Kenya_pneumococcal_genome_sequencing_project

This work is a collaboration to characterise pneumococci recovered from both children and adults residing in Kilifi, Kenya. Pneumococci have been collected from healthy children (via nasopharyngeal swabs) during the course of several large-scale carriage studies in Kilifi and from patients of all ages with invasive disease who presented to the district hospital in Kilifi. 3400 of these pneumococcal isolates have been selected for whole genome sequencing: 2500 from carriage and 900 from invasive disease. These pneumococcal genomes will be investigated to determine 1) Pneumococcal population structure pre- and post-vaccine introduction. 2) Evidence for vaccine-induced changes in the population structure, including in the distribution of circulating serotypes and genetic lineages. 3) The prevalence and diversity of pneumococcal bacteriocins in this strain collection, and the associations between pneumococcal serotypes and genetic lineages and their respective bacteriocins. 4) Changes in the distribution of bacteriocins post-vaccine implementation.