6, and its genomic and phenotypic characterization in a multidrug-resistant E. brevis isolate.

Findings

A multidrug-resistant Empedobacter brevis strain GBW-1 was identified from ground beef with resistance to carbapenems and cephalosporins.

Genome sequencing revealed a novel blaEBR-6 metallo-beta-lactamase variant with 84.98% amino acid identity to EBR-3.

In silico docking predicted mutations in blaEBR-6 alter meropenem binding, and mobile genetic elements suggest potential for spread.

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. Data collection from whole genome sequencing of this strain detected a 3.74 Mb genome with 32.8% GC content containing 3780 coding genes. Among these genes, at least three known antimicrobial resistance (AMR) genes were identified from the dataset with qacG, vanT gene within the vanG cluster, and a novel variant of the metallo-β-lactamase blaEBR-6. This 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. Data collection from in silico molecular docking experiments predicted these mutations change the binding to meropenem. Furthermore, nearly 100 annotated regions associated with mobile genetic elements, including the presence of tra operons, were identified on the genome. Together, this dataset provides, genomic, phenotypic, and in silico data that may be reused to monitor the evolution of EBR from a One Health perspective.

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