Methicillin-resistant Staphylococcus aureus (MRSA) were first isolated in 1961, soon after the introduction of methicillin for therapeutic treatments. Since then, the rate of MRSA isolates among S. aureus has continuously increased to reach 60% in some healthcare institutions. The resistance to methicillin is conferred by the acquisition of the mecA gene, which is located on a large mobile genetic element called the Staphylococcal chromosome cassette mec (SCCmec), and, so far 11 types of SCCmec elements have been described (types I–XI). The population structure of S. aureus has been shown to be highly clonal, and previous genomic comparisons showed that about 75% of the S. aureus genome is highly conserved (core genome), while the remaining 25% varies significantly among strains (accessory genome). The accessory genome consists mostly of mobile genetic elements (MGEs), such as bacteriophages, pathogenicity islands, genomic islands, plasmids, transposons, and the SCCmec element. The importance of understanding the patterns of evolution of MGEs is illustrated by the SCCmec element, which has been acquired and/or transferred on multiple occasions during the evolution of the species.
The study of the population genetics of S. aureus has been addressed using multilocus sequence typing. Based on these data, the population structure of S. aureus was classified into related groups of strains defined as clonal complexes and their isolated sequence types. Extensive typing showed that the S. aureus population associated with humans consists of 10 major lineages and most MRSA belong to 6 of them. The presence of the same clones in different geographical regions suggested their rapid dissemination. Moreover, the epidemiology of MRSA is highly dynamic, and clonal replacement of predominant clones within a given locale has been widely documented. Although the reasons why some clones replace others are unclear, the emergence and replacement of clones might have significant consequences for public health, as different clones possess differing resistance and virulence attributes.