Fig. 1

Whole genome sequence dated phylogeny, antimicrobial resistance, and genetic polymorphisms in the ST-1901-associated core-genome group. Left: A clonal dated phylogeny with corrected branch lengths to account for homologous recombination. In the heat map, the 3rd column titled “complete genome” shows the three Japanese strains harboring penA-34 from 2005 in blue and the ancestral Japanese strain (at the bottom) harboring penA-5 in green, whereas the WHO_Y (F89) strain is in pink. In the 4th column titled “ST”, ST-1901 and its single locus-variants are colored using different colors as shown in our previous study [11]. In the 6th and 7th column, susceptible/resistant (S/R) categories according to the EUCAST breakpoint of 3GCs (cefixime CFM and ceftriaxone CRO) are shown. The columns were colored gray when the MIC values were missing. In the 8th column, the presence (light yellow-green) or absence of any non-mosaic penA allele is shown. In the 9th–12th columns, the presence (light yellow-green) or absence of a specific non-mosaic penA allele is shown. The 13th column shows the presence (cyan) or absence any mosaic penA allele. The 14th–18th columns show presence (cyan) or absence a specific mosaic penA allele (specifically, 34 and its variants [35], 10 and its variants [35], and 35 [17]). The 19th column shows the susceptible/resistant (S/R) categories of fluoroquinolones (mostly ciprofloxacin, and much less frequently, levofloxacin) according to the EUCAST breakpoint. The 20th–21st columns show the presence (yellow-green) or absence of nonsynonymous amino acid changes compared to the wild type in GyrA. The 22nd–24th 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, a red circle indicates emergence of the sub-lineage 34, whereas two purple lines indicate 95% confidence intervals examined in the main text (emergence time of the sub-lineage 34, and that of one of the three sub-lineages harboring penA-10)