Figure 5: Mapping plot representing the presence of the 89k pathogenicity region in the sequenced isolates.

(A) Maximum Likelihood tree, created by Gubbins, on the core genome using only the sequenced isolates. Branch lengths were ignored for clarity. (B) Annotated pathogenicity island extracted from isolate 05ZYH33 and visualized by Artemis. The salK/salR two component signaling system is indicated by the magenta coding sequences. (C) Heat map demonstrating the presence/absence of the pathogenicity island. The reads from the sequenced isolates were mapped against the 89k pathogenicity island from isolate 05ZYH33 and a maximum read coverage was set at 50 to demonstrate a presence by red and an absence by blue. Each row describes the presence/absence for one isolate. Only CC20 isolates contained the salK/salR system and the synteny of the pathogenicity island was checked in the assemblies of the CC20 isolates.