title: Phylogenetic analysis of human Chlamydia pneumoniae strains reveals a distinct Australian indigenous clade that predates European exploration of the continent.
abstract: BACKGROUND
  The obligate intracellular bacterium Chlamydia pneumoniae is a common respiratory pathogen, which has been found in a range of hosts including humans, marsupials and amphibians. Whole genome comparisons of human C. pneumoniae have previously highlighted a highly conserved nucleotide sequence, with minor but key polymorphisms and additional coding capacity when human and animal strains are compared.
  
  
  RESULTS
  In this study, we sequenced three Australian human C. pneumoniae strains, two of which were isolated from patients in remote indigenous communities, and compared them to all available C. pneumoniae genomes. Our study demonstrated a phylogenetically distinct human C. pneumoniae clade containing the two indigenous Australian strains, with estimates that the most recent common ancestor of these strains predates the arrival of European settlers to Australia. We describe several polymorphisms characteristic to these strains, some of which are similar in sequence to animal C. pneumoniae strains, as well as evidence to suggest that several recombination events have shaped these distinct strains.
  
  
  CONCLUSIONS
  Our study reveals a greater sequence diversity amongst both human and animal C. pneumoniae strains, and suggests that a wider range of strains may be circulating in the human population than current sampling indicates.
authors.affiliation: Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia. eileen.roulis@qut.edu.au.
authors.forename: Eileen
authors.initials: E
authors.lastname: Roulis
authors.affiliation: Centre for Animal Health Innovation, Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia. nbachman@usc.edu.au.
authors.forename: Nathan
authors.initials: N
authors.lastname: Bachmann
authors.affiliation: Institute for Genomic Sciences, University of Maryland, Baltimore, MD, USA. MHumphrys@som.umaryland.edu.
authors.forename: Michael
authors.initials: M
authors.lastname: Humphrys
authors.affiliation: i3 Institute, University of Technology, Sydney, NSW, Australia. Garry.Myers@uts.edu.au.
authors.forename: Garry
authors.initials: G
authors.lastname: Myers
authors.affiliation: Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia. w.huston@qut.edu.au.|i3 Institute, University of Technology, Sydney, NSW, Australia. w.huston@qut.edu.au.
authors.forename: Wilhelmina
authors.initials: W
authors.lastname: Huston
authors.affiliation: Centre for Animal Health Innovation, Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia. apolking@usc.edu.au.
authors.forename: Adam
authors.initials: A
authors.lastname: Polkinghorne
authors.affiliation: Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia. ptimms@usc.edu.au.|Centre for Animal Health Innovation, Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia. ptimms@usc.edu.au.
authors.forename: Peter
authors.initials: P
authors.lastname: Timms
mesh_terms: D000595:Amino Acid Sequence; D001315:Australia / Q000453:epidemiology; D001483:Base Sequence; D023521:Chlamydophila Infections / Q000453:epidemiology / Q000382:microbiology*; D016993:Chlamydophila pneumoniae / Q000145:classification* / Q000235:genetics*; D016000:Cluster Analysis; D019143:Evolution, Molecular; D023061:Gene Order; D005819:Genetic Markers; D014644:Genetic Variation; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D010802:Phylogeny; D011995:Recombination, Genetic; D016415:Sequence Alignment; D000095283:Australian Aboriginal and Torres Strait Islander Peoples
chemical_list: D005819:Genetic Markers