Fig. 2

Genome-to-genome networks provide insight into population structure and associations. A Phylogenetic tree of all S. aureus isolates produced using ParSNP v1.2. Largest clonal complexes (CCs) are coloured and labelled, with minor CCs in white. B Relationship network between genomes based on the accessory genome visualised in 3D. Nodes represent individual isolates, edges represent shared accessory gene content (JSC > 0.8 filter applied), and a k-NN (k = 8) edge filter has been applied. The largest CCs are coloured and labelled, corresponding to the phylogeny in A. C The same network as in B but visualised using a 2D layout. Ci shows only CC5 isolates, demonstrating sub-structures within the network with nodes coloured by sequence type. D The same network as in C and Di the same network as in Ci, coloured by host