Clonal population structure of Legionella pneumophila inferred from allelic profiling

Abstract

The population structure of Legionella pneumophila was investigated by analysing nucleotide sequences from six loci (flaA, pilE, asd, mip, mompS and proA) of 335 globally distributed isolates from clinical and environmental sources over a 29-year period (1977-2006). Data were obtained from unrelated isolates from Europe (n5270), Japan (n531), Canada (n57), the USA (n524) and Australia (n51). The country of origin of two strains was unknown. Analysis of these isolates indicated significant linkage disequilibrium between the six loci. Application of six sequence-based recombination detection tests did not reveal evidence of recombination, but estimates of rates of recombination and mutation made by a seventh test suggested that recombination could have occurred at a rate similar to, but probably lower than, that of mutation.Genealogies inferred under models with and without recombination were congruent with each other, providing no definitive evidence regarding recombination, and were in agreement with sequence clusters identified by graph methods. Further evidence supporting the distinct nature of two of the three subspecies of L. pneumophila, subsp. fraseri and subsp. pascullei, was also found. The ratios of non-synonymous to synonymous nucleotide polymorphisms for each of the allele sets were examined and revealed that the putative virulence loci mompS and pilE are under diversifying pressure, while the allelic regions of three other loci linked to virulence (flaA, proA and mip) do not appear to be. INTRODUCTIONFollowing the recognition of the aetiological agent of Legionnaires' disease in 1977(McDade et al., 1977, phenotypic and genotypic analyses of Legionella pneumophila have mainly focused on the short-term epidemiology of the bacterium. In this scenario, the aim has been to demonstrate potential environmental sources of infection, thereby allowing timely intervention, in order to prevent further infection. Many such methods have been developed and applied with the purpose of discriminating between epidemiologically unrelated strains of L. pneumophila, particularly those belonging to serogroup (sg) 1 (Edelstein et al., 1986;Fry et al., 1999; Saunders et al., 1990;Schoonmaker et al., 1992;van Ketel et al., 1984).The utility of the multi-locus sequence typing (MLST) approach, in which sequences from five to 10 housekeeping genes are determined, in the identification of major bacterial lineages associated with invasive disease was first described in 1998 (Enright & Spratt, 1998;Maiden et al., 1998). Since then, this robust and portable technique (or variations of it) has been applied to the study of genetic diversity and clonal expansion, and to the long-term epidemiological analysis of microbial populations (see http://pubmlst.org/ and http://www.mlst.net/) (Giske et al., 2006;Paraskevopoulos et al., 2006;Vassileva et al., 2006).Recently, a similar approach, termed sequence-based typing (SBT), developed by members of the European Working Group for Legionella Infections (EWGLI), was applied to the epidemiolo...

Distribution of lag-1 Alleles and Sequence-Based Types among Legionella pneumophila Serogroup 1 Clinical and Environmental Isolates in the United States

“…In addition, we observed that STs tend to associate with a single lag-1 allele type. This suggests the existence of clonal groups of L. pneumophila serogroup 1 that rarely recombine (7). Further studies should indicate if combining SBT and lag-1 data will define a hierarchy of virulence genotypes that require greater scrutiny to prevent human disease.…”

“…The SBT database, which is available through the website of the European Working Group for Legionella Infections (EWGLI) (www.ewgli.org), allows assignment of the sevendigit allelic profile for alleles in a predetermined order (flaA, pilE, asd, mip, mompS, proA, and neuA) and a corresponding sequence type (ST) to L. pneumophila isolates. SBT is based on the same approach as multilocus sequence typing (28) and, similarly to multilocus sequence typing, may be applied to the study of genetic diversity and clonal expansion of microbial populations (7,37). Analysis of the phylogenetic relationships between L. pneumophila serogroup 1 STs identified in our study was used to provide insight on how the MAb2 epitope might have emerged and imparted enhanced virulence.…”

Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses?

“…L. pneumophila exhibits also strong LD (Edwards et al, 2008). MLST analysis reveals the presence of 'sequence clusters' (near-clades) in this species (Edwards et al, 2008).…”

“…McManus and Coleman (2014) b Edwards et al (2008) e Feretzaki and Heitman (2013) c Ngamskulrungroj et al (2009) b,e Fargier et al (2011) b,e…”

Molecular Pathogenesis of Infections Caused byLegionella pneumophila

“…The gene encoding the peptidylprolyl cis-trans isomerase (PPIase) Mip was one of the first genes associated with the ability of L. pneumophila to replicate in eukaryotic cells, and the mip nucleotide sequence has been used extensively as a target for Legionella molecular diagnostics and typing for 2 decades (69,115,118,185,203,269). Mip stands for macrophage infectivity potentiator, and mip mutants of L. pneumophila are defective for replication in macrophages, epithelial cells, and amoebae and are attenuated in both guinea pig and mouse models of infection (81,83,358).…”