Rhys White

Rhys White

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

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

2 minute read

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.

Abstract

Fowl cholera caused by Pasteurella multocida has re-emerged in Australian poultry production since the increasing adoption of free-range production systems. Currently, autogenous killed whole-cell vaccines prepared from the isolates previously obtained from each farm are the main preventative measures used. In this study, we use whole-genome sequencing and phylogenomic analysis to investigate outbreak dynamics, as well as monitoring and comparing the variations in the lipopolysaccharide (LPS) outer core biosynthesis loci of the outbreak and vaccine strains. In total, 73 isolates from two different free-range layer farms were included. Our genomic analysis revealed that all investigated isolates within the two farms (layer A and layer B) carried LPS type L3, albeit with a high degree of genetic diversity between them. Additionally, the isolates belonged to five different sequence types (STs), with isolates belonging to ST9 and ST20 being the most prevalent. The isolates carried ST-specific mutations within their LPS type L3 outer core biosynthesis loci, including frameshift mutations in the outer core heptosyltransferase gene (htpE) (ST7 and ST274) or galactosyltransferase gene (gatG) (ST20). The ST9 isolates could be separated into three groups based on their LPS outer core biosynthesis loci sequences, with evidence for potential phase variation mechanisms identified. The potential phase variation mechanisms included a tandem repeat insertion in natC and a single base deletion in a homopolymer region of gatG. Importantly, our results demonstrated that two of the three ST9 groups shared identical rep-PCR (repetitive extragenic palindromic PCR) patterns, while carrying differences in their LPS outer core biosynthesis loci region. In addition, we found that ST9 isolates either with or without the natC tandem repeat insertion were both associated with a single outbreak, which would indicate the importance of screening more than one isolate within an outbreak. Our results strongly suggest the need for a metagenomics culture-independent approach, as well as a genetic typing scheme for LPS, to ensure an appropriate vaccine strain with a matching predicted LPS structure is used.

Read the full publication here: https://doi.org/10.1099/mgen.0.000772

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 PRJNA643588

Raw Illumina sequence read data have been deposited to the NCBI SRA under the accession numbers SRR12130700 through to SRR12130770

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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.

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.