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Mid-point rooted phylogenetic tree of S. aureus USA300 isolates. Two most closely related non-USA300 isolates were included as an out-group (isolates PFESA2332 and PFESA1492, red branches). Also, two reference genomes were included and corresponding nodes are marked with a star. Branches were highlighted to show consecutive clades of the nested clade structure, and labelled 1 to 6. SNPs that define each labelled clade are described in Table 2.
