Monomorphic genotypes within a generalist lineage of <i>Campylobacter jejuni</i> show signs of global dispersion
Bibliographic record
Abstract
Abstract The decreased costs of genome sequencing have increased capability to apply whole-genome sequence on epidemiological surveillance of zoonotic Campylobacter jejuni . However, knowledge about how genetically similar epidemiologically linked isolates can be is vital for correct application of this methodology. To address this issue in C. jejuni we investigated the spatial and temporal signals in the genomes of a major clonal complex and generalist lineage, ST-45 CC, by exploiting the population structure and genealogy and applying genome-wide association analysis of 340 isolates from across Europe collected over a wide time-range. The occurrence and strength of the geographical signal varied between sublineages and followed the clonal frame when present, while no evidence of a temporal signal was found. Certain sublineages of ST-45 CC formed discrete and genetically isolated clades to which geography and time had left only negligible traces in the genomes. We hypothesize that these ST-45 CC clades form globally expanded monomorphic clones possibly spread across Europe by migratory birds. In addition, we observed an incongruence between the genealogy of the strains and MLST typing, thereby challenging the existing clonal complex definition and use of a common MLST-based nomenclature for the ST-45 CC of C. jejuni .
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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 | 0.000 |
| 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 | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 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".