DISPATCHES Genomic Analysis of emm59 Group A Streptococcus
Bibliographic record
Abstract
Genomic analysis of type emm59 group A Streptococcus invasive strains isolated in the United States discovered higher than anticipated genetic heterogeneity among strains and identifi ed a heretofore unrecognized monoclonal cluster of invasive infections in the San Francisco Bay area. Heightened monitoring for a potential shift in the epidemic behavior of emm59 group A Streptococcus is warranted. Group A Streptococcus (GAS) causes human diseases ranging in severity from uncomplicated pharyngitis to life-threatening necrotizing fasciitis (1). GAS strains have traditionally been classified based on a serologic reaction against the M protein, a polymorphic cell surface adhesin and anti-phagocytic factor; GAS strains are currently typed by sequencing the 5 ′ hypervariable region of the emm gene, encoding M protein (2–4). Studies of large numbers of GAS isolates causing invasive infections and pharyngitis worldwide have shown that type emm59 GAS strains rarely cause disease (5,6). However, an increase in the frequency and severity of invasive infections caused by type emm59 strains (>500 cases since 2006) has been reported recently in Canada (7). One of the most striking features of the emm59 epidemic in Canada was its rapid spread; invasive emm59 disease was reported in most Canadian provinces and territories in a matter of only a few years (7). By using whole-genome sequencing and animal models of invasive disease, we recently discovered that virtually all type emm59 GAS invasive cases in Canada were caused by a single, recently emerged, hypervirulent emm59 clone (8). Whole-genome sequence analysis also revealed distinct spatiotemporal patterns of subclone diversification of the epidemic clone in Canada (8). Furthermore, we discovered that several geographically clustered cases of type
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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 | 0.002 | 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) | 0.001 | 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".