A Clostridioides difficile surveillance study of Canadian retail meat samples from 2016-2018: a possible source of human clinical infections?
Bibliographic record
Abstract
Introduction: C. difficile spores are dispersed throughout the environment and can asymptomatically colonize and/or infect animals. Previous studies have shown that C. difficile spores can be isolated from commercially available beef, veal, pork, vegetables, and seafood. However, a definitive link has yet to have been made between food contamination and hospitalized cases. This study aims to isolate C. difficile from retail meat samples and compare them to human isolates. Methods: Frozen retail pork, beef, and veal samples were obtained from the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) program and FoodNet Canada. These samples were analyzed for C. difficile contamination by direct plating on selective media and by inoculation in enrichment broth. Suspected C. difficile colonies were confirmed by polymerase chain reaction (PCR). Toxigenic C. difficile isolates were molecularly characterized by ribotyping and pulsed-field gel electrophoresis (PFGE). Antibiotic susceptibility was determined by ETEST® strips. Whole genome sequencing (WGS) was performed on all C. difficile isolates from retail meats and from select human cases. Results: Overall, toxigenic C. difficile was isolated from 10 of 644 retail meat samples (1.6%). All 10 isolates were A/B toxin positive. Additionally, 2 isolates were found to harbor binary toxin. All retail meat isolates were susceptible to vancomycin, metronidazole, tigecycline, rifampin, and clindamycin, excluding 1 NAP1 isolate that was resistant to moxifloxacin. Molecular typing revealed strain types commonly found in human clinical isolates (e.g. NAP1 (RT027), NAP4 (RTNS195), and NAP11 (RT106)). The closest related human clinical isolate to the C. difficile isolates from retail meats differed by 8-34 SNVs when analyzed at the highest resolution (84.54%-95.02% core genome). Conclusion: A low percentage of retail meats (1.6%) were contaminated by C. difficile. All ribotypes and NAP types of C. difficile isolates from retail meats have been previously identified in human cases. Through WGS, half of the C. difficile isolates from retail meats were determined to be closely related to a C. difficile isolate from a human case (≤10 SNVs), while the other half were genetically distinct (>10 SNVs), suggesting that retail meats may be a vector of dissemination for C. difficile in the community.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 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".