Pre-vaccine serotype composition within a lineage signposts its serotype replacement – a carriage study over 7 years following pneumococcal conjugate vaccine use in the UK

This is the first description of the population structure of this collection of pneumococcal carriage isolates in the UK. This study sought to define dominant lineages and their dynamics over the study period. When a non-vaccine type (NVT) was detected in a vaccine type (VT) lineage in the pre-pneumococcal conjugate vaccine (PCV) era, that NVT was observed to expand, replacing the vaccine serotype. If it can be predicted which NVT/genotype combinations are likely to be involved in replacement, the clinical impact can be assessed, via the lineages antibiotic resistance and virulence determinants profile and the invasive potential of the serotype expressed. Establishing the population structure and serotype mixture of lineages in countries thinking about PCV implementation could therefore offer additional, geographically specific, information during the PCV selection process.