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Background   Chlamydia pneumoniae  is a widespread pathogen causing upper and lower respiratory tract infections in addition to a range of other diseases in humans and animals. Previous whole genome analyses have focused on four essentially clonal (> 99% identity)  C. pneumoniae  human genomes (AR39, CWL029, J138 and TW183), providing relatively little insight into strain diversity and evolution of this species.    Results  We performed individual gene-by-gene comparisons of the recently sequenced  C. pneumoniae  koala genome and four  C. pneumoniae  human genomes to identify species-specific genes, and more importantly, to gain an insight into the genetic diversity and evolution of the species. We selected genes dispersed throughout the chromosome, representing genes that were specific to  C. pneumoniae , genes with a demonstrated role in chlamydial biology and/or pathogenicity (n = 49), genes encoding nucleotide salvage or amino acid biosynthesis proteins (n = 6), and extrachromosomal elements (9 plasmid and 2 bacteriophage genes).    Conclusions  We have identified strain-specific differences and targets for detection of  C. pneumoniae  isolates from both human and animal origin. Such characterisation is necessary for an improved understanding of disease transmission and intervention.

Comparison of koala LPCoLN and human strains of Chlamydia pneumoniae highlights extended genetic diversity in the species