While globally published data suggests that chlamydial species are essentially ubiquitous in livestock, little is known about the epidemiology of livestock C. pecorum infections, particularly in Australia. Although C. pecorum infections are regularly reported across most of Australia’s mainland koala populations, the genetic diversity of infecting C. pecorum strains is not well understood. The encroachment of koala habitats by sheep and cattle farming along the east coast of Australia is common and raises serious questions over the relationships and potential role that cross-host transmission may have in the epidemiology of chlamydial disease in these hosts. Infections in wild ruminants (e.g. ibex and chamois) and domesticated pigs have also been reported, yet almost nothing is known about the genetic diversity of C. pecorum in these animal hosts and their relationships to livestock and koala strains either. Previous typing studies for C. pecorum utilised highly polymorphic genes, however the derived phylogenies and genotyping schemes were often in contrast to each other. In order to evaluate the overall C. pecorum genetic diversity in various hosts, I developed a C. pecorum-specific Multi Locus Sequence Typing (MLST) scheme. This scheme was then applied to a range of samples from koalas, Australian sheep and cattle, as well as C. pecorum livestock isolates from Europe and the USA and wild ruminants from Switzerland. C. pecorum-specific MLST provided the first molecular epidemiological data on infections in sheep and cattle in Australia, and in characterising novel C. pecorum genotypes, highlighting an unexpected level of diversity for this pathogen.
Submitted in the fulfilment of the requirements of the degree of Doctor of Philosophy, University of the Sunshine Coast, 2016.