Multiple major disease-associated clones ofLegionella pneumophilahave emerged recently and independently

Abstract

Legionella pneumophila is an environmental bacterium and the leading cause of Legionnaires’ disease. Just five sequence types (ST), from more than 2000 currently described, cause nearly half of disease cases in northwest Europe. Here, we report the sequence and analyses of 364 L. pneumophila genomes, including 337 from the five disease-associated STs and 27 representative of the species diversity. Phylogenetic analyses revealed that the five STs have independent origins within a highly diverse species. The number of de novo mutations is extremely low with maximum pairwise single-nucleotide polymorphisms (SNPs) ranging from 19 (ST47) to 127 (ST1), which suggests emergences within the last century. Isolates sampled geographically far apart differ by only a few SNPs, demonstrating rapid dissemination. These five STs have been recombining recently, leading to a shared pool of allelic variants potentially contributing to their increased disease propensity. The oldest clone, ST1, has spread globally; between 1940 and 2000, four new clones have emerged in Europe, which show long-distance, rapid dispersal. That a large proportion of clinical cases is caused by recently emerged and internationally dispersed clones, linked by convergent evolution, is surprising for an environmental bacterium traditionally considered to be an opportunistic pathogen. To simultaneously explain recent emergence, rapid spread and increased disease association, we hypothesize that these STs have adapted to new man-made environmental niches, which may be linked by human infection and transmission.

Diverse conjugative elements silence natural transformation inLegionellaspecies

“…For instance, all isolates belonging to the branch of the Paris strain are consistently transformable. This is concordant with the high rates or recombination observed in this ST1 lineage, with an average of nearly 10% of the genome of isolates originating from recombination (34). Similarly, all isolates of the ST47 cluster are consistently poorly transformable.…”

“…Although conserved, the phenotype is not homogeneously distributed. The ST1 clade groups a majority of transformable isolates, consistent with high recombination rates observed in this clade (33,34). This contrasts with the absence of transformable isolates in the ST47 clade in which no recombination events could be detected (34).…”

Genomic investigation of a suspected outbreak of Legionella pneumophila ST82 reveals undetected heterogeneity by the present gold-standard methods, Denmark, July to November 2014

“…Underwood et al also found that some isolates of the same ST (interestingly the close ST47) that were separated by several years and geographic location differed by just four SNPs [31]. The diversity could be different in other L. pneumophila lineages, however similar results have recently been shown in several other STs 1, 23, 36, 37, 47 and 62 [33,34]. …”

A Unique cis -Encoded Small Noncoding RNA Is Regulating Legionella pneumophila Hfq Expression in a Life Cycle-Dependent Manner

“…1B). Comparison of the Hfq amino acid sequence among more than 300 L. pneumophila strains sequenced in the last years (19, 29–32) revealed that Hfq is 100% conserved across the different L. pneumophila strains. Analyses of four non- pneumophila Legionella species (33) showed that Hfq is 80% conserved (Fig.…”