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Genetic diversity of the obligate intracellular bacterium Chlamydophila pneumoniae by genome-wide analysis of single nucleotide polymorphisms: evidence for highly clonal population structure

Thomas Rattei, Stephan Ott, Michaela Gutacker, Jan Rupp, Matthias Maass, Stefan Schreiber, Werner Solbach, Thierry Wirth, Jens Gieffers

Department of Genome-Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Am Forum 1, 85354 Freising, Germany, Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Schittenhelnstrasse 12, 24105 Kiel, Germany, Instituto Cantonale di Microbiologia, Via Mirasole 22, 6501 Bellinzona, Switzerland, Institute of Medical Microbiology and Hygiene, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany, Institute of Medical Microbiology, Hygiene and Infectious Diseases, University Hospital Salzburg, Muellner Hauptstrasse 48, 5020 Salzburg, Austria and Department of Biology, Lehrstuhl für Zoologie und Evolutionsbiologie, University Konstanz, Universitätstrasse 10, 78457 Germany



Background: Chlamydophila pneumoniae is an obligate intracellular bacterium that replicates in a biphasic life cycle within eukaryotic host cells. Four published genomes revealed an identity of > 99 %. This remarkable finding raised questions about the existence of distinguishable genotypes in correlation with geographical and anatomical origin.

Results: We studied the genetic diversity of C. pneumoniae by analysing synonymous single nucleotide polymorphisms (sSNPs) that are under reduced selection pressure. We conducted an in silico analysis of the four sequenced genomes, chose 232 representative sSNPs and analysed the loci in 38 C. pneumoniae isolates. We identified 15 different genotypes that were separated in four major clusters. Clusters were not associated with anatomical or geographical origin. However, animal lineages are basal on the C. pneumomiae phylogeny, suggesting a recent transmission to humans through successive bottlenecks some 150,000 years ago. A lack of detectable variation in 17 isolates emphasizes the extraordinary genetic conservation of this species and the high clonality of the population. Moreover, the largest cluster, which encompasses 80% of all analysed strains, is an extremely young clade, that went through an important population expansion some 3,300 years ago.

Conclusion: sSNPs have proven useful as a sensitive marker to gain new insights into genetic diversity, population structure and evolutionary history of C. pneumoniae.