Fig. 2

Whole genome sequence dated phylogeny, antimicrobial, and genetic polymorphisms in the ST-7363-associated core-genome group. The columns in the heat map are almost the same as those in Fig. 1, although the first five columns in Fig. 1 have been omitted here. The 1st and 2nd columns show the susceptible/resistant (S/R) categories according to the EUCAST breakpoint of cefixime (CFM) and ceftriaxone (CRO). The 3rd column shows the presence (light yellow-green) or absence of any non-mosaic penA allele. The 4th–6th columns show the presence (light yellow-green) or absence of a specific non-mosaic penA allele. The 7th column shows the presence (cyan) or absence of any mosaic penA allele. The 8th–9th columns show the presence (cyan) or absence a specific mosaic penA allele (specifically, 10, and 34 or 37 (H041-type) [7]). The 10th column shows the susceptible/resistant (S/R) categories of fluoroquinolones (mostly ciprofloxacin, and much less frequently, levofloxacin) according to the EUCAST breakpoint. The 11th–12th columns show the presence (yellow green) or absence of nonsynonymous amino acid changes compared to the wild type in GyrA. The 13th–14th columns show the presence (green) or absence of nonsynonymous amino acid changes compared to the wild type in ParC. In the clonal dated phylogeny at the left, the two branches of interest examined in the main text are colored cyan and green, with 95% confidence interval of the two evolutionary events (acquisition of penA-10 and simultaneous amino acid substitutions at GyrA 95 and ParC 87-88) colored purple