Kenya_pneumococcal_genome_sequencing_project. Kenya_pneumococcal_genome_sequencing_project

This work is a collaboration between Anthony G. Scott (LSHTM), Angela B. Brueggemann (Imperial) and Stephen D Bentley (WTSI) 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. The pneumococci will be prepared in Kilifi by Anthony Scott’s group and shipped to Angela Brueggemann’s group at Imperial, where the DNA will be extracted. Angela Karani, from Anthony Scott’s group, will spend a period of time at Imperial helping to extract the DNA. Genomic DNA will be sent to the Sanger Institute for sequencing and data analyses will be performed collaboratively by all three research groups. These pneumococcal genomes will be investigated to determine: a) Pneumococcal population structure pre- and post-vaccine introduction. b) Evidence for vaccine-induced changes in the population structure, including in the distribution of circulating serotypes and genetic lineages. c) The prevalence and diversity of pneumococcal bacteriocins in this strain collection, and the associations between pneumococcal serotypes and genetic lineages and their respective bacteriocins. d) Changes in the distribution of bacteriocins post-vaccine implementation. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/