Extra-intestinal Pathogenic Escherichia coli Bloodstream Infections (BSIs) in 2016: Antibiotic Susceptibility Patterns in Calgary, Alberta, Canada
Bibliographic record
Abstract
Extra-intestinal pathogenic Escherichia coli (ExPEC) is one of the most common causes of BSIs in North America. Studies show that 20–45% of ExPEC are resistant to first line antibiotic therapies, and the frequency of extended spectrum β-lactamases (ESBLs) is increasing. Our surveillance data in Calgary, Alberta, Canada demonstrates a steady increase in the incidence of E.coli BSIs and antibiotic resistance in our population, most markedly since 2007. This study aims to assess our current burden of ExPEC BSIs and the evolving antibiotic resistance patterns. Adult and pediatric blood cultures processed at a centralized laboratory between January 1, 2016 and December 31, 2016 were eligible for inclusion. Patients with blood cultures positive for E.coli were retrospectively identified and antibiotic susceptibility profiles were retrieved using laboratory software. Antibiotic susceptibilities were determined using CLSI breakpoints for Enterobacteriaceae. The presence of ESBLs was confirmed by CLSI disk confirmation testing. There were a total of 748 confirmed sets of positive blood cultures for E.coli. Thirty-six duplicates were removed, for a total of 712 unique patient isolates. Only 298 isolates (41.9%) were susceptible to all antibiotics tested, with the remaining isolates demonstrating variable resistance to all other antibiotic classes including ampicillin (53.7%), amoxicillin-clavulanic acid (7.6%), piperacillin-tazobactam (1.1%), cefazolin (23.9%), ciprofloxacin (27.9%), and trimethoprim-sulfamethoxazole (33.3%). 120 ESBL-producing organisms were identified (16.9%). Of these, many had additional resistance to ciprofloxacin (51.7%), trimethoprim-sulfamethoxazole (55%), and carbapenems (1.7%). ExPEC is a common cause of BSIs in our patient population, and a particularly concerning finding is the presence of multi-drug resistance to cephalosporins, fluoroquinolones, and trimethoprim-sulfamethoxazole in a number of isolates. Detailed epidemiological studies are required to characterize key microbial and clinical factors driving antibiotic resistance of E.coli in our population and will be relevant to clinical practice, informing local guidelines on empiric antibiotic choices. 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 | 0.001 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.003 | 0.007 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.002 | 0.000 |
| Open science | 0.002 | 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".