Figure 2: Characteristics and virulence gene content for each isolate in relation to a maximum likelihood phylogenetic tree.

(A) Maximum likelihood tree of S. suis based on 55464 non-recombinant core genome SNPs as determined by Gubbins. The phylogenetic tree included all 116 S. suis isolates from this study and BAPS population grouping is overlaid on the branches. The tree illustrates how the isolates from BAPS groups 2 and 6 cluster together on a branch that only consists of Dutch isolates and none of the reference isolates. BAPS group 3, consisting solely of the MLST singleton isolate 9401240, is the most outlying isolate. (B) Characteristics of isolates in relation to population group. The serotype, clonal complex and host species from which the isolate was obtained are indicated with colored strips. (C) The presence and absence matrix of each of 84 virulence factors for each isolate. Presence is indicated with a black box, and absence with a white box. The name or description of each virulence factor is indicated above the matrix and further information for each factor is provided in Supplementary Table 2. (D) Presence and absence of the 18.5 kb prophage region encoding a type I restriction modification system and the extracellular protein variants. Presence of the prophage is indicated with a solid red box, and absence is indicated with a white box. The composition of the prophage is illustrated in Supplementary Fig. 13. Presence of a variant of the extracellular protein for each of the isolates. Green: EF, magenta: EF* and Cyan: EF+.