The four clades were distinguished by differences in genes that fell into GO categories such as DNA exchange (probably species-specific phages, transposons and plasmids) and signal transduction. Recent genome analysis has shown that the repertoire of secreted effector proteins with highly variable protein domains is largely species-specific19. Based on our PCA analysis, the species within each clade formed non-overlapping groups and were also more similar regarding accessory gene families. This suggests that Legionella as a group may use broadly similar and conserved machinery for intracellular infection and growth in humans as in a myriad of soil and water protists5 but differ from each other in the presence of genes that promote adaptations to specific niches by providing environmental sensing and shifts in virulence. For example, Clade 1 represents all Lp serogroups. For Lp1, a recent study of 21 clinical isolates (ST191) from an outbreak of LD in Scotland identified mutation, recombination and HGT that had occurred in the environmental Legionella population before human infection46. WGS of the isolates revealed three regions of high SNP density and four distinct subtypes. Included in the set of genes transferred horizontally were those encoding the Lvh T4ASS located on a plasmid-like element that has been implicated in host cell entry and intracellular replication28 at low temperature. Variation in clinical virulence was linked to strain-dependent differences in T4ASS46. In our study, the Lvh T4ASS was identified in only 10 genomes: 6 of 9 Clade 1 Lp1 genomes, and Clade 3 L. bozemanii serogroup 2 and L. dumoffii. Our findings suggest that Lvh T4ASS is not an essential virulence factor and confirms that the Lvh system is not widespread among Legionella species outside of Lp4748. Additionally, we found that the P-type T4ASS was present in all Legionella genomes whereas the F-type T4ASS was missing in Lp2, 3 and 6, and in L. cherii. Such a heterogeneous distribution of these different T4ASS across the Legionella species is additional evidence of the plasticity of these genomes.