Development of multiple resistances to antibiotics in staphylococci, enterococci and pneumococci became a health threat during the past 20 years, not only with respect to nosocomial infections. This resistance development is based on acquisition of resistance genes by predominant epidemic subpopulations (clonal complexes). Although emergence and spread of methicillin-resistant Staphylococcus aureus is associated with a limited number of epidemic clones which have been widely disseminated, acquisition of SCCmec elements by susceptible ancestors has taken place at different times and at different locations. Among Staphylococcus epidermidis and Enterococcus faecium, one clonal complex, which had acquired resistance genes at several occasions, is widely disseminated in hospitals. Also in Streptococcus pneumoniae, antibiotic resistance is preferentially associated with clonal lineages which have a capacity for spreading. They became, however, more rare after introduction of the 7-valent conjugate vaccine.