Additional file 2 of Drivers of methicillin-resistant Staphylococcus aureus (MRSA) lineage replacement in China

Additional file 2: Fig. S1. Core genome phylogeny for ST239 and ST59. Fig. S2. Regression of root-to-tip distance against sampling time for core genome alignments. Fig. S3. Global core genome phylogenies for ST239 and ST59. Fig. S4. Shared core and accessory genes amongst Chinese ST239 and ST59 isolates. Fig. S5. Conservation of accessory genome homology groups (HGs) across the Chinese ST239 and ST59 isolates. Fig. S6. Presence/absence of mobile genetic elements (MGEs) amongst Chinese ST239 and ST59 isolates. Fig. S7. Presence/absence of antimicrobial resistance genes amongst Chinese ST239 and ST59 isolates. Fig. S8. Presence/absence of virulence genes amongst Chinese ST239 and ST59 isolates. Fig. S9. Number of resistance (AMR) genes carried between ST sub-lineages. Fig. S10. Changing trends of antimicrobial resistance (AMR) mutations/elements within ST239 and ST59 lineages over time. Fig. S11. Number of virulence genes carried between ST sub-lineages and within ST239 and ST59 sub-lineages. Fig. S12. Trends of virulence mutations/elements within Chinese ST239 and ST59 lineages over time. Fig. S13. Core genome phylogeny for ST239 annotated for sasX. Fig. S14. Methicillin resistance acquisition analyses. Fig. S15. Presence absence of virulence genes against cell lysis phenotype. Fig. S16. Colony counts at 0 hours and 96 hours for three ST59 isolates (wild-type and knock-out) compared to two possible ST239 control strains. Table S2. Inferred tMRCA, clock rates and marginal likelihoods inferred by Bayesian dating analyses. Table S3. The distribution of mobile genetic elements (MGEs) in different sub-lineages. Table S4. Bonferroni corrected p-values following fitting of a generalized linear model (GLM) for VFDB virulence gene presence / absence against cell lysis phenotype. Table S5. Relative adaptive difference (S), fitness (F) and fitness cost (C) estimated from the in vitro competition experiment between ST59-WT and ST59 ��chp.