The graphical output from the BRIG analysis comparing the genomes to the Corby sequence displays an overview of the major regions of variability among these genomes such that 14 regions of substantial variation were observed (Figure  5 and Additional file 1: Table S1). Many of the genes present in these regions are phage or transposable-element associated, suggesting selleckchem that much of this variability is driven by

mobile elements. Many of these regions are adjacent to or have a tRNA sequence within them, a common location for mobile element integration [39]. Several of the variable regions have genes involved in a conjugation/type IV secretion system (T4SS). The excision, transfer and re-integration of genetic loci by this class of genes has been implicated in HGT [34]. Variability p38 MAPK activity in T4SS genes has been shown previously to be a major contributor to the genome plasticity of L. pneumophila[23]. Other classes of genes include those encoding transporter/eflux proteins, proteins

involved in glycosylation, putative virulence proteins, restriction endonuclease system proteins, and antibiotic resistance proteins. None of these proteins are involved in core metabolic functions and variability in the presence and absence of these genes is likely to result in phenotypic changes that alter the ability of the organism to survive within its environment. Plasmid analysis Apart from acquisition of genomic islands another common way that bacteria gain genetic elements that confer phenotypic differences is by plasmid

acquisition. In order to investigate the presence of plasmids in the genomes the plasmids of the Lens and Paris genomes were compared. A shared 9.2 kb region was used to query both the assembled and GenBank genomes. Although there may be plasmids circulating in the population that do not contain this shared locus, the same sequence is also present in the plasmid of another Legionella species, Legionella longbeachae (NSW150 plasmid pLLO: Accession FN650141) suggesting that this is a conserved sequence present in at least some of plasmids of the Legionella genus. Blast analysis detected this conserved plasmid sequence in a small proportion of the Fludarabine in vivo strains (8/33) and the these plasmids sequence itself was variable. The following genomes produced a hit whose e-score was less than 1×10-20: Lens: (100% identity over 9299 bases), Paris: (83% identity over 8319 bases), ST154: (83% identity over 7270 bases), ST336: (83% identity over 7270 bases), ST44: (88% identity over 249 bases), ST54: (99% identity over 9299 bases), ST707: (83% identity over 7373 bases), ST74: (82% identity over 8239 bases), ST78: (83% identity over 7323 bases). It can be seen that there are some closely related strains (ST 154 and 336 in the same cluster) that share a very similar plasmid whereas other closely related strains (e.g. Paris, ST5 and ST152) have different plasmid content.