FIG 3.

Phylogenetic analysis of the 142 Sheffield HIC isolate genomes. A maximum likelihood phylogenetic tree was generated with the core gene alignment (1,185,813 bp) by using RAxML (51) with 100 bootstraps. All isolates clustered by emm type. The presence (black)/absence (white) of superantigen genes speA, speC, speG, speH to speM, speQ, speR, ssa, and smeZ and DNase genes sda1, sda2, sdn, spd1, spd3, and spd4 is indicated. Antimicrobial resistance genes (AMR) tetM, ermA, and ermB were also identified in some isolates (white, absent; black, present). The positivity for serum opacity factor (sof) is also shown, but in all emm12 types, this gene would produce a truncated variation of serum opacity factor (gray). The scale bar represents substitutions per site. emm types are colored for easy visualization, and type numbers are also given.