Prediction of Genetic Relatedness of Escherichia coli Using Long-Read Sequencing Paired with Neighbour Typing: A Tool for Rapid Antibiotic-Resistant Organism Outbreak Detection - Updated E. coli database
Bibliographic record
Abstract
The enhanced E. coli database used for the initial analyses in this publication and the iterative databases used for the intermediate steps in the long outbreak analysis. The enhanced database consists of the initial isolates included in the previously published E. coli database (DOI: 10.5281/zenodo.11042579) with additional isolates added for missing and under-represented STs (ecoli_enhanced_mlst_db.zip). Additional MLST isolates were downloaded from NCBI. The iterative databases for the long outbreak have also been included (ecoli_extout_dbs.zip), with outbreak isolates added to the above enhanced database. Files from the databases (.k18.tar.gz and .k18.tsv) and original metadata (.tsv) and genetic trees (.tree) have been included for each database.
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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 | 0.002 | 0.006 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.003 | 0.004 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.002 | 0.002 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.010 | 0.011 |
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".