Progressive changes in pneumococcal carriage in children attending daycare in Portugal after 6 years of gradual conjugate vaccine introduction show falls in most residual vaccine serotypes but no net replacement or trends in diversity

► Pneumococcal ecology and its trends differ between settings. ► Disappearance of PCV7 serotypes takes longer if vaccine coverage is modest and 19F may persist. ► Net falls in pneumococcal carriage rates (and thus incomplete replacement) sometimes occur. ► High serotype diversity may persist without trends during changes in serotype distribution.