Variations in carbapenem resistance associated with the VIM-1 metallo-β-lactamase across the Enterobacterales

Abstract

The VIM-1 metallo-{beta}-lactamase enzyme, encoded as a cassette within class 1 integrons, is found in Gram-negative clinical isolates worldwide and has been linked to outbreaks of bacterial pathogens in nosocomial settings. Six vim-1+ clinical isolates, from the genera Escherichia, Klebsiella, and Enterobacter, were obtained from Kingston, Ontario, Canada. Whole genome sequencing revealed that vim-1 was plasmid-borne in all strains and situated as the first gene in In916 or In110 integrons. Analysis of related plasmids suggested that these vim-1-containing plasmids are globally disseminated and have spread via horizontal gene transfer and autochthonous vertical spread within Ontario. Interestingly, the minimum inhibitory concentrations of ertapenem and meropenem, two clinically relevant carbapenem antibiotics, against these six isolates varied more than tenfold, suggesting the effects of VIM-1 are dependent on the genomic content of the host microbe. To further study the genomic content dependency of VIM-1, we introduced vim-1 into three common Enterobacterales laboratory strains. Although introduction of vim-1 into Escherichia coli DH5 resulted in little resistance to ertapenem or meropenem, multiple rounds of adaptive laboratory evolution allowed us to identify variants with extremely high levels of resistance to both carbapenems. DNA sequencing revealed that the increase in carbapenem resistance was due to a combination of increased vim-1 gene dosage and epistatic interactions with mutations of ompC that likely would have decreased outer membrane permeability to these antibiotics. Together, these results provide additional support for the role of gene epistasis is modulating the antimicrobial resistance phenotypes of acquired resistance genes, as well as previous results suggesting that the presence of a {beta}-lactamase gene is insufficient to confer strong resistance to carbapenems without being paired with reduced outer membrane permeability.