FIG 5 .

Prophage content of the emm89 strains. Shown is the phylogeny inferred by neighbor-joining for the 1,193 clade 1, 2, and 3 isolates based on 8,989 core SNPs filtered to exclude SNPs acquired by horizontal gene transfer events. Isolates are colored by phage genotype (PG) as indicated in the index. PGs were assigned in order of prevalence of occurrence in the strain sample. With the exception of PG02 (absence of phage), most of the PGs are exclusive to a single clade. PG01 was first present in the strain sample in 2003 in two isolates, one each of clades 2 and 3. The year 2003 is also when epidemic clade 3 strains were first present in the strain sample.