The Seed - Biosecurity Innovation Hub

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Welcome to The Seed, our biosecurity innovation hub where you can learn more about exciting developments in the biosecurity space.

This initiative was an outcome of the inaugural Biosecurity Innovation Exchange 2018.

Each issue will feature stories about exciting initiatives and profiles of people who are making great strides in innovation.

You can also plant your ideas in our ideas patch and subscribe so you don’t miss out on the latest news.

Welcome to The Seed, our biosecurity innovation hub where you can learn more about exciting developments in the biosecurity space.

This initiative was an outcome of the inaugural Biosecurity Innovation Exchange 2018.

Each issue will feature stories about exciting initiatives and profiles of people who are making great strides in innovation.

You can also plant your ideas in our ideas patch and subscribe so you don’t miss out on the latest news.

  • Investing in agriculture’s next generation

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    Written by Compliance division

    We’re inviting Australia’s brightest minds to apply for a grant in the 2021 Science and Innovation Awards for Young People in Agriculture, Fisheries and Forestry.

    10 awards of up to $22,000 will be given for new and creative research projects that help overcome industry challenges in agriculture.

    Applications are open now to young agricultural innovators, scientists and researchers between 18 and 35 years of age.

    Chief Scientist & Chief Plant Protection Officer Dr. Robyn Cleland said ”We’re happy to support the emerging careers of Australia’s young agricultural innovators“.

    The 10 award categories were developed in partnership with research and development corporations and industry associations. They are:

    • biosecurity and digital innovation
    • cotton
    • eggs and poultry (layers)
    • forest and wood products
    • grains
    • horticulture
    • meat and livestock
    • red meat processing
    • viticulture and oenology
    • wool.

    The winners will then be invited to apply for the Minister for Agriculture, Drought and Emergency Management’s Award. This provides additional funding for an extended research project.

    The 2020 Minister’s Award winner was Dr Meagan Craven from Deakin University. Her project investigated whether pigeon milk can combat deadly Salmonella outbreaks on Australian egg farms.

    Applications close 5pm AEST Friday 2 October 2020. Find out how to apply.

  • Embracing technology in environmental biosecurity engagement

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    Image: Webinar 2 – It’s all about the people (August 2020)

    Written by

    In place of the biannual Environmental Biosecurity Roundtables, this year the Chief Environmental Biosecurity Office is hosting a series of webinars. They will take place from July to November 2020.

    Each webinar will focus on a different theme relating to environmental biosecurity. These themes are inclusive of attitudes and behaviours that influence biosecurity management.

    A Have Your Say page supports the webinars, with a discussion forum for participants.

    Philippe Frost, from the Environmental Biosecurity Office, said that this year the department had to think of other ways for interested stakeholders to stay connected.

    ‘With so much happening, it's important to have a space to learn and collaborate together. The webinars offer a great opportunity to continue these collaborations,’ Mr Frost said.

    ‘They’ve also helped us expand our audience this year. Stakeholders now have a new way to connect with us from around Australia.

    ‘We didn't expect such a strong uptake — the numbers are double what we would have at a roundtable meeting.

    ‘We're delighted to offer this opportunity for people to talk about environmental biosecurity,’ he said.

    The July and August webinars attracted over 150 participants. We received positive feedback from participants about the webinar format and content.

    You can register to take part in the next webinar. For recordings, slides, and related information from past webinars, visit Have Your Say.

  • Modelling the potential spread of African swine fever

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    Written by Biosecurity Animal Division

    A new animal disease planning model will strengthen Australia’s preparedness to biosecurity threats. The Australian Animal Disease spread model (AADIS) was funded by the Department of Agriculture, Water and Environment (DAWE) and is used to model the spread and control of a disease in a population for emergency planning.

    This national-scale modelling capability is being adapted to look at the possible impacts of African Swine Fever (ASF) where an outbreak in Australia could cost millions from economic losses. ASF poses a threat to the Australian pig industry. Recently, ASF has spread throughout Asia and has now reached Papua New Guinea.

    Sharon Roche is a veterinary officer at DAWE. She explains that AADIS is a useful tool to help understand how an exotic diseases, like ASF, may spread in Australia. ‘It can provide insights into how to control the disease’ Ms Roshe said. Once we have AADIS set up for ASF, we will be able to model potential ASF outbreaks in Australia.’

    ‘This will allow us to identify where ASF may be more likely to spread, or situations that allow spread to occur. Insights on the effectiveness of potential control programs can inform response policies.’ said Ms Roche. AADIS is an internationally recognised epidemiological model being adapted for the Australian context as part of the Biosecurity Innovation Program. This will help in our efforts to plan for possible outbreaks of animal diseases in Australia.





  • How do you help train AI, protect Kakadu and win a prize? Now that’s innovation

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    Image caption: Types of labelled imagery and use cases

    Written by Heritage, Reef and Wildlife division

    Calling on citizen scientists to help ID fish and protect the park

    Kakadu National Park has remained protected from the effects of uranium mining for more than 40 years.

    Technological advancements and safety driven innovation means we can keep better track of freshwater fish communities. This allows us to detect mining related impacts on the park. Scientists now use drones and underwater video cameras. This helps to safely conduct annual surveys of billabongs throughout the national park. The cameras allow our scientists to measure the presence and abundance of freshwater fish species. It also enables the collection of hundreds of hours of fish videography every year.

    We are now working with Microsoft engineers to develop an innovative artificial intelligence (AI) model. It will help automate the identification of fish species.

    When completed, the AI model will be able to identify and count fish from video. This will significantly increase the efficiency and accuracy in our data processing. But we need your help and are calling on the support of citizen scientists!

    In order to fully automate the process, the model needs to be trained. This is done by providing more than 100,000 annotated and labelled images of fish. If you can help with the annotations, your actions will help train artificial intelligence. There is also a prize for the participant with the highest number of labelled images!

  • Supporting our biosecurity system to manage risk through innovation

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    Written by the compliance division

    We’re proud to be able to support our biosecurity system to manage risk through innovation, and to be able to fund projects which will help us manage biosecurity risk smarter in the future.

    Two projects funded through our Biosecurity Innovation Program have been nominated for innovation awards.

    Last week the 3D x-ray technology and algorithm project was announced as one of the 12 finalists in Australia’s 2020 Public Sector Innovation Awards digital and data category. This project is a ground-breaking trial by using 3D x-ray technology and is a world first algorithm to automatically detect biosecurity risk. This is inclusive of materials including fruit, meat and seafood. This project has the potential to improve the rates of early detection of biosecurity pests and diseases. Further details can be seen on the IPAA website.


    The second nomination is the Deep Learning Artificial Intelligence used for the detection of Brown Marmorated Stink Bug (BMSB) project.It has been nominated for the CSIRO 2020 Digital, National Facilities and Collections Awards under the Breakthrough Innovation category. The project is a proof of concept to determine whether a mobile phone app could be used to identify BMSB from other similar stink bugs. The app uses Microsoft Azure’s Computer Vision and the results of the feasibility study are extremely promising.

    We look forward to sharing the outcome with you shortly.

  • The power of new diagnostics to enable faster identification of biosecurity threats

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    Written by compliance division

    Having ready access to diagnostic capability is of critical importance to the Department of Agriculture, Water and the Environment, particularly when dealing with emerging pests and diseases of biosecurity concern. Historically we’ve relied on external providers to develop diagnostic tests. In many cases, this has delayed our ability to perform the required tests in response to new biosecurity threats.

    This project is building an in-house diagnostic capability to develop and validate new molecular technologies. Which means we will be more agile in our ability to prepare and respond to emerging threats.

    ‘We have successfully established a brand new, cutting-edge molecular diagnostic development laboratory within the PIC@PEQ team based at PEQ Mickleham. Using an important family of plant viruses called Begomoviruses as a test-case, we are now close to finalising significantly improved diagnostic tools to detect these viruses in plant hosts. This advancement benefits not just the department, but also colleagues in state government and international jurisdictions said Mark Whattam, Director of PIC@PEQ.

    PIQ@PEQ is continuing to enhance their diagnostic development capability which will further enhance the department’s ability to respond efficiently to new and emerging biosecurity threats.

    Funded by the Biosecurity Innovation Program.

  • DNA testing in cows is reducing superbug risk

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    The dairy industry is embracing new technology to help address antimicrobial resistance (AMR). It allows a more precise identification of mastitis in dairy cattle. Mastitis is a painful condition that reduces milk production and quality.

    The technology uses DNA technology to address the important and growing issue of AMR. AMR reduces the ability to treat serious bacterial infections in animals and humans. Though a natural defence mechanism, inappropriate antibiotic use can increase resistance. This makes infections more difficult to treat.

    The dairy industry is an important contributor to the Australian economy. In 2017–18, it accounted for around 7 percent ($4.4 million) of the gross value of agricultural production (ABS 2019). It also accounted for around 7 percent ($3.5 billion) of agricultural export income.

    Poor udder health costs Australian dairy farmers $150 million per year. The major cause is mastitis, which is usually treated with antibiotics.

    It can be challenging though, to know which antibiotic to use, and whether they will help at all. Preventative use of broad-spectrum antibiotics is common by veterinarians and dairy farmers. They also administer them while awaiting culture results from the laboratory.

    The Biosecurity Animal Division is collaborating with the CSIRO. Together they are producing a cow-side, point-of-care test. This is possible through funding from the Biosecurity Innovation Program.

    The test identifies common, causative bacteria for mastitis. It is based on polymerase chain reaction (PCR) technology.

    The test process is for bacterial DNA to be extracted from fresh milk. Target bacteria is then identified in under 30 minutes, creating a ‘laboratory in a drop’.

    CSIRO is working with Queensland biotechnology company, XING, and the dairy industry. Together, they are developing this proof-of-concept project. This will ensure that the technology fits with workflows in Australian dairies.

    The dairy industry wants a reliable, quick and affordable test. This will help inform treatment decisions for mastitis.

    Dr Jenny Baird said the test will help treatment decisions to be better informed. Dr Baird is a Veterinary Officer in Animal Health Policy.

    ‘They desire a cost effective, fast and reliable test for on-farm use,' she said.

    'Real-time information could lead to more selective antibiotic use. This would reduce the likelihood of ‘superbugs’, which are difficult to treat.

    In 2020–21, further laboratory testing and in field trials will be undertaken.





  • eDNA project crawls out of the water

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    Image caption: EcoDNA scientist Allejandro with export premesis health manager Malee down in the waste water pit. The best place to get an eDNA sample from the whole facility.

    Written by: Biosecurity Analytics and Intelligence Services

    Last year on The Seed we reported on eDNA and portable DNA technology research.

    Early work took us to Kasetsart University in Bangkok. We hooked up with ornamental fish exporters. They helped us understand how to apply this new technology to biosecurity risk-management.

    We are now entering the second year of research. In this phase, we are expanding our partnerships beyond the aquatic environment. Moreover, into new priority pest and disease targets.

    This year, we focused on eDNA tests using platforms like MinION and iSeq. Additionally, portable technology like Biomeme mobile qPCR thermolcyclers. These are easy to use by our own experts in the field to produce results in as little as 20 minutes.

    Geoff Grossel is a scientist at the Department of Agriculture, Water and the Environment. He says an example of how this could support border control is testing eDNA samples. Also, targeted DNA with mobile qPCR.

    ‘This would provide officers with a quick, cheap and accurate tool,' he says. 'The tool would detect high-risk pest hitchhikers and diseases. These pests could be entering the country with all types of imported products.

    There are a number of new priorities for the project, including:

    • developing a quick and accurate I.D. test for exotic invasive ants
    • monitoring for white nose disease in bats from soil samples
    • rummaging through imported bulk seed samples for signs of disease. These include tomato and cucurbit diseases.

    We are starting to realise the tremendous potential of these new DNA technologies. Like the cross-sectoral application to produce benefits for biosecurity risk management. This would impact pre-border to post-border biosecurity across all our divisions. Across state, territory and international governments and exporters. National and international research partnerships are also possible.

    We can also announce our new project partners:

    • Chief Environmental Biosecurity Officer, Ian Thompson
    • Biosecurity Plant Division
    • Post Entry Quarantine at Mickleham in Melbourne
    • state and territory biosecurity departments
    • Western Sydney University.

    The University of Canberra EcoDNA lab is a partner we have already been working with. Also, the Centre for Invasive Species Solutions. The diversity of these partnerships makes the project more interesting and exciting.

    We will provide an update on implementation and application of this mobile technology. This includes both in the field and at the border.

    We are hoping to answer some questions like: Will it work? Will it be more efficient? Will it improve the service we offer our clients? Will it be better than what we are doing now?



  • Polly want a lab test ?

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    Article written by Biologicals and Avian branch

    Exciting things are happening in the world of animal biosecurity. The Department of Agriculture, Water and the Environment is close to releasing its draft risk assessment for the import of live psittacine birds. Most of us know these better as parrots and their various relatives like cockatoos and lovebirds.

    This will mean imports of these birds may shortly be permitted for the first time in decades.

    But a policy is only as good as its implementation and implementation was looking a bit tricky. Why? Because there are no commercially available tests in the world for some of the exotic viruses we need to protect against. Specifically, psittacine bornavirus and herpesvirus.

    ‘A lot of people want to import psittacines, but we can’t afford to risk the health of any of our native birds in the process’ said a departmental spokesperson.

    So, the department, through the Biosecurity Innovation Program, turned to the Australian Centre for Disease Preparedness (ACDP) for help developing suitable tests that we can use to ensure imported psittacine birds aren’t carrying any hidden nasties.

    The ACDP is on track to have the new tests up and running shortly. This will be welcome news for Australia’s psittacine fanciers and for people who have had to leave a pet bird behind when immigrating to Australia.

    ‘Psittacine birds are often very long lived, intelligent and closely bonded with their owner. We are expecting several happy reunions in the not too distant future,’ said a departmental spokesperson.

  • FMD preparedness training goes virtual

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    Image: Early screenshot of clinical examination in the pilot VR experience

    Article written by Animal Health Epidemiology and One Health division

    We’re turning to virtual reality to enhance foot-and-mouth disease (FMD) preparedness, by transforming live training courses into simulated learning experiences.

    Since 2012, the department has been working with the European Commission for the Control of Foot-and-Mouth Disease (EuFMD) to run training courses in FMD-endemic countries, such as Nepal. These face to face training courses give livestock workers, industry representatives and veterinarians first-hand experience diagnosing and investigating FMD outbreaks. They also play an important role in raising awareness of FMD when they return home. However, providing this training in person is resource intensive, and inaccessible to some.

    Virtual reality has been shown to be a successful, cost effective and practical method for training large numbers of people using task-based scenarios. So, in the search for an alternative, the department asked Novus Res, a virtual reality games studio in Adelaide, to conduct a pilot virtual reality experience and develop a research report on the efficacy of the training.

    The pilot experience includes activities such as clinical examination of cows, laboratory sampling, and setting up a biosecurity control point. The pilot will evaluate the effectiveness of the technology for biosecurity training, with a focus on FMD preparedness. The research report will provide insights into the possibilities of virtual reality as a training tool, and how it could potentially be rolled out.

    Project manager, Corrie Croton, said ‘the report and pilot outcomes will help show government and industry the current state, and the potential, of virtual reality training. It will provide a foundation for future virtual reality training projects. This is an emerging field with the potential to enhance future training programs.’

    The department expects to release the report in July 2020.