Genetic Analysis of Invasive Pneumococcal Isolates from Children in Ontario, Canada, 2007–2012
Bibliographic record
Abstract
BACKGROUND: Multilocus sequence typing (MLST) is commonly used to understand the genetic background of invasive pneumococcal disease (IPD) isolates. This study was conducted to identify serotype and genetic change among IPD isolates in Canadian children following vaccine use. METHODS: Clinical isolates collected from children ≤5 years old of Ontario, Canada with IPD during 2007-2012 were characterized with serotyping, multilocus sequence typing and antimicrobial susceptibility testing. RESULTS: One year after 13-valent pneumococcal conjugate vaccine (PCV13) implementation, a decline in 19A and 7F was observed in 2012, coincident with the rise of serogroup 15 and 22F. Clonal complex (CC) 199, CC320 and CC695 are 3 major CCs in 19A (74%). From 2007 to 2012, clonal shift was detected in the 19A population as CC320 and CC199 declined, whereas CC695 rose to a majority. Genetically, serogroup 15 was composed of 2 CCs and 7 sequence types (STs), making it more diverse than serotypes 3, 7F and 22F. Interestingly, 60% of 15C isolates were a novel ST, suggesting high single nucleotide polymorphism frequency in house-keeping genes of 15C. Several newly appeared STs found in 19A and 15 indicate the possibility of recent serotype switching events. CONCLUSION: Genetic shift because of PCV13 impact may have resulted in the decline of 19A in IPD. Recent rise of serogroup 15 infections in children could be because of its selective advantage conferred by genetic diversity, frequent recombination in the population plus drug resistance potential related to CC63 genotype. Close monitoring of serotype replacement and genetic change in IPD among children post-PCV13 is warranted.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| 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 | 0.001 |
| 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 teacher head, 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".