Evolving genomic landscape of pediatric pneumococcus in two Canadian urban centers following conjugate vaccination
Background and aimPneumococcal 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 lon...
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Frontiers Media S.A.
2025-08-01
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1642658/full |
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| author | Sarah Teatero Allison McGeer Allison McGeer Agron Plevneshi Leah J. Ricketson James D. Kellner James D. Kellner James D. Kellner James D. Kellner James D. Kellner Nahuel Fittipaldi Nahuel Fittipaldi |
| author_facet | Sarah Teatero Allison McGeer Allison McGeer Agron Plevneshi Leah J. Ricketson James D. Kellner James D. Kellner James D. Kellner James D. Kellner James D. Kellner Nahuel Fittipaldi Nahuel Fittipaldi |
| author_sort | Sarah Teatero |
| collection | DOAJ |
| description | Background and aimPneumococcal 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.MethodsWe 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.ResultsPCV 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.ConclusionOur 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. |
| format | Article |
| id | doaj-art-54ef675848964b5890bf6b1e87eccff2 |
| institution | DOAJ |
| issn | 1664-302X |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj-art-54ef675848964b5890bf6b1e87eccff22025-08-20T03:06:58ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2025-08-011610.3389/fmicb.2025.16426581642658Evolving genomic landscape of pediatric pneumococcus in two Canadian urban centers following conjugate vaccinationSarah Teatero0Allison McGeer1Allison McGeer2Agron Plevneshi3Leah J. Ricketson4James D. Kellner5James D. Kellner6James D. Kellner7James D. Kellner8James D. Kellner9Nahuel Fittipaldi10Nahuel Fittipaldi11Public Health Ontario, Toronto, ON, CanadaDepartment of Microbiology, Sinai Health System, Toronto, ON, CanadaDepartment of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, CanadaDepartment of Microbiology, Sinai Health System, Toronto, ON, CanadaDepartment of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, CanadaDepartment of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, CanadaAlberta Children's Hospital Research Institute, Calgary, AB, CanadaDepartment of Community Health Sciences, University of Calgary, Calgary, AB, CanadaDepartment of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, AB, CanadaAlberta Health Services, Calgary, AB, CanadaPublic Health Ontario, Toronto, ON, CanadaGREMIP and CRIPA, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, CanadaBackground and aimPneumococcal 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.MethodsWe 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.ResultsPCV 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.ConclusionOur 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.https://www.frontiersin.org/articles/10.3389/fmicb.2025.1642658/fullStreptococcus pneumoniaepneumococcal conjugate vaccine (PCV)serotype replacementantimicrobial resistancewhole-genome sequencinggenomic epidemiology |
| spellingShingle | Sarah Teatero Allison McGeer Allison McGeer Agron Plevneshi Leah J. Ricketson James D. Kellner James D. Kellner James D. Kellner James D. Kellner James D. Kellner Nahuel Fittipaldi Nahuel Fittipaldi Evolving genomic landscape of pediatric pneumococcus in two Canadian urban centers following conjugate vaccination Frontiers in Microbiology Streptococcus pneumoniae pneumococcal conjugate vaccine (PCV) serotype replacement antimicrobial resistance whole-genome sequencing genomic epidemiology |
| title | Evolving genomic landscape of pediatric pneumococcus in two Canadian urban centers following conjugate vaccination |
| title_full | Evolving genomic landscape of pediatric pneumococcus in two Canadian urban centers following conjugate vaccination |
| title_fullStr | Evolving genomic landscape of pediatric pneumococcus in two Canadian urban centers following conjugate vaccination |
| title_full_unstemmed | Evolving genomic landscape of pediatric pneumococcus in two Canadian urban centers following conjugate vaccination |
| title_short | Evolving genomic landscape of pediatric pneumococcus in two Canadian urban centers following conjugate vaccination |
| title_sort | evolving genomic landscape of pediatric pneumococcus in two canadian urban centers following conjugate vaccination |
| topic | Streptococcus pneumoniae pneumococcal conjugate vaccine (PCV) serotype replacement antimicrobial resistance whole-genome sequencing genomic epidemiology |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1642658/full |
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