We study pneumococcal infection that are major contributors to morbidity and mortality worldwide. New conjugated pneumococcal vaccines have been launched targeting only a minor proportion of pneumococcal strains circulating in the society. Here 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. We have recently developed an ultra-sensitive meta-transcriptomic flow screen for investigating, coinfections, and host response during respiratory infections. We have mapped differences in virus and bacterial microbiota between healthy children, and from children with lower respiratory tract infections. We are also using this method to investigate the role of co-infections during covid-19 disease. Earlier observations has reported a possible link between co-infection of S pneumoniae and disease outcome of Covid-19. We have currently collected and sequenced lower respiratory samples from patients at Karolinska University Hospital and are in the process of expanding the spread and number of these samples. We plan to add an additional 250 samples covering the disease progression and more severe cases of the disease.