2468. The Genomic Epidemiology of Carbapenemase-Producing Enterobacterales (CPE) in Ontario, Canada, 2016
Bibliographic record
Abstract
Abstract Background Carbapenemase-producing Enterobacterales (CPE) are among the most urgent of antimicrobial resistance threats. In south-central Ontario, Canada, over one-third of CPE cases are associated with local healthcare and the incidence of such CPE cases is rising steadily. We integrated whole-genome sequencing (WGS) and CPE population-based surveillance data to gain insights into CPE transmission dynamics in Ontario, Canada. Methods We included all incident CPE isolates received at the Public Health Ontario Laboratory as part of a voluntary surveillance program from Jan. 1 to Dec. 31, 2016 in Ontario, Canada (population ∼13.5 million). All isolates underwent Illumina WGS. MLST was determined for all isolates, and single nucleotide variant (SNV) analysis was performed by species. SNV analyses were combined with epidemiological data from the Toronto Invasive Bacterial Diseases Network to identify transmission clusters. Results There were 206 incident CPE isolates from 176 patients. Most common species were Escherichia coli (95, 46%) and Klebsiella pneumoniae (76, 37%), and most common carbapenemases produced were NDM (77, 37%), OXA-48-like (68, 33%), and KPC (45, 22%). There was variability in MLST, with ST167 being most common among E. coli (10, 11%), and ST147 being most common among K. pneumoniae (13, 17%). There were 14 clusters with 34 (17%) CPE isolates belonging to 33 (20%) unique patients total (Table). Cluster size range was 2-5 patients. Time from first to last identified case in clusters ranged from 0 to 258 days. In 8 clusters, the index case likely acquired CPE during prior hospitalization abroad, with subsequent direct or indirect transmission to other patients in the cluster. In 5 clusters, all patients likely acquired CPE at the Ontario hospital where their CPE was detected. Conclusion There was variability in CPE species and MLST as well as carbapenemase produced. Almost one fifth of patients belonged to a transmission cluster, with transmission lasting many months in some clusters. These data highlight challenges with CPE local transmission and a need to intensify control measures. Disclosures 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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.002 | 0.005 |
| Science and technology studies | 0.003 | 0.001 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.003 | 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".