Clonal diversity of Streptococcus pneumoniae serotype 19A collected from children < 5 years old in Québec, Canada, 2016-2021

Alyssa R Golden; Brigitte Lefebvre; Geneviève Deceuninck; Nicholas Brousseau; Philippe De Wals; Caroline Quach; Walter H B Demczuk; Irene Martin

doi:10.1016/j.vaccine.2023.09.042

Clonal diversity of Streptococcus pneumoniae serotype 19A collected from children < 5 years old in Québec, Canada, 2016-2021

Vaccine. 2023 Oct 20;41(44):6612-6618. doi: 10.1016/j.vaccine.2023.09.042. Epub 2023 Sep 25.

Authors

Alyssa R Golden¹, Brigitte Lefebvre², Geneviève Deceuninck³, Nicholas Brousseau⁴, Philippe De Wals⁵, Caroline Quach⁶, Walter H B Demczuk⁷, Irene Martin⁷

Affiliations

¹ National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada. Electronic address: alyssa.golden@phac-aspc.gc.ca.
² Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada.
³ Centre de recherche du Centre hospitalier universitaire de Québec, Équipe de recherche en vaccination, Québec, QC, Canada.
⁴ Centre de recherche du Centre hospitalier universitaire de Québec, Équipe de recherche en vaccination, Québec, QC, Canada; Institut national de santé publique du Québec, Direction des risques biologiques, Québec, QC, Canada.
⁵ Institut national de santé publique du Québec, Direction des risques biologiques, Québec, QC, Canada; Département de médecine sociale et préventive, Université Laval, Québec, QC, Canada.
⁶ Department of Microbiology, Infectious Diseases and Immunology, University of Montreal, Montreal, QC, Canada.
⁷ National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.

PMID: 37758569
DOI: 10.1016/j.vaccine.2023.09.042

Abstract

Streptococcus pneumoniae serotype 19A is a highly diverse, often antimicrobial-resistant Gram-positive bacterium which can cause invasive pneumococcal disease (IPD). In 2021, public health authorities in the Canadian province of Québec observed an increase of serotype 19A IPD in children <5 years. The purpose of this study was to determine the clonal composition of serotype 19A isolates collected from this age group in Québec, from 2016 to 2021. Forty-one and 37 IPD isolates from children <5 years from Québec and the remainder of Canada, respectively, were sequenced using the Illumina NextSeq platform. Phylogenetic analysis using SNVPhyl identified three clusters, corresponding to three common clones of serotype 19A: CC199, CC320 and ST695. CC199, predominantly represented by ST416, accounted for similar proportions of serotype 19A isolates collected from children in Québec (19.5 %) and other Canadian jurisdictions (OCJs, 21.6 %), with significant presence of ermB (62.5 % and 60 % of ST416 isolates, respectively). CC320 was more commonly identified from OCJs in comparison to Québec (18.9 % vs. 7.3 %, respectively), but were highly antimicrobial-resistant regardless of region. ST695 was the most common clone of serotype 19A collected in Québec from children <5 years, representing 65.9 % of isolates collected over the study period (40.5 % of isolates collected in OCJs). Phylogenetic analysis identified geographical differences in ST695 across Canada; including a large clade specific to Québec (with both susceptible and macrolide-resistant [ermB] subclades), and a separate macrolide-resistant (mefA) clade associated with OCJs. The Québec-specific ermB-ST695 clone represented 48.1 % of ST695 collected from the province. Continued genomic surveillance of S. pneumoniae serotype 19A is required to: i) track the prevalence and clonal composition of serotype 19A in Québec in future years; ii) characterize the clonal distribution of serotype 19A in adult populations; and iii) monitor whether the currently geographically restricted ermB-ST695 clone observed in Québec expands to OCJs.

Keywords: Canada; Children; Serotype 19A; Streptococcus pneumoniae; Whole genome sequencing.