Multigenome analysis identifies a worldwide distributed epidemic Legionella pneumophila clone that emerged within a highly diverse species

Abstract

Genomics can provide the basis for understanding the evolution of emerging, lethal human pathogens such as Legionella pneumophila, the causative agent of Legionnaires’ disease. This bacterium replicates within amoebae and persists in the environment as a free-living microbe. Among the many Legionella species described, L. pneumophila is associated with 90% of human disease and within the 15 serogroups (Sg), L. pneumophila Sg1 causes over 84% of Legionnaires’ disease worldwide. Why L. pneumophila Sg1 is so predominant is unknown. Here, we report the first comprehensive screen of the gene content of 217 L. pneumophila and 32 non-L. pneumophila strains isolated from humans and the environment using a Legionella DNA-array. Strikingly, we uncovered a high conservation of virulence- and eukaryotic-like genes, indicating strong environmental selection pressures for their preservation. No specific hybridization profile differentiated clinical and environmental strains or strains of different serogroups. Surprisingly, the gene cluster coding the determinants of the core and the O side-chain synthesis of the lipopolysaccaride (LPS cluster) determining Sg1 was present in diverse genomic backgrounds, strongly implicating the LPS of Sg1 itself as a principal cause of the high prevalence of Sg1 strains in human disease and suggesting that the LPS cluster can be transferred horizontally. Genomic analysis also revealed that L. pneumophila is a genetically diverse species, in part due to horizontal gene transfer of mobile genetic elements among L. pneumophila strains, but also between different Legionella species. However, the genomic background also plays a role in disease causation as demonstrated by the identification of a globally distributed epidemic strain exhibiting the genotype of the sequenced L. pneumophila strain Paris.

Large-scale identification and translocation of type IV secretion substrates by Coxiella burnetii

“…In addition, similar to the finding in L. pneumophila type IV substrates (5,22), several C. burnetii Dot/Icm substrates have more than one homolog in its genome (Table S6), which suggests that functional redundancy of T4SS substrates may also exist in C. burnetii. Furthermore, except for one protein (CBUA0014) encoded by a plasmid carried gene, only 18 substrates are fully conserved among C. burnetii isolates (Table S5), a phenomenon in contrast to L. pneumophila, in which T4SS substrates are highly conserved among different isolates of the same species (43). The majority of missing homologs were presented as pseudogenes in different isolates.…”

Genome Dynamics in Legionella: The Basis of Versatility and Adaptation to Intracellular Replication

“…This region can be integrated in the chromosome but can also excise in a site-specific manner to exist as a low copy number plasmid that is undoubtedly transferable among strains (Doleans-Jordheim et al 2006). Indeed, it is present in five of the eight sequenced L. pneumophila strains, in L. longbeachae strain D-4968 (Kozak et al 2010), and according to hybridization results also partly in Legionella rubrilucens (Cazalet et al 2008). Interestingly, in the Legionella strains where the Lvh T4SS is not present, another Tra system, a Ptype T4SS that codes for short and rigid pili that allow surface mating for conjugation, is present in the same chromosomal position (Gomez-Valero et al 2011b).…”

“…Likewise, L. longbeachae strain NSW150 possesses a plasmid of 72 kb, and also strain D-4968 seems to contain a plasmid (Kozak et al 2010). These replicons show a heterogeneous distribution among the different genomes, as the same plasmids or partially similar plasmids are present in different strains (Cazalet et al 2008). Likewise, a comparative analysis of these plasmids revealed that the 30.4 kb Tra region present in the plasmid of L. pneumophila strain Paris shows much higher identity with the Tra region located on the L. longbeachae plasmid, than with those of the other L. pneumophila strains sequenced (Gomez-Valero et al 2011b).…”

“…In 2004, more than 60 of these proteins were described in the genomes of strains Paris and Lens (Cazalet et al 2004) and in 2005, in strain Philadelphia (de Felipe et al 2005). Later, the analysis of the distribution of these genes among more than 200 L. pneumophila strains using DNA arrays showed that the conservation of certain eukaryotic-like genes within the species L. pneumophila was high, indicating strong environmental selection pressures for their preservation (Cazalet et al 2008).…”

“…Taking into account that these strains belong to the same species and serogroup, the genomic diversity among them is relatively high. Further analysis of the gene content of 217 L. pneumophila strains using a Legionella DNA array confirmed that the gene content of the L. pneumophila genome is highly diverse (Cazalet et al 2008). Both studies suggested that the main source of diversity among the Legionella genomes is mobile genetic elements and horizontal gene transfer among L. pneumophila strains, but also among strains belonging to different Legionella species, other bacterial species, and most surprisingly, probably also between Legionella and their eukaryotic hosts (Cazalet et al 2004(Cazalet et al , 2008.…”