FIG 3.

Seventh pandemic core genome phylogeny with MGT2 and MGT3 assignments. A 7P seventh pandemic (7P) core genome phylogeny based on MGT8 alleles was calculated and visualized with GrapeTree. Allelic distances of 4,770 7P isolates were used to generate a phylogeny using the rapid neighbor-joining algorithm (43). Nodes were MGT8 STs and node sizes were proportional to the number of isolates with the same MGT8 ST. Clades corresponding to 7P waves are indicated. Nodes are colored by MGT3 ST. The number of isolates per ST is shown in square brackets. MGT3 STs with less than 10 isolates were grouped into “Other” and are marked in white. Branches longer than 50 allelic differences were truncated and are represented as dashed lines.