Accumulation of Single Nucleotide Polymorphism (SNP) Mutations in Escherichia coli Grown Under Food Production Conditions and Their Importance in Outbreak Strain Epidemiology
Bibliographic record
Abstract
Food borne illness outbreak investigations require accurate genotyping to identify outbreak clusters and link them to isolates recovered from possible sources of infection.Traditional genotyping methods such as PFGE lack the resolution to differentiate highly similar but epidemiologically unrelated isolates.Single Nucleotide Polymorphism (SNP) analysis of whole genome sequences shows promise in providing the required level of resolution, but lacks field relevant data to aid interpretation of results.Here, three E. coli strains of serotypes commonly associated with foodborne illness outbreaks were used to inoculate lettuce growing under field conditions and recovered weekly for SNP analysis.This pilot study indicates that the number of SNP differences accumulated in these strains while growing under field relevant conditions is very low, but that variability exists between strains and further study is warranted.These results will aid interpretation of SNP analyses during food outbreak investigations and help support resulting regulatory decisions.
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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 | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.001 |
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".