Oral Presentation Australian Society for Microbiology Annual Scientific Meeting 2014

Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum provides novel insight into chlamydial host adaptation (#131)

Nathan Bachmann 1 , Tamieka Fraser 2 , Martina Jelocnik 2 , Claire Bertelli 3 , Garry Myers 4 , Peter Timms 1 , Adam Polkinghorne 1
  1. University of the Sunshine Coast, Sippy Downs, QLD, Australia
  2. Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, 4059, Australia
  3. Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
  4. Institute of Genome Sciences, University of Maryland, Baltimore, USA

Chlamydia pecorum is a widespread pathogen of cattle, sheep, goats and pigs. C. pecorum also causes debilitating ocular and urogenital tract disease in koalas.  In this study, the genomes of koala and sheep C. pecorum strains were compared to identify potential genes involved in adaptation to different hosts.

Four C. pecorum isolates were sequenced as a part of this study, including three koala strains isolated from the genital tracts and conjunctiva of diseased koalas and a joint isolate from a sheep with polyarthritis. A C. pecorum E58 genome, isolated from a calf, was previously available. The reads of each strain were mapped individually against the E58 genome and SNPs were predicted by the variant caller program, VarScan.

Whole genome comparison revealed that the genomes analyzed have identical core and pan genome contents, with a DNA sequence similarity from 98.5 to 98.8%. Two regions in the koala strain appear to be accumulating SNPs, regions that were nearly identical between cattle and sheep strains. These regions include a 77 kbp region, encoding putative type III effector and structural proteins, chaperones and other virulence related proteins. The majority of  non-synonymous SNPs were associated with putative Type III effector proteins. The second region includes the plasticity zone, which also has a high SNP frequency in the three koala strains and yet it is conserved in livestock strains.

A few pseudogenes were also identified in the three koala strains, including putative toxin, metabolic and hypothetical protein-encoding genes. PCR/DNA sequencing of these pseudogenes in koala C. pecorum clinical samples confirmed that they are also present in field strains.

An accumulation of genetic changes in koala C. pecorum strains alone adds to increasing evidence of a recent introduction of this bacteria into koalas from livestock hosts. Genome sequencing of more C. pecorum strains will validate these evolutionary hypotheses and identify additional evidence for the role of genetic variation in host and tissue adaptation.