Respiratory_pathogen_and_microbiome_co_colonisation_study

This is a small supplement to Study G3376 which is designed to look for associations between seasonal changes in climatic conditions in the meningitis belt of Africa and the microbiome of human nasopharynx. In this supplement we wish to study the genomes of 384 pathogens, Streptococcus pneumoniae and Neisseria meningitidis, isolated from nasopharynx in the same cohort. The data will allow the following analyses 1. Genomic characterisation of the pathogens circulating within the cohort, analysed in the context of broder regional/global genome datasets 2. Association of pathogen genotype and microbiome profile 3. Evidence of recombination between pathogens and other members of the microbiome This study will serve as a pilot for subsequent larger studies.