Expanding the range of the respiratory infectome in Australian feedlot cattle with and without respiratory disease using metatranscriptomics

Barbara P Brito; Melinda J Frost; Kay Anantanawat; Frederick Jaya; Tony Batterham; Steven P Djordjevic; Wei-Shan Chang; Edward C Holmes; Aaron E Darling; Peter D Kirkland

doi:10.1186/s40168-023-01591-1

Expanding the range of the respiratory infectome in Australian feedlot cattle with and without respiratory disease using metatranscriptomics

Microbiome. 2023 Jul 25;11(1):158. doi: 10.1186/s40168-023-01591-1.

Authors

Barbara P Brito^{1

2

3}, Melinda J Frost⁴, Kay Anantanawat^{5

6}, Frederick Jaya⁵, Tony Batterham⁷, Steven P Djordjevic⁵, Wei-Shan Chang⁸, Edward C Holmes⁸, Aaron E Darling^{5

6}, Peter D Kirkland⁴

Affiliations

¹ Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, New South Wales, Australia. barbara.britorodriguez@dpi.nsw.gov.au.
² New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, Australia. barbara.britorodriguez@dpi.nsw.gov.au.
³ Present Address: Biosecurity and Food Safety, NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute (EMAI), Menangle, New South Wales, Australia. barbara.britorodriguez@dpi.nsw.gov.au.
⁴ New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, Australia.
⁵ Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, New South Wales, Australia.
⁶ Illumina Australia, Ultimo, New South Wales, Australia.
⁷ Apiam Animal Health, East Bendigo, Australia.
⁸ Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia.

Abstract

Background: Bovine respiratory disease (BRD) is one of the most common diseases in intensively managed cattle, often resulting in high morbidity and mortality. Although several pathogens have been isolated and extensively studied, the complete infectome of the respiratory complex consists of a more extensive range unrecognised species. Here, we used total RNA sequencing (i.e., metatranscriptomics) of nasal and nasopharyngeal swabs collected from animals with and without BRD from two cattle feedlots in Australia.

Results: A high abundance of bovine nidovirus, influenza D, bovine rhinitis A and bovine coronavirus was found in the samples. Additionally, we obtained the complete or near-complete genome of bovine rhinitis B, enterovirus E1, bovine viral diarrhea virus (sub-genotypes 1a and 1c) and bovine respiratory syncytial virus, and partial sequences of other viruses. A new species of paramyxovirus was also identified. Overall, the most abundant RNA virus, was the bovine nidovirus. Characterisation of bacterial species from the transcriptome revealed a high abundance and diversity of Mollicutes in BRD cases and unaffected control animals. Of the non-Mollicutes species, Histophilus somni was detected, whereas there was a low abundance of Mannheimia haemolytica.

Conclusion: This study highlights the use of untargeted sequencing approaches to study the unrecognised range of microorganisms present in healthy or diseased animals and the need to study previously uncultured viral species that may have an important role in cattle respiratory disease. Video Abstract.

Keywords: Bovine respiratory disease; Infectome; Metagenomics; Metatranscriptomics; Microbiome; Virome.

Publication types

Video-Audio Media
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Australia
Cattle
Cattle Diseases* / microbiology
Respiratory Tract Diseases*
Rhinitis*
Viruses* / genetics