title: Dynamics of genome change among Legionella species.
abstract: Legionella species inhabit freshwater and soil ecosystems where they parasitize protozoa. L. pneumonphila (LP) serogroup-1 (Lp1) is the major cause of Legionnaires' Disease (LD), a life-threatening pulmonary infection that can spread systemically. The increased global frequency of LD caused by Lp and non-Lp species underscores the need to expand our knowledge of evolutionary forces underlying disease pathogenesis. Whole genome analyses of 43 strains, including all known Lp serogroups 1-17 and 17 emergent LD-causing Legionella species (of which 33 were sequenced in this study) in addition to 10 publicly available genomes, resolved the strains into four phylogenetic clades along host virulence demarcations. Clade-specific genes were distinct for genetic exchange and signal-transduction, indicating adaptation to specific cellular and/or environmental niches. CRISPR spacer comparisons hinted at larger pools of accessory DNA sequences in Lp than predicted by the pan-genome analyses. While recombination within Lp was frequent and has been reported previously, population structure analysis identified surprisingly few DNA admixture events between species. In summary, diverse Legionella LD-causing species share a conserved core-genome, are genetically isolated from each other, and selectively acquire genes with potential for enhanced virulence.
authors.affiliation: Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA.
authors.forename: Sandeep J
authors.initials: SJ
authors.lastname: Joseph
authors.affiliation: Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Cox
authors.affiliation: Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
authors.forename: Bernard
authors.initials: B
authors.lastname: Wolff
authors.affiliation: Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
authors.forename: Shatavia S
authors.initials: SS
authors.lastname: Morrison
authors.affiliation: Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
authors.forename: Natalia A
authors.initials: NA
authors.lastname: Kozak-Muiznieks
authors.affiliation: Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Frace
authors.affiliation: Department of Infectious Disease Epidemiology, Imperial College, Norfolk Place, London, United Kingdom.
authors.forename: Xavier
authors.initials: X
authors.lastname: Didelot
authors.affiliation: Programa de Genomica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
authors.forename: Santiago
authors.initials: S
authors.lastname: Castillo-Ramirez
authors.affiliation: Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
authors.forename: Jonas
authors.initials: J
authors.lastname: Winchell
authors.affiliation: Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA.|Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA.
authors.forename: Timothy D
authors.initials: TD
authors.lastname: Read
authors.affiliation: Department of Medicine and University of California, San Francisco, San Francisco, California, USA.|Department of Biomedical Engineering, University of California at San Francisco and Berkeley, San Francisco and Berkeley, California, USA.|9Center for Immunobiology and Vaccine Development, UCSF Benioff Children's Hospital Oakland Research Institute, Oakland, California, USA.
authors.forename: Deborah
authors.initials: D
authors.lastname: Dean
mesh_terms: D058947:Bacterial Secretion Systems / Q000235:genetics; D001483:Base Sequence; D064113:CRISPR-Cas Systems / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D022761:Gene Transfer, Horizontal / Q000235:genetics; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D023281:Genomics; D007875:Legionella / Q000235:genetics*; D010802:Phylogeny; D011995:Recombination, Genetic / Q000235:genetics; D012641:Selection, Genetic; D013045:Species Specificity
chemical_list: D058947:Bacterial Secretion Systems; D004269:DNA, Bacterial