Fig. 3

Venn diagrams showing co-occurrence of tfs ICE modules/types with each other and the cagPAI. a Non-T4SS accessory/cargo tfs genes located within tfs4 L1/L2 modules and the tfs3 left segment. b tfs4 R1/R2 modules and the tfs3 right segment comprising the majority complement of tfs T4SS transfer genes. c Intact tfs3 and L1C1R1 and L2C1R1f tfs4 ICE types. Plots a. and b. highlight a complex history of tfs ICE/module acquisition in which cargo/accessory modules (a) are more commonly maintained in strain genomes compared with transfer modules (b). Erosion of transfer modules is further reflected by the low co-occurrence of intact tfs3 with either of the most prevalent tfs4 types, L1C1R1 (dupA+) or L2C1R1f (partial dupA), co-resident with tfs3 in 22 and 26% of strains respectively (c). Although most commonly co-resident with the cagPAI, all tfs modules and ICE types were also apparent in strains which lacked it. Representation of intact elements was determined in 181, 168 and 164 H. pylori genomes (a-c respectively). tfs4 ‘Lm’ hybrid left flanks were included with L2 counts in a. and L2C1R1f counts in c