Despite its inclusion in pneumococcal conjugate vaccine 13 (PCV13), Streptococcus pneumoniae serotype 3 remains a major cause of invasive pneumococcal disease in England and Wales. Previous studies have indicated that there are distinct lineages within serotype 3 clonal complex 180 and the clade distributions have shifted in recent years with the emergence of clade II. We undertook whole genome sequencing and genomic analysis of 616 serotype 3 isolates from England and Wales between 2003 and 2018, including invasive and carriage isolates. Our investigations showed that clade II has expanded since 2014 and now represents 50% of serotype 3 invasive pneumococcal disease (IPD) isolates in England and Wales. Genomic analysis of antibiotic resistance and protein antigen genes showed that distinct profiles are present within the clades which could account for the recent emergence of this clade. This investigation highlights the importance and utility of routine whole genome sequencing and its ability to identify new and emerging variation at the single nucleotide level which informs surveillance and will impact future vaccine development.
Bibliographical noteFunding Information:
The authors would like to thank the Public Health England Central Sequencing Laboratory for the production of the sequencing data used within this project. The authors would also like to thank Taj Azarian and Ben Metcalfe for sharing their expertise and data with us to enable the completion of this project.
© 2019 by the authors. Licensee MDPI, Basel, Switzerland.
- Serotype 3
- Streptococcus pneumoniae
- Whole genome sequencing