Using genomics to examine the persistence of Streptococcus pneumoniae serotype 19A in Ireland and the emergence of a sub-clade associated with vaccine failures

Streptococcus pneumoniae serotype 19A remains a significant cause of invasive pneumococcal disease (IPD) in Ireland despite the successful introduction 13-valent conjugate vaccine (PCV13) 2010 which reduced overall incidence IPD children. Invasive isolates from Irish reference laboratory between 2007–08 and 2017–18 were analysed using whole genome sequencing (WGS) to investigate persistence this vaccine-preventable serotype. We compared entire national collection other international collections standardised nomenclature Global Pneumococcal Sequencing Clusters (GPSC). Expansion GPSCs clonal complexes (CCs) may have been associated with antimicrobial prescribing policies. A sub-clade GPSC1-CC320 (n = 25) unique Ireland, included five ten failures/breakthrough cases identified (p 0.0086). This was not observed global collection. All within contained galE gene variant rarely 37/13454, p < 0.001) nor 19/227) 0.001). The estimated emerged at start PCV-vaccine era (ancestral origin 2000, range 1995–2004) expanded most isolated after PCV13 24/25). identification sub-clade/variant highlights benefit WGS analyse genotypes preventable S. pneumoniae. Particularly as more likely be vaccinated children than genotypes. It is possible that changes gene, involved capsule production but outside capsular polysaccharide biosynthesis locus, affect bacterial population. Discrete vaccine-serotype should further investigated inform strategies.