Fig. 1

Prevalence of tfs ICE and selected cag genes in 187 H. pylori genomes (for a high resolution version of this figure, please see Additional file 6). a Clustering defines the strain representation and integrity of tfs ICEs relative to each other and cagPAI status. Distinct clusters (1–4) identify strains with similar representation of tfs and cag gene complements. Colouring of tfs4 gene subsets corresponds to different complements of orthologous genes contained within each of two left (L1 and L2), central (C1 and C2) or right (R1 and R2) ICE segment modules which may be contiguous with, isolated from or additional to the tri-module complement of a particular tfs4 ICE type. The tfs3 ICE lacks an equivalent pattern of modular variation and is more broadly defined by left and right segments. b tfs ICE and cag gene content data was transformed to reflect phylogeographic lineage of the originating strain as determined by MLST relative to a subset of 347 reference sequences obtained from the MLST database (Additional file 3: Figure S1). tfs and cag gene complements were coloured according to the phylogeographic population assigned to each strain, as indicated in the inset key. Hierarchical clustering identifies extensive erosion of the tfs ICEs in hpEurope strain populations