Rhys White

Rhys White

PhD in Microbial Genomics | Comparative Genomics | Bioinformatics | Antibioic Resistance | Phylogenomics

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

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Published:

In Australia, novel C. psittaci infections in horses raise biosecurity concerns. Here, we used limited whole-genome sequencing to figure out ’who is giving it to who’ and when these modern C. psittaci strains may have appeared in Australia. Our findings suggest that strains from parrots and horses have likely descended from a single progenitor strain.

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.

Read the full publication here: https://doi.org/10.1099/mgen.0.000888

SCImago Journal & Country Rank

Data availability

Sequence read data has been submitted to the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject PRJNA798154

Raw Illumina sequence read data have been deposited to the NCBI SRA under the accession numbers SRR17649252 through to SRR17649264

Twitter thread

The first genomic insight into Chlamydia psittaci sequence type (ST)24 from a healthy captive psittacine host in Australia demonstrates evolutionary proximity with strains from psittacine, human, and equine hosts

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Published:

In 2022, we went into a pet shop and collected a faecal sample from a healthy (asymptomatic) pet bird. We discovered that a strain of Chlamydia psittaci found in a pet bird in 2022 is very similar to the C. psittaci strains that caused foal loss in horses in 2016. This is a bit concerning because it means that there’s a possibility that people and animals could get sick from C. psittaci, so we need to keep a close eye on it to make sure everyone stays healthy. To do that, we need to figure out who is giving C. psittaci to whom so we can come up with evidence-based ways to stop C. psittaci from spreading.

Phase variation in the glycosyltransferase genes of Pasteurella multocida associated with outbreaks of fowl cholera on free-range layer farms

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Published:

In poultry, P. multocida causes fowl cholera which leads to acute and fatal septicaemia with significant economic loss on the poultry industry. In Australia, gene-centric molecular studies are valuable in studying the epidemiology of outbreaks and guiding autogenous vaccination programmes. But these techniques do not provide the resolution for insight into the LPS structure of strains - enter whole-genome sequencing.

Completing the genome sequence of Chlamydia pecorum strains MC/MarsBar and DBDeUG: New insights into this enigmatic koala (Phascolarctos cinereus) pathogen

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Published:

We present the first two complete C. pecorum genomes sequenced from diseased koalas. With these genomes, we expand on previous works by improving the gene annotations and by providing the genomic context of important virulence and accessory gene content. These findings lay the foundations for identifying and understanding species specificity and host adaptation behind chlamydial infections affecting koalas.