Phylogenetic trees based on (A) MLST, (B) entire aur genes and (C) shortened aur sequences. Phylogenetic trees for 50 S. aureus strains were constructed by using the neighbor-joining method based on the Kimura two-parameter model with MEGA 3.1. All branch lengths are drawn to scale. Bootstrap values were calculated for 1,000 replicates and are given for each branch. Strains used represent all combinations of STs and aur alleles. Each strain is abbreviated with the isolate designation, followed by the MLST (ST) designation in panel A, and the aur allele designation in panel B. CCs and supergroups are indicated in panel A. Phylogenetic analysis based on housekeeping gene sequences placed strains in groups which corresponded to CCs (Table 1) identified by the BURST analysis with the exception of the ST188 strains which were sorted as unique (panel A). The Supergroup is based on a reconstruction of S. aureus phylogeny conducted in this study and those presented previously [17, 18].