Emerging antimicrobial resistance among <i>Escherichia coli</i> strains in bloodstream infections in Toronto, 2006–2016: a retrospective cohort study
Bibliographic record
Abstract
Background: Enterobacteriaceae that produce extended-spectrum β-lactamase (ESBL) have emerged as a serious threat, with variable rates depending on geographic region. We determined the prevalence of ESBL-producing Escherichia coli, Klebsiella pneumoniae, K. oxytoca and Proteus mirabilis in bloodstream infections in Toronto from 2006 through 2016. Methods: All patients with E. coli, K. pneumoniae, K. oxytoca and P. mirabilis isolated from blood in a tertiary care microbiology laboratory in Toronto between 2006 and 2016 (1 isolate per species per patient per year) were included in this retrospective cohort study. Organisms were identified by conventional methods, and susceptibility testing was performed according to Clinical and Laboratory Standards Institute standards. Screening for ESBL and phenotypic confirmatory testing were done with a modified Clinical and Laboratory Standards Institute method. ST131 clonal type was determined by means of an established protocol. Results: The proportion of ESBL-producing E. coli isolates increased significantly between 2006 and 2016, from 6.4% (19/296) to 17.3% (89/513) (p < 0.001). This trend was seen in both intensive care units and emergency departments. Concurrently, the proportion of ST131 among ESBL-producing E. coli also increased significantly, from 31.6% (6/19) in 2006 to 73.0% (65/89) in 2016 (p = 0.03). Among ESBL-producing E. coli, significant resistance was noted to multiple antimicrobial classes. Comparable increases in the proportion of ESBL-producing K. pneumoniae, K. oxytoca and P. mirabilis were not noted. Interpretation: We observed a significant increase in the proportion of ESBL-producing E. coli in bloodstream infections in Toronto temporally correlated with an increase in the ST131 clonal type. Recognition of this dramatic rise is important to inform empiric antibiotic treatment.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| 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".