ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Infectious Agents and Disease
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1642658
Evolving Genomic Landscape of Pediatric Pneumococcus in Two Canadian Urban Centers Following Conjugate Vaccination
Provisionally accepted
Sarah Teatero1
Allison McGeer2,3
Agron Plevneshi2
Leah J. Ricketson4
James D. Kellner4,5,6,7
Nahuel Fittipaldi1,8*- 1Public Health Ontario, Toronto, Canada
- 2Mount Sinai Hospital, Toronto, Canada
- 3University of Toronto Department of Laboratory Medicine and Pathobiology, Toronto, Canada
- 4University of Calgary Department of Pediatrics, Calgary, Canada
- 5Alberta Children's Hospital Research Institute, Calgary, Canada
- 6University of Calgary Department of Microbiology Immunology and Infectious Diseases, Calgary, Canada
- 7University of Calgary Department of Community Health Sciences, Calgary, Canada
- 8Universite de Montreal, Montreal, Canada
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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 (1998Calgary ( -2016) ) and Toronto (2009)(2010)(2011)(2012)(2013)(2014)(2015)(2016). Phylogenetic analyses, serotype characterization, and AMR profiling were performed to assess temporal trends across three vaccine eras.Results. PCV implementation reduced VT disease 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% to 29.3%), distributed across multiple lineages; penicillin resistance remained infrequent.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.
Keywords: Streptococcus pneumoniae, pneumococcus, Vaccines, PCV, Whole-genome sequencing, Genomic epidemiology, Canada, Calgary, Alberta
Received: 06 Jun 2025; Accepted: 26 Jul 2025.
Copyright: © 2025 Teatero, McGeer, Plevneshi, Ricketson, Kellner and Fittipaldi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Nahuel Fittipaldi, Universite de Montreal, Montreal, Canada
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