CC8 pangenome and phylogeny.

(a) Pangenomic analysis of CC8 genomes shows the distribution of genes and mutations in ORFs and regulatory regions. (b) Prevalence of USA300 specific genetic markers, PVL and SCCMecIVa, as you traverse up the phylogenetic tree from TCH1516. The gray dashed line represents the node where the USA300 root is placed. (c) Phylogenetic tree of CC8 genomes classified into USA300 and non-USA300 strains.

USA300 strains associated mutations.

(a) DBGWAS recovers components associated with USA300 previously described markers of USA300 strains including mecA (SCCMec IVa), arcA (ACME), cap5e mutation, seq, sek and Phi-PVL. In addition, components with many other mutations scattered throughout the genome (NC_010079) are also enriched. Each ‘significant node’ represents a k-mer sequence (with minimum size of 31 nucleotides) that are associated with USA300 strains (adjusted p-value < 0.05).

Linkage Disequilibrium and de novo mutations in USA300 strains.

(a) Enriched k-mers showed high linkage disequilibrium, with some k-mers at 1.4 Mbp distance still having r2 of greater than 0.98. (b) Schematic of position specific entropy analysis. Positions with heterogeneous sequences have higher calculated entropy than more conserved sequences with fewer mutations. (c) Using position specific entropy, we only found one example of shared enriched mutation in ORFs of USA300 and non-USA300 strains. (d) Distance (in base pairs) between the position of enriched mutation in USA300 strains and the position of the nearest entropy peak in other non-CC8 strains.

Strain-specific regulatory changes in the CC8 clade.

(a) ICA analysis of USA300 and non-USA300 RNA-sequencing data identified an iModulon with strain specific activity.(b) The strain-specific iModulon contained various horizontally acquired elements (e.g. ACME, PhiPVL) that are prevalent in USA300 lineage as well as conserved genes with strain-specific expression patterns. (c) Comparing the 5’ regulatory region of the gene isdH from various S. aureus strains revealed a unique deletion containing Fur binding site in USA300 reference strain TCH1516.