Group A Streptococcus emm Gene Types in Pharyngeal Isolates, Ontario, Canada, 2002–2010
Bibliographic record
Abstract
Group A Streptococcus (GAS) is a human-adapted pathogen that causes a variety of diseases, including pharyngitis and invasive infections.GAS strains are categorized by variation in the nucleotide sequence of the gene (emm) that encodes the M protein.To identify the emm types of GAS strains causing pharyngitis in Ontario, Canada, we sequenced the hypervariable region of the emm gene in 4,635 pharyngeal GAS isolates collected during 2002-2010.The most prevalent emm types varied little from year to year.In contrast, fi ne-scale geographic analysis identifi ed inter-site variability in the most common emm types.Additionally, we observed fl uctuations in yearly frequency of emm3 strains from pharyngitis patients that coincided with peaks of emm3 invasive infections.We also discovered a striking increase in frequency of emm89 strains among isolates from patients with pharyngitis and invasive disease.These fi ndings about the epidemiology of GAS are potentially useful for vaccine research.G roup A Streptococcus (GAS) is a gram-positive bacterial pathogen responsible for ≈600 million cases of pharyngitis each year worldwide (1).The widespread prevalence of this disease results in considerable costs, estimated to exceed $200 million annually in the United States alone (2).In addition to acute pharyngitis, GAS causes several other human diseases, ranging from relatively mild to more severe, such as necrotizing fasciitis, soft tissue infections, glomerulonephritis, acute rheumatic fever, and streptococcal toxic shock syndrome.Thus, infections caused by GAS are a major public health concern in the United States and Canada and throughout the world.GAS strains are classifi ed mainly on the basis of variation in a cell-surface molecule known as M protein, encoded by the emm gene (3,4).M protein is a critical virulence factor and a major site of the human antibody response against GAS.M type-specifi c immunity develops in persons recovering from some GAS infections (5,6).As a result, the portion of the emm gene that encodes the amino-terminal 100 residues of M protein is under strong diversifying selection pressure, and this region is hypervariable in terms of GAS types (7).Currently, >120 distinct emm types of GAS are recognized.Despite the considerable diversity of emm types of GAS isolates, epidemiologic studies have found that relatively few emm types tend to predominate within a local population; most isolates are composed of a small number of emm types (8,9).In distinct geographic areas, the predominant emm types often vary in frequency from year to year for reasons not fully understood.In addition, sizeable outbreaks can be caused by strains of a single emm type or of a small number of emm types.Overall, this combination of factors results in a complex epidemiologic situation for GAS pharyngitis.Recently, vaccine candidates have been identifi ed in an effort to reduce the prevalence of GAS disease and the number of human deaths it causes (10).Some of these experimental vaccines are based on the amino-terminus of Group A Streptococcus emm Gene Types in Pharyngeal Isolates, Ontario, Canada, 2002-2010
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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 | 0.002 |
| Science and technology studies | 0.001 | 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 | 0.000 |
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".