First identification and whole-genome characterization of human-associated Enterobacter roggenkampii and Enterobacter sichuanensis carrying blaIMI-4 carbapenemase in Costa Rica
Bibliographic record
Abstract
• Two Enterobacter isolates from Costa Rica carrying the rare chromosomal bla IMI-4 gene are reported. • The genetic variant associated with carbapenem resistance is embedded within a 25-kb integrative mobile element resembling EcloIMEX-2. • This study highlights the urgent need to incorporate next-generation genomic tools into active antimicrobial resistance surveillance to enable the timely detection of emerging and unusual antimicrobial resistance genes, thereby improving epidemiological monitoring and patient outcomes. All carbapenem-resistant Gram-negative bacterial isolates obtained in the Costa Rican National Network of Bacteriology Laboratories are routinely referred to the National Reference Center for Bacteriology for the national-laboratory for the surveillance and characterization of their carbapenem-related mechanism of resistance. As a result of this healthcare-associated infection surveillance, two bacterial isolates with unknown mechanisms for carbapenem resistance were investigated. The isolates were subjected to taxonomic identification, antimicrobial susceptibility testing, and whole-genome characterization, using Illumina and Oxford Nanopore technologies, and bioinformatic analyses. The isolates were identified as Enterobacter roggenkampii and Enterobacter sichuanensis . Although the isolates presented different antimicrobial resistance profiles, both were resistant to carbapenems, positive for the modified carbapenem inactivation method (mCIM), and showed inhibition of carbapenem resistance with boronic acid. The full characterization of the isolates’ genomes, revealed the presence of the rare chromosomal bla IMI-4 gene inserted within 25-kb integrative mobile elements, closely related to EcloIMEX-2. The limited global distribution of the bla IMI-4 variant, along with its identification in two distinct bacterial species in Costa Rica within integrative mobile elements, underscores the critical need for regular antibiotic resistance surveillance using next-generation sequencing technologies. This study demonstrates that this practice allows the timely detection of novel or rare mechanisms of antibiotic resistance.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| 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 teacher head, 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".