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Evolving genomic landscape of pediatric pneumococcus in two Canadian urban centers following conjugate vaccination

Sarah Teatero1, Allison McGeer2,3, Agron Plevneshi2

  • 1Public Health Ontario, Toronto, ON, Canada.

Frontiers in Microbiology
|September 3, 2025
PubMed

Insights

Pneumococcal conjugate vaccines (PCVs) reduced disease but led to new serotypes and antimicrobial resistance. Ongoing genomic surveillance is crucial for monitoring these evolving trends in pediatric invasive pneumococcal disease (IPD).

Area of Science:

  • Microbiology
  • Epidemiology
  • Genomics

Background:

  • Pneumococcal conjugate vaccines (PCVs) have decreased pediatric invasive pneumococcal disease (IPD).
  • Concerns persist regarding vaccine escape variants, emergence of non-vaccine serotypes (NVTs), and antimicrobial resistance (AMR).

Purpose of the Study:

  • To analyze long-term trends in serotype distribution, lineage composition, and AMR patterns of pediatric IPD.
  • Focus on Calgary and Toronto, Canada, post-PCV introduction.

Main Methods:

  • Whole-genome sequencing and epidemiological data from 818 pediatric IPD isolates (1998-2016).
  • Phylogenetic analysis, serotype characterization, and AMR profiling across three vaccine eras.

Main Results:

  • PCV reduced vaccine serotypes but NVT expansion occurred (e.g., 22F, 33F, 15B), with regional variations.
  • Serotypes 19A and 3 persisted; capsular switching led to re-emergence of pre-vaccine lineages.
  • Macrolide resistance increased significantly in Calgary; penicillin resistance remained low.

Conclusions:

  • Pneumococcus demonstrates sustained adaptation via serotype replacement, vaccine escape, and AMR spread.
  • Genomic surveillance is vital for tracking trends and informing vaccination strategies.
Abstract

Keywords:
Canada (Calgary, Alberta, Toronto, Ontario)Streptococcus pneumoniaeantimicrobial resistancegenomic epidemiologypneumococcal conjugate vaccine (PCV)serotype replacementvaccine escapewhole-genome sequencing

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