We study pneumococcal infection that are major contributors to morbidity and mortality world wide. New conjugated pneumococcal vaccines have been launched targeting only a minor proportion of pneumococcal strains circulating in the society. He we aim at studying the genomic content of pneumococcal strains as well as perform transcriptomic analyses on different conditions. We aim at investigating why certain non-vaccine pneumococcal strains/clonal types are emerging after vaccination.Hence we are sequencing a large collection of clinical isolates of pneumococci. The project includes several bioinformaticians and is a collaboration between professor Jens Lagergrens (KTH) and professor Birgitta Henriques Normarks (KI/KS) groups.