One clone to rule them all: Culture-independent genomics of Chlamydia psittaci from equine and avian hosts in Australia

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.

Whole-genome sequencing of Chlamydia psittaci from Australasian avian hosts: A genomics approach to a pathogen that still ruffles feathers

“…To combat these challenges, extensive sampling followed by WGS of C. psittaci -positive samples is needed from a broader range of atypical hosts, as shown by the approach utilised in our previous sampling [16] and genomic [6] studies.…”

“…The probes were designed to cover the complete chromosome and plasmid of C. psittaci , using two reference genomes (CP3; GenBank: CP003797 and Horse_pl; GenBank: CP025423) and the plasmid pCpHorse_placenta (GenBank: CP025424), as previously described [6].…”

“…Notably, five Australian samples (LittleCorella, Corella_41C, Corella_42_pooled, Bustard1C and Sshearwater1_pooled) were described in our previous study [16]. For the Australian swab samples, we followed the swab processing and DNA extraction protocols previously described [6,16]. For the isolates collected in New Zealand, DNA was extracted using standard DNA extraction protocols in the New Zealand Ministry for Primary Industries (MPI) laboratories.…”

“…Genomic studies further investigated and highlighted the intraspecies strain diversity of C. psittaci, providing novel insights into the evolution, genome content and phylogeny [1,3,6,7,12]. For example, Herrmann and colleagues successfully isolated and provided novel insights into the origin of fulmar-derived zoonotic strains from the Faroe Islands [13], whilst other genomic studies described the emergence and spillover into humans and horses of the global virulent and clonal 'parrot-type 6BC'/sequence type (ST)24 strains [1,6,7,14]. Despite the valuable insights the scarcity of such C. psittaci phylogenomic studies is striking, particularly when compared to the large-scale genomic analyses of Chlamydia trachomatis that can encompass over 500 genomes in a single study [15].…”

“…Recent studies in Australia have also detected C. psittaci in atypical hosts, such as the Australian white ibis (Threskiornis moluccus), Australian bustard (Ardeotis australis) and sooty shearwater (Ardenna grisea), with genotyping revealing that novel genetically diverse strains could be infecting atypical hosts, while 'traditional genotypes' are common in traditional hosts (e.g. clonal ST24/ompA genotype A in parrots and diverse STs/ompA genotypes E/B in pigeons) [6,10,16,17].…”