Emerging antimicrobial resistance among <i>Escherichia coli</i> strains in bloodstream infections in Toronto, 2006–2016: a retrospective cohort study
Bibliographic record
Abstract
<h3>Background:</h3> 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 <i>Escherichia coli</i>, <i>Klebsiella pneumoniae</i>, <i>K. oxytoca</i> and <i>Proteus mirabilis</i> in bloodstream infections in Toronto from 2006 through 2016. <h3>Methods:</h3> All patients with <i>E. coli</i>, <i>K. pneumoniae</i>, <i>K. oxytoca</i> and <i>P. mirabilis</i> 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. <h3>Results:</h3> The proportion of ESBL-producing <i>E. coli</i> isolates increased significantly between 2006 and 2016, from 6.4% (19/296) to 17.3% (89/513) (<i>p</i> < 0.001). This trend was seen in both intensive care units and emergency departments. Concurrently, the proportion of ST131 among ESBL-producing <i>E. coli</i> also increased significantly, from 31.6% (6/19) in 2006 to 73.0% (65/89) in 2016 (<i>p</i> = 0.03). Among ESBL-producing <i>E. coli,</i> significant resistance was noted to multiple antimicrobial classes. Comparable increases in the proportion of ESBL-producing <i>K. pneumoniae</i>, <i>K. oxytoca</i> and <i>P. mirabilis</i> were not noted. <h3>Interpretation:</h3> We observed a significant increase in the proportion of ESBL-producing <i>E. coli</i> 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.
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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 | 0.001 | 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 | 0.001 | 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".