Chlamydia pecorum is an important global pathogen of livestock and is a burden to primary producers in a number of agriculturally productive regions in Australia. The same pathogen is also recognized as the major pathogen of the koala, causing debilitating ocular and reproductive tract diseases and threatening the long-term survival of Australia’s koala populations. Molecular typing studies by our group have previously suggested a link between C. pecorum strains infecting sheep, cattle and koalas, however, further genetic inference has been limited by the requirement to culture strains in vitro for the purpose of whole genome sequencing.
This study employed a culture-independent DNA capture approach to sequence C. pecorum genomes directly from clinical swabs samples collected from koalas with chlamydial disease as well as from sheep with arthritis and conjunctivitis. Investigations into single nucleotide polymorphisms within each of the swab samples revealed that a portion of the reads in each sample belonged to separate C. pecorum strains, suggesting that all of the clinical samples analyzed contained mixed populations of genetically distinct C. pecorum isolates. This observation was independent of the anatomical site sampled and the host species. Using the genomes of strains identified in each of these samples, whole genome phylogenetic analysis revealed that a clade containing a bovine and a koala isolate is distinct from other clades comprised of livestock or koala C. pecorum strains. Providing additional evidence to support exposure of koalas to Australian livestock strains, two ‘minor’ strains assembled from the koala swab samples clustered with livestock strains rather than koala strains.
Culture-independent probe-based genome capture and sequencing of clinical samples provides the strongest evidence yet to suggest that sheep and cattle C. pecorum strains can be transmitted to koalas and raises further questions about the evolutionary origin of this pathogen in native Australian animals.