Evolving genomic landscape of pediatric pneumococcus in two Canadian urban centers following conjugate vaccination
Bibliographic record
Abstract
Background and aim: Pneumococcal conjugate vaccines (PCVs) have significantly reduced pediatric invasive pneumococcal disease (IPD). However, vaccine escape variants, the emergence of non-vaccine serotypes (NVTs), and antimicrobial resistance (AMR) remain ongoing concerns. We aimed to characterize long-term trends in serotype distribution, lineage composition, and AMR patterns among pediatric IPD cases following PCV introduction in two major Canadian urban centers: Calgary, Alberta, and Toronto, Ontario. Methods: We combined whole-genome sequencing with epidemiologic data from 818 pediatric IPD isolates collected through population-based, active surveillance in Calgary (1998-2016) and Toronto (2009-2016). Phylogenetic analyses, serotype characterization, and AMR profiling were performed to assess temporal trends across three vaccine eras. Results: PCV implementation reduced vaccine type serotypes but was followed by expansion of NVTs, including serotypes 22F, 33F, and 15B, with regional differences in prevalence. Serotypes 19A and 3 persisted despite PCV13 inclusion. Several pre-vaccine-associated lineages re-emerged under NVT capsules, indicating capsular switching. Macrolide resistance increased in Calgary (7.4-29.3%), distributed across multiple lineages; penicillin resistance remained infrequent. Conclusion: Our findings highlight sustained pneumococcal adaptation through serotype replacement, vaccine escape, and AMR dissemination. Ongoing genomic surveillance is essential to monitor these trends and inform vaccination policies.
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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) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.002 | 0.004 |
| Science and technology studies | 0.003 | 0.001 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 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 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".