The Genomics of Streptococcus pneumoniae carriage isolates from children and their household contacts, pre-PCV7 to post-PCV13.

We used WGS analysis to investigate the population structure of 877 Streptococcus pneumoniae isolates from five carriage studies from 2002 (N=346), 2010 (N=127), 2013 (N=153), 2016 (N=187) and 2018 (N=64) in UK households which covers the period pre-PCV7 to post-PCV13 implementation. The genomic lineages seen in the population were determined using MLST and PopPUNK which was used for local and global comparisons. A Roary core genome of all the carriage genomes was to investigate phylogenetic relationships between the lineages. The results showed an influx of previously undetected sequence types after vaccination associated with non-vaccine serotypes. A small number of lineages persisted throughout, associated with both non-vaccine and vaccine types (ST199), or that were examples of serotype switching from vaccine to non-vaccine types (ST177 and ST162). Serotype 3 persisted throughout the study years, represented by ST180 and Global Pneumococcal Sequencing Cluster (GPSC) 12; however, the local PopPUNK analysis and core genome maximum likelihood phylogeny separated them into two clades, one clade only seen in later study years. The genomic data showed that serotype replacement in the carriage studies was mostly due to a change in genotype as well as serotype, but that some important genetic lineages, previously associated with vaccine types persisted.