Rhys White

Rhys White

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

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.

Abstract

Chlamydia pecorum, an obligate intracellular pathogen, causes significant morbidity and mortality in livestock and the koala (Phascolarctos cinereus). A variety of C. pecorum gene-centric molecular studies have revealed important observations about infection dynamics and genetic diversity in both koala and livestock hosts. In contrast to a variety of C. pecorum molecular studies, to date, only four complete and 16 draft genomes have been published. Of those, only five draft genomes are from koalas. Here, using whole-genome sequencing and a comparative genomics approach, we describe the first two complete C. pecorum genomes collected from diseased koalas. A de novo assembly of DBDeUG_2018 and MC/MarsBar_2018 resolved the chromosomes and chlamydial plasmids each as single, circular contigs. Robust phylogenomic analyses indicate biogeographical separation between strains from northern and southern koala populations, and between strains infecting koala and livestock hosts. Comparative genomics between koala strains identified new, unique, and shared loci that accumulate single-nucleotide polymorphisms and separate between northern and southern, and within northern koala strains. Furthermore, we predicted novel type III secretion system effectors. This investigation constitutes a comprehensive genome-wide comparison between C. pecorum from koalas and provides improvements to annotations of a C. pecorum reference genome. These findings lay the foundations for identifying and understanding host specificity and adaptation behind chlamydial infections affecting koalas.

Read the full publication here: https://doi.org/10.3390/pathogens10121543

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Data availability

Sequence read data has been submitted to the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject PRJNA747116

Raw Illumina sequence read data have been deposited to the NCBI SRA under the accession numbers SRR15170907 and SRR15170908

The high-quality draft assemblies have been deposited to GenBank under the accession numbers CP080401 to CP080404

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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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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.

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

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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.

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.