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Streptococcus pneumoniae is a major cause of morbidity and mortality in all age groups. In a few years, penicillin non-susceptible pneumococci (PNSP) have emerged worldwide as a new threat. In order to better understand the mechanisms behind the rapid expansion of these strains, the virulence of 10 clinical and two transformed PNSP strains were compared with the virulence of three fully susceptible strains in a mouse model of bacteremia and a rat model of acute otitis media. Serotype, antibiotic susceptibility, and to some extent also genetic profile and growth rate of the strains were investigated before inoculation. The animals were monitored for up to 7 days after challenge by clinical examinations/otomicroscopy and cultures from middle ears and blood. The results of the study demonstrated that the PNSP strains had a significantly reduced ability to persist at the infectious site, and to some extent also to induce infections, compared with fully susceptible strains. The reduction was most evident for strains isolated from sources other than blood. It is therefore possible that other factors than virulence factors are of importance for the ability of PNSP strains to expand.