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

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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. We used culture-independent probe-based 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 spatial clusters and lineage diversity. We utilised a single-nucleotide polymorphism (SNP) based clustering and multi-locus sequence typing (MLST) approach. Based on core-genome SNP-based phylogeny, C. psittaci has three major distinct clades (Clade I-III). Clade I contained clonal global and Australian equine, psittacine, and human ST24 genomes, with a median pairwise SNP distance of 68 SNPs. Clades II and II 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 Clade III 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. 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 with another global strain. This work describes a comprehensive phylogenomic characterisation of ST24 of potential bird-to-equine spillover events.