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One clone to rule them all Culture-independent genomics of Chlamydia psittaci from equine and avian hosts in Australia1.32 MB
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Journal article
One clone to rule them all: Culture-independent genomics of Chlamydia psittaci from equine and avian hosts in Australia
Microbial Genomics, Vol.8(10), pp.1-12
2022
PMID: 36269227
Appears in UniSC Supported Open Access Outputs
Abstract
Chlamydia psittaci is an avian pathogen with zoonotic potential. In Australia, C. psittaci has been well reported as a cause of reproductive loss in mares which subsequently have been the source of infection and illness in some in contact humans. To date, molecular typing studies describe the predominant and clonal C. psittaci sequence type (ST)24 strains in horse, psittacine, and human infections. We sought to assess the clonality between ST24 strains and the emergence of equine ST24 with a comprehensive genomics approach. We used culture independent probe based and metagenomic whole genome sequencing to investigate 13 C. psittaci genomes from horses, psittacines, and a pigeon from Australia. Published genomes of 36 C. psittaci strains were also used to contextualise our Australian dataset and investigate lineage diversity. We utilised a single nucleotide polymorphism (SNP) based clustering and multi locus sequence typing (MLST) approach. C. psittaci has four major phylogenetic groups (PG1-4) based on core genome SNP based phylogeny. PG1 contained clonal global and Australian equine, psittacine, and human ST24 genomes, with a median pairwise SNP distance of 68 SNPs. PG2, PG3, and PG4 had greater genomic diversity, including diverse STs collected from birds, livestock, human, and horse hosts from Europe and North America and a racing pigeon from Australia. We show that the clustering of C. psittaci by MLST was congruent with SNP based phylogeny. The monophyletic ST24 clade has four major sub lineages. The genomes of 17 Australian human, equine, and psittacine strains collected between 2008 and 2021 formed the predominant ST24 sub-lineage 1 (emerged circa 1979). Despite a temporal distribution of 13 years, the genomes within sub lineage 1 had a median pairwise SNP distance of 32 SNPs, suggesting a recent population expansion or potential cross host transmission. However, two C. psittaci genomes collected in 2015 from Victorian parrots clustered into distinct ST24 sub lineage 4 (emerged circa 1965) with ovine strain C19/98 from Germany. This work describes a comprehensive phylogenomic characterisation of ST24 and identifies a timeline of potential bird to equine spillover events.
Details
- Title
- One clone to rule them all: Culture-independent genomics of Chlamydia psittaci from equine and avian hosts in Australia
- Authors
- Rhys T White (Author) - University of the Sunshine Coast, Queensland, Centre for BioinnovationSusan I Anstey (Author) - University of the Sunshine Coast, Queensland, Centre for BioinnovationVasilli Kasimov (Author) - University of the Sunshine Coast, Queensland, Centre for BioinnovationCheryl Jenkins (Author) - New South Wales Department of Primary IndustriesJoanne Devlin (Author) - The University of MelbourneCharles El-Hage (Author) - The University of MelbourneYvonne Pannekoek (Author) - University of AmsterdamAlistair R Legione (Author) - The University of MelbourneMartina Jelocnik (Corresponding Author) - University of the Sunshine Coast, Queensland, Centre for Bioinnovation
- Publication details
- Microbial Genomics, Vol.8(10), pp.1-12
- Publisher
- The Microbiology Society
- Date published
- 2022
- DOI
- 10.1099/mgen.0.000888
- ISSN
- 2057-5858
- PMID
- 36269227
- Copyright note
- © 2022 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
- Organisation Unit
- GeneCology Research Centre - Legacy; School of Science, Technology and Engineering; Centre for Bioinnovation
- Language
- English
- Record Identifier
- 99681395602621
- Output Type
- Journal article
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