title: Genomic factors related to tissue tropism in Chlamydia pneumoniae infection.
abstract: BACKGROUND
  Chlamydia pneumoniae (Cpn) are obligate intracellular bacteria that cause acute infections of the upper and lower respiratory tract and have been implicated in chronic inflammatory diseases. Although of significant clinical relevance, complete genome sequences of only four clinical Cpn strains have been obtained. All of them were isolated from the respiratory tract and shared more than 99% sequence identity. Here we investigate genetic differences on the whole-genome level that are related to Cpn tissue tropism and pathogenicity.
  
  
  RESULTS
  We have sequenced the genomes of 18 clinical isolates from different anatomical sites (e.g. lung, blood, coronary arteries) of diseased patients, and one animal isolate. In total 1,363 SNP loci and 184 InDels have been identified in the genomes of all clinical Cpn isolates. These are distributed throughout the whole chlamydial genome and enriched in highly variable regions. The genomes show clear evidence of recombination in at least one potential region but no phage insertions. The tyrP gene was always encoded as single copy in all vascular isolates. Phylogenetic reconstruction revealed distinct evolutionary lineages containing primarily non-respiratory Cpn isolates. In one of these, clinical isolates from coronary arteries and blood monocytes were closely grouped together. They could be distinguished from all other isolates by characteristic nsSNPs in genes involved in RB to EB transition, inclusion membrane formation, bacterial stress response and metabolism.
  
  
  CONCLUSIONS
  This study substantially expands the genomic data of Cpn and elucidates its evolutionary history. The translation of the observed Cpn genetic differences into biological functions and the prediction of novel pathogen-oriented diagnostic strategies have to be further explored.
authors.affiliation: Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, 1090, Vienna, Austria. Thomas.Weinmaier@univie.ac.at.
authors.forename: Thomas
authors.initials: T
authors.lastname: Weinmaier
authors.affiliation: Department of Genome Oriented Bioinformatics, Technical University Munich, 85354, Freising, Germany. Jonathan.Hoser@helmholtz-muenchen.de.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Hoser
authors.affiliation: Center for Human Genetics and Laboratory Diagnostics Dr. Klein, Dr. Rost and Colleagues, 82152, Martinsried, Germany. Sebastian.Eck@medizinische-genetik.de.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Eck
authors.affiliation: Department of Molecular and Clinical Infectious Diseases, University of Luebeck, 23538, Luebeck, Germany. Inga.Kaufhold@uksh.de.
authors.forename: Inga
authors.initials: I
authors.lastname: Kaufhold
authors.affiliation: Department of Molecular and Clinical Infectious Diseases, University of Luebeck, 23538, Luebeck, Germany. Kensuke.shima@uksh.de.
authors.forename: Kensuke
authors.initials: K
authors.lastname: Shima
authors.affiliation: Institute of Human Genetics, Helmholtz Center Munich, 85764, Neuherberg, Germany. TimStrom@helmholtz-muenchen.de.
authors.forename: Tim M
authors.initials: TM
authors.lastname: Strom
authors.affiliation: Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, 1090, Vienna, Austria. Thomas.Rattei@univie.ac.at.|Department of Genome Oriented Bioinformatics, Technical University Munich, 85354, Freising, Germany. Thomas.Rattei@univie.ac.at.
authors.forename: Thomas
authors.initials: T
authors.lastname: Rattei
authors.affiliation: Department of Molecular and Clinical Infectious Diseases, University of Luebeck, 23538, Luebeck, Germany. Jan.Rupp@uksh.de.
authors.forename: Jan
authors.initials: J
authors.lastname: Rupp
mesh_terms: D000818:Animals; D001769:Blood / Q000382:microbiology; D023521:Chlamydophila Infections / Q000382:microbiology* / Q000662:veterinary; D016993:Chlamydophila pneumoniae / Q000235:genetics* / Q000254:growth & development / Q000302:isolation & purification*; D003331:Coronary Vessels / Q000382:microbiology; D016680:Genome, Bacterial; D006801:Humans; D054643:INDEL Mutation; D008168:Lung / Q000382:microbiology; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods; D018523:Tropism