Antimicrobial susceptibility profiles of invasive isolates of anaerobic bacteria from a large Canadian reference laboratory: 2012–2019
Bibliographic record
Abstract
Anaerobic bacteria can cause severe and life threatening infections. Susceptibility data are relatively limited on anaerobic organisms despite the clinical importance in guiding empiric treatment of infections. To determine antimicrobial susceptibility profiles of clinically significant anaerobic bacteria, isolates obtained from sterile sites submitted to Public Health Ontario Laboratory (2012-2019) were included in this study (N = 5712). Cefoxitin, clindamycin, metronidazole, meropenem, penicillin and piperacillin-tazobactam were tested using the gradient strip method with MICs interpreted based on Clinical and Laboratory Standards Institute guidelines. Bacteroides spp. (N = 958; 16.7%), Clostridium spp. (N = 798; 14.0%), Cutibacterium spp. (N =659; 11.5%) and Actinomyces spp. (N = 551; 7.0%) were the most commonly isolated genera. Bacteroides fragilis isolates were susceptible to cefoxitin (88.4%), clindamycin (68.4%), metronidazole (96.0%), meropenem (99.0%) and piperacillin-tazobactam (98.4%). Other Bacteroides spp. showed reduced susceptibility to several antimicrobials. Clostridium spp. isolates were susceptible to penicillin (69.7%), clindamycin (69.7%) and cefoxitin (76.3%); C. perfringens and C. ramosum showed distinct susceptibility profiles. Susceptibility rates among anaerobes remained relatively unchanged over 8 years with a few exceptions: C. perfringens susceptibility to clindamycin decreased from 91.3% to 60% (p = 0.03); Clostridium spp. susceptibility to penicillin similarly decreased from 82.1% to 65.9% (p = 0.03); Eggerthella spp. susceptibility to piperacillin-tazobactam decreased from 100% to 24.3% (p < 0.001); B. fragilis group susceptibility to cefoxitin decreased from 70.4% to 48.2% (p = 0.05); and Parabacteroides spp. susceptibility to piperacillin-tazobactam decreased from 100% to 25% (p = 0.01). Our findings underscore the need for ongoing surveillance and periodic monitoring of antimicrobial resistance in order to guide empiric therapy.
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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 | 0.004 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.002 | 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) | 0.001 | 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".