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Pathogen profiling of Australian rabbits by metatranscriptomic sequencing.

Maria Jenckel¹, Robyn N Hall^1,2, Tanja Strive^1,2

¹CSIRO Health and Biosecurity, Canberra, Australia.

Transboundary and Emerging Diseases

|June 10, 2022

Summary

Rabbit deaths in Australia are not always due to known viruses like RHDV. Metatranscriptomic sequencing identified various bacteria and parasites, but also revealed some deaths had no identified pathogen, suggesting complex causes.

Keywords:

Oryctolagus cuniculus metagenomics metatranscriptomics pathogen identification

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Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Published on: December 22, 2014

Area of Science:

Veterinary Pathology
Wildlife Disease Ecology
Genomics

Background:

Australia utilizes biocontrol agents like myxoma virus (MYXV) and rabbit haemorrhagic disease virus (RHDV) for wild rabbit population management.
Surveillance revealed approximately 40% of deceased rabbits tested negative for RHDV, prompting investigation into other causes of mortality.

Purpose of the Study:

To identify infectious agents responsible for rabbit deaths in Australia when RHDV is absent.
To explore the utility of host transcriptome data in differentiating infectious from non-infectious causes of death.

Main Methods:

Metatranscriptomic sequencing of liver samples from RHDV-negative rabbits.
Host transcriptome analysis to assess host immune responses.

Main Results:

Identified transcripts of known rabbit pathogens including Clostridia species, Pasteurella multocida, Pseudomonas spp., and Eimeria stiedae.
Hepatitis E virus and Cyniclomyces yeast were detected but not typically associated with severe disease.
One-third of samples lacked identifiable infectious agents; some showed host immune up-regulation, unlike samples with detected E. stiedae, Pseudomonas, or yeast.

Conclusions:

While no novel rabbit pathogens were discovered, the study established a reliable workflow for investigating rabbit mortality events.
Host transcriptome analysis aids in distinguishing pathogenic microbes from commensals or contaminants.
Some rabbit deaths may result from non-infectious causes or unidentified pathogens, indicated by host immune responses.