Epidemiological and genomic characterisation of an outbreak of Streptococcus pyogenes emm5.23
Bibliographic record
Abstract
OBJECTIVES: This retrospective cross-sectional study examined the epidemiology, clinical presentations, and genomics of Streptococcus pyogenes genotype emm5.23, linked to severe outcomes in Scotland. METHODS: Between 2014 and 2022, 58 cases of invasive Group A Streptococcus (iGAS) disease associated with emm5.23 were reported in Scotland. Surveillance data from 45 cases were analysed for clinical characteristics and risk factors. Whole-genome sequencing (WGS) included all available emm5.23 strains from Scotland (n=58), a subset from England (n=29), and emm5 strains of non-5.23 subtypes from Scotland (n=10), England (n=2), and Canada (n=1). RESULTS: Nearly all cases (96%, 43/45) were hospitalised, of whom 33% (15/45) required intensive care and 20% (9/45) died with iGAS. The most common presentations were bacteraemia (51%, 23/45) and pneumonia (24%, 11/45). WGS identified an emerging emm5.23 clade in Scotland, encompassing most isolates, which shared highly similar genomes and three non-synonymous polymorphisms. CONCLUSIONS: Although genomic traits known to increase GAS virulence potential were not found, polymorphisms that may affect the emm5.23 phenotype were detected. This suggests this emm5.23 genotype was transiently successful rather than hypervirulent, with low population-level immunity contributing to its spread. This study emphasises the need for integration of real-time genomic data in public health surveillance to enhance source attribution and guide interventions.
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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 | 0.001 | 0.002 |
| 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 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 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".