Natural_trends_in_pneumococcal_population_evolution_over_25_years_in_Israel

Streptococcus pneumoniae is commonly found as a coloniser of the nasopharynx of healthy humans. Colonisation is a prerequisite for progression to disease but the mechanisms which lead to disease are only partially understood. Through this collaboration we will build a longitudinal dataset which comprises genomes from bacterial isolates collected from both healthy carriers and cases of disease, specifically children with pneumonia who represent the most important burden of pneumococcal disease. Comparison of genetic variants found in the isolates found in disease and healthy carriage will allow the identification of genes and variants important in the process of pathogenesis. Such genetic associations are often hindered by biases in the dataset. In this study we will have a rich and balanced dataset with equivalent numbers of disease and carriage samples collected from children over a 20-year period in the same geographic setting providing unprecedented analytical power. Furthermore, the longitudinal nature of the data will allow greater detection of epistatic interactions between disease-associated genes as external forces affect the balance of gene variant frequencies.