Oral Presentation Australian Society for Microbiology Annual Scientific Meeting 2022

Whole-genome sequencing of Australian equine and avian Chlamydia psittaci strains: One clone to rule them all? (82407)

Rhys T White 1 2 3 , Susan I Anstey 1 , Vasilli Kasimov 1 , Cheryl Jenkins 4 , Joanne Devlin 5 , Charles El-Hage 5 , Alistair R Legione 5 , Yvonne Pannekoek 6 , Martina Jelocnik 1
  1. Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
  2. Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Queensland, Australia
  3. School of Chemistry and Molecular Biosciences, Australian Infectious Disease Research Centre, The University of Queensland, Brisbane, Queensland, Australia
  4. NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, Australia
  5. Asia Pacific Centre for Animal Health, The University of Melbourne, Parkville, Victoria, Australia
  6. Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, North Holland, The Netherlands

Introduction. Chlamydia psittaci is an avian pathogen with zoonotic potential. In Australia, C. psittaci also causes reproductive loss in Thoroughbred mares. To date, molecular typing studies describe the predominant and clonal C. psittaci sequence type (ST)24 strains in horse, psittacine, and human infections. Therefore, we sought to assess the clonality between global and Australian ST24 strains and the emergence of ST24 with a comprehensive genomics approach.

 

Methods. We used culture-independent probe-based whole-genome sequencing to investigate 13 C. psittaci genomes from horses, psittacines, and a pigeon across Australia. Published genomes of 36 C. psittaci strains were also used to contextualise our Australian dataset and investigate spatial clusters and lineage diversity. We utilised a single-nucleotide polymorphism (SNP) based clustering and multi-locus sequence typing (MLST) approach.

 

Results. Based on core-genome SNP-based phylogeny, C. psittaci has four major distinct phylogenetic groups (PG1-4). 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 several STs collected from birds, livestock, human, and horse hosts from Europe and North America, and a racing pigeon from Australia (clustering in PG4 with other “pigeon-type STs”). We show that the clustering of C. psittaci by MLST was congruent with ‘gold-standard’ SNP-based phylogenies. The monophyletic ST24 clade has four major host generalist 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 another global strain.

 

Conclusion. This work describes a comprehensive phylogenomic characterisation of ST24 and identifies a timeline of potential bird-to-equine spillover events.