Fig. 4: Bayesian phylogeny and population dynamics of major MRSA clones in Japan.

The three major MRSA clones are shown in (a), CC1; (b), CC8; and (c), CC5. Upper panel indicates the Bayesian maximum clade credibility time-calibrated phylogenies based on non-recombining regions of the core genome of each CC. Arrow nodes indicate the divergence date (median estimate with 95% highest posterior). Blue horizontal bars at each node represent 95% confidence intervals. Lower panel, Bayesian skyline plots showing changes in effective population size over time. Median is represented by a dark blue line, and 95% confidence intervals are in light blue. Index No. 1–5 represents the STs, SCCmec type, ACME type, spa typing, and VFGs/AGRs, respectively. In index No. 5 of each CC, ant(9)-Ia and erm(A) harbored in Tn554 are indicated in red. In CC8 (b), MRSA/J acquired SCCmecIVl, genomic island vSa4, and se1-harboring plasmid somewhere between 1957 and 1986. sec, tst-1, and sel on vSa4 and se1-harboring plasmid are indicated in blue (see also Supplementary Fig. 7a and b). Some strains of ST8-SCCmecIVj and ST8-SCCmecI acquired tet(M)-harboring Tn916-like transposable unit somewhere between the late 1980s and 1990s. tet(M) is indicated in green (see also Supplementary Fig. 7c). In CC5 (c), in the process leading to the emergence of ST5-SCCmecII (N/J clone) and ST764-SCCmecII, it is estimated that SCCmecII, genomic islands, and transposons were acquired stepwise. The related VFGs are indicated in blue, and tet(M) is indicated in green (see also Supplementary Fig. 8).