Culture-Independent Genome Sequencing of Clinical Samples Reveals an Unexpected Heterogeneity of Infections by Chlamydia pecorum
Nathan L. Bachmann,a Mitchell J. Sullivan,a Martina Jelocnik,a Garry S. A. Myers,b Peter Timms,a Adam Polkinghornea
Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australiaa
i3 Institute, University of Technology, Sydney, New South Wales, Australiab
Chlamydia pecorum is an important global pathogen of livestock, and it is also a signiﬁcant threat to the long-term survival of Australia’s koala populations. This study employed a culture-independent DNA capture approach to sequence C. pecorum genomes directly from clinical swab samples collected from koalas with chlamydial disease as well as from sheep with arthritis and conjunctivitis. Investigations in to 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 livestockstrains, 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 naturally occurring chlamydial infections are comprised of multiple genetically distinct strains.