Salmonella Thompson outbreak associated with consumption of chicken shawarma and the usefulness of genome sequencing in the investigation
Bibliographic record
Abstract
BACKGROUND: . Thompson) cases distributed throughout three border regions in the province of Quebec in November 2016 triggered a provincial investigation to identify a common source of contamination and to put the appropriate control measures into place. OBJECTIVE: To report on the outbreak and to describe the use of genomic sequencing to identify the salmonella serotype responsible. METHODS: serogroup C1 that had occurred between October 1, 2016 and February 15, 2017 was conducted. A case definition was developed. Pulsed field gel electrophoresis supplemented by analyses of genome sequences using the single nucleotide variant phylogenomics method were used to demarcate and manage the outbreak. RESULTS: Thompson were identified through whole genome sequencing. The onset dates of symptoms for the 16 cases that presented enteric symptoms were November 21-December 2, 2016. Two cases that presented with atypical symptoms were not reported until February 2017. Among the 18 cases, 16 had eaten or probably eaten chicken shawarma at the same restaurant chain and nine of these cases ate it at the same restaurant. In total, five restaurants from this chain, spread throughout three border regions of Quebec, were identified. CONCLUSION: Outbreaks associated with chicken shawarma have been identified in the past. Efforts must be made to ensure that the owners of this type of restaurant know the contamination risk associated with this type of cooking and take the necessary steps to reduce this risk. The use of the genome sequencing method was very useful in defining the outbreak.
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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 | 0.001 |
| 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 | 0.001 |
| 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".