Variations in carbapenem resistance associated with the Verona integron-encoded metallo-beta-lactamase across the order Enterobacterales
Bibliographic record
Abstract
The Verona integron-encoded metallo-β-lactamase (VIM), encoded as a cassette within class 1 integrons, is found in gram-negative clinical isolates worldwide and has been linked to outbreaks in nosocomial settings. Here, we obtained six vim-1+ clinical isolates from the genera Escherichia, Klebsiella, and Enterobacter. Antimicrobial susceptibility testing revealed that the minimum inhibitory concentrations of ertapenem, a clinically relevant carbapenem antibiotic, against these six isolates ranged from ≤ 0.25 μg/mL to > 32 μg/mL. Variations within vim-1 were not responsible for the phenotypic variation as whole genome sequencing showed that all strains contain identical vim-1 alleles with identical proximity to the promoter. However, other antimicrobial resistance genes, including additional β-lactamases, were identified in each strain that likely contribute to β-lactam resistance. A dendrogram of vim-1+ plasmids from these isolates produced using hierarchical clustering suggests both global dissemination of plasmids via horizontal gene transfer and autochthonous vertical spread within Ontario. To test the impact of genomic background on VIM-1 functionality, the vim-1 gene was cloned into a broad host range plasmid and introduced into laboratory strains of Escherichia coli DH5α and MG1655, and Klebsiella grimontii KP5022. Initial susceptibility testing revealed that the introduction of vim-1 alone was insufficient to confer carbapenem resistance in these strains. Next, KP5022 and DH5α vim-1+ strains were subjected to adaptive lab evolution experiments to identify epistatic mutations increasing ertapenem resistance. Sequencing data from evolved KP5022 and DH5α strains showed plasmid recombinations resulting in increased vim-1 copy number, although they were not resistant to ertapenem or meropenem. In contrast, when evolved plasmids were transformed into DH5α and subjected to adaptive lab evolution, evolved strains were extensively carbapenem resistant. Experiments suggest that chromosomal mutations contribute to increased resistance in the evolved DH5α vim-1+ strains. Sequence data showed that these mutations resulted in the deletion of nucleotides within ompC or deletion of the entire ompC gene, which encodes a non-specific outer membrane porin that plays a role in antibiotic transport into the cell. Overall, our results support the current literature on vim-1 in Ontario and find additional support for the role of gene epistasis in conferred resistance phenotypes of acquired genes.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".