An extended multi-locus molecular typing schema for Streptococcus pneumoniae demonstrates that a limited number of capsular switch events is responsible for serotype heterogeneity of closely related strains from different countries

► We define a molecular typing schema for Streptococcus pneumoniae (96-MLST). ► 96-MLST was able to partition strains into groups homogenous for capsular serotype. ► Changes of serotype occur occasionally during the short term expansion of clones. ► The geographical expansion of clones was due to a small number of transmissions.