P2f: Infectious Diseases – New tools for diagnosing causes of scours and respiratory diseases in dairy calves.

Dairy UP Project P2

You can help

if you are interested in this project or think you may want to be involved at some stage, please contact anyone from the team here:

Team Leader:

  • Dr Barbara Brito Rodriguez – NSW DPI – barbara.britorodriguez@dpi.nsw.gov.au

Project Team:

  • Dr Ian Lean – Scibus – ianl@scibus.com.au
  • Dr Helen Golder – Scibus – heleng@scibus.com.au


  • Aleksandra Ola – UTS PhD Student
  • Chloe Wilson – USyd
  • David Sheedy – USyd PhD Student
  • John Webster
  • Joyce To – UTS
  • Karen Smith – EMAI
  • Monica Suann – EMAI
  • Sopheak Hem – UTS
  • Steve Djordjevic – UTS
  • Zain UI Abedien – UTS PhD Student

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Barbara Brito Rodriguez on Dairy UP

Barbara Brito Rodriguez (Project Leader P1b & P2f) talks about reducing antimicrobial use.

This project aims to determine the occurrence and spread of viruses and bacteria in NSW dairy herds. The information will provide a foundation for tools to help farmers and vets monitor and treat diseases such as scours and respiratory disease.

Scours and respiratory diseases are common causes of death in young calves. Currently, calves with scours or respiratory disease are often treated on the basis of symptoms, without identifying the microbe responsible.

The research team is using an approach called “metagenomics” to build a library of genomes of bacteria and viruses found in NSW dairy cattle. They aim to work with up to 300 dairy farmers from all of NSW’s dairying regions to collect nasal and faecal swabs from sick and healthy calves. The genome of bacteria and viruses detected in the swabs will be sequenced to build the genome library. The genetic sequence will allow them to identify specific ‘strains’ of bacteria or viruses that cause more severe disease than others and therefore guide the focus for disease control.

Samples taken from sick calves can be matched with microbes in the library, for quick and easy detection of the virus or bacteria responsible for causing disease. This would enable early treatment with the appropriate drugs, improving survival rates and reducing overall use of antimicrobials.

Although this work is focussed on calf scours and respiratory diseases in NSW dairy calves, the findings have the potential for broader application. For example, the diagnostic tools developed may be relevant to dairy regions outside NSW.


February 2022
A pilot study was conducted in 2021 which involved collecting nasal and faecal swabs from two NSW dairy farms. The results from this work will inform the design of the broader project with representative samples from NSW dairy farms. A new microbe of potential interest has already been identified.

July 2023
Dairy UP’s Infectious Diseases project has made significant progress recently. As at July 2023, more than 1800 swabs have been collected from about 550 cows and calves  on 26 farms.  Analysis of samples is underway, while sampling from more farms continues. Initial analysis has identified a number of viruses that have not been recently studied . The next step is to determine if these viruses have a role in disease.

Timeframe: July 2021 – June 2026
Project contact: Dr Barbara Brito Rodriguez, DPI NSW (EMAI) email: barbara.britorodriguez@dpi.nsw.gov.au