Carbapenemase Gene Transfer among Canadian Patients Colonized or Infected with Carbapenemase-Producing Enterobacteriaceae
Bibliographic record
Abstract
Carbapenemase-producing Enterobacteriaceae (CPE) has been declared an emerging global health threat. Plasmid transfer between species is of particular concern, allowing carbapenem resistance to spread rapidly to invasive or hypervirulent organisms which could potentially lead to severe infections. The rate of carbapenemase gene transfer between species has not been quantified to date. CPE isolates from 754 patients whom had either clinical or surveillance specimens submitted to our reference laboratory between January 2011 and December 2016 were reviewed. Patients with multiple Enterobacteriaceae species possessing the same carbapenemase gene were analyzed. Additionally, we reviewed data from a study in which rectal and groin swabs were collected from 88 patients at 3-month intervals to determine the average duration of CPE colonization prior to gene transfer. Thirty-nine out of 754 patients (5.2%) showed evidence of carbapenemase gene transfer between species. The majority (34/39 patients, 87.2%) had specimens submitted at a single point in time. Most commonly, multiple species with the same carbapenemase gene were found in rectal swabs (25/286 CPE-positive rectal swabs, 8.7%) followed by urine cultures (3/327 CPE-positive urine cultures, 0.9%). In the follow-up study, 8/88 patients with at least one follow-up specimen (9.1%) showed evidence of gene transfer over time. Out of a total of 10 instances of gene transfer, 3, 2, 3, 1, and 1 were detected at the 1-, 3-, 6-, 9-, and 15-month follow-up periods, respectively. Distribution of species and gene types was similar among the index isolates and second isolates (Table 1). Distribution of CPE isolates in the follow-up study A significant minority of CPE-colonized patients will be colonized with multiple species of Enterobacteriaceae. Gene transfer to new species continues to occur over time in persistently colonized patients. All authors: No reported disclosures.
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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 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.001 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.003 |
| Science and technology studies | 0.003 | 0.001 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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".