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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.

bmc genomics

Phylogenetic analysis of human Chlamydia pneumoniae strains reveals a distinct Australian indigenous clade that predates European exploration of the continent