| Summary: | <p>Abstract</p> <p>Background</p> <p><it>Chlamydia pneumoniae </it>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) <it>C. pneumoniae </it>human genomes (AR39, CWL029, J138 and TW183), providing relatively little insight into strain diversity and evolution of this species.</p> <p>Results</p> <p>We performed individual gene-by-gene comparisons of the recently sequenced <it>C. pneumoniae </it>koala genome and four <it>C. pneumoniae </it>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 <it>C. pneumoniae</it>, 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).</p> <p>Conclusions</p> <p>We have identified strain-specific differences and targets for detection of <it>C. pneumoniae </it>isolates from both human and animal origin. Such characterisation is necessary for an improved understanding of disease transmission and intervention.</p>
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