Culture-independent genome sequencing of clinical samples reveals an unexpected heterogeneity of infections by Chlamydia pecorum

Journal of Clinical Microbiology
Nathan L BachmannAdam Polkinghorne

Abstract

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 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-ind...Continue Reading

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Citations

Oct 10, 2015·Bioinformatics·Mitchell J SullivanAdam Polkinghorne
Mar 22, 2016·International Journal of Microbiology·Cory Ann LeonardNicole Borel
Aug 25, 2015·Microbes and Infection·Marie de BarsyGilbert Greub
Oct 2, 2015·Mediators of Inflammation·Tamsyn DerrickMartin J Holland
Mar 28, 2017·Transboundary and Emerging Diseases·R ChahotaH Fukushi
Jan 10, 2018·Microbial Genomics·Alyce Taylor-BrownAdam Polkinghorne

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