The Seed - Biosecurity Innovation Hub

aThe Plant Innovation Centre at Post-Entry Quarantine (PIC@PEQ)

The Plant Innovation Centre at Post-Entry Quarantine (PIC@PEQ), part of the Department of Agriculture, Water and the Environment, is a team of dedicated scientists who:

Since 2017, PIC@PEQ have worked closely with a range of external partners including universities, state governments and biosecurity treatment providers, to champion new and innovative initiatives to improve business outcomes ­– particularly in relation to cutting-edge diagnostic technologies and novel treatment strategies.

One such project is ‘High Throughput Sequencing (HTS) for high-risk plant diagnostics in PEQ’, a collaborative effort between PIC@PEQ, Science and Surveillance Group, Queensland University of Technology, Agriculture Victoria, Hort Innovation and the New Zealand Ministry of Primary Industries.

Mark Whattam, the Director and founder of PIC@PEQ, said that HTS will be a game-changer for how we detect and identify viruses in high-risk plants imported into Australia.

“At present, we run dozens of individual tests for viruses which is expensive and time-consuming,” Mr Whattam said.

“HTS will replace all of these with a single test. It will result in improved detections, cheaper imports, and faster clearance times with less resources.”

HTS is scheduled for implementation in late 2022, with the necessary policy settings currently under development via a divisional working group chaired by David Dall, the department’s head of Plant Science and Risk Assessment.

ROVs can be used to detect pests that threaten Australia’s marine environments and industries

Marine pests, such as the Asian green mussel, can hitch a ride to Australia on ships or other vessels. Once established, marine pests have impacts on Australia’s unique environment, economy and way or life. We need to constantly be on the lookout for marine pests, to stop their introduction and spread.

Remotely Operated underwater Vehicles (ROVs) are emerging as a powerful new tool to detect introduced marine pests. These underwater drones can search for pests on the underside of ships, port infrastructure or in the natural environment.

The Department of Agriculture, Water and the Environment has funded the modification of ROVs to make them more powerful surveillance tools, and trained biosecurity personnel in their use. Features such as high-resolution cameras, live streaming of footage, sonar and sample collection tools have been tested and a report outlining the results is now available.

Training videos and documents will also be published on the marine pest website late this year and will be used to support the use of ROVs for biosecurity surveillance.

ROVs are already being used for biosecurity surveillance around Australia and interest is expected to grow as new features are developed, experience in their use is gained and prices continue to drop.

Check out the video of ROVs in action, or find out more about developments in marine biosecurity surveillance using ROVs

Dr Kim Ritman Award for Science & Innovation winner is plant biosecurity expert Professor Brendan Rodoni

Professor Brendan Rodoni is the inaugural winner of the Dr. Kim Ritman Award for Science and Innovation. The win is recognition of his efforts to improve Australia’s capability for managing plant biosecurity risks.

Professor Rodoni is a strong advocate for biosecurity research. He has made a substantial contribution to plant virology and bacteriology research over his 35-year career.

Professor Rodoni was involved in the national response to the reported detection of fire blight in Melbourne in 1997. This report resulted in one of the most intense survey and diagnostic programs in the history of plant industries in Australia.

In 2010, he was involved in the development of advanced molecular diagnostic methods for the detection of plant viruses. This resulted in the adoption of new polymerase chain reaction tests for post-entry quarantine operations.

In 2012, he investigated new approaches for diagnosing high-priority exotic plant bacterial pathogens. This led to improvements in diagnostic capability for Australia, New Zealand and the United States. This improved detections of fire blight, zebra chip, citrus canker and kiwi fruit blight.

Prof Rodoni has led innovative work in emerging genomics technologies and field-deployable detection systems.

Since 2018 he has worked on a national high-throughput sequencing (HTS) project. This includes his advocacy role in developing a framework and guidelines for using HTS.

He is currently engaged in a 5-year industry-funded surveillance project that will change how airborne emergency plant pests are detected.

Prof Rodoni’s has a strong commitment to delivering outcomes for government, industry and the community. His efforts have contributed significantly to innovations in biosecurity.

Insect under low energy x-ray

Currently, seeds make up around 80% of all detections at our mail gateway facilities. Everyday hundreds of seed packets are intercepted by biosecurity officers.

Seeds come in varying shapes and are often small and low density. Current detection technologies have challenges in identifying seeds at our border.

This is being addressed with an innovative technical solution to reduce biosecurity risk.

The technology uses real-time video imagery and a computer algorithm to automatically identify seed packets and then uses a low-energy, high resolution x-ray to confirm the presence of seeds inside the packet.

Project director, Jessica Mitchell, explains that high energy x-ray cannot be absorbed by small items so will generally not detect the presence of seeds.

‘Unlike high energy x-ray, low energy x-ray is able to be absorbed by smaller items such as insects and seeds,’ says Ms. Mitchell.

’Low-energy beams are not as powerful and are able to show an incredibly defined image, perfect for detecting small hidden seeds.’

Funded by the Biosecurity Innovation Program, this world-first, proof of concept trial began in May 2020. It has already proven successful, demonstrating that computer algorithms and low energy x-ray is an effective way to identify and confirm the presence of seeds.

The project team is now preparing for phase 2. This involves operational trials and integrating this technology into current processes. Watch this space for future updates!

DAWE is working collaboratively in partnership with Rapiscan to develop this technology.

Bruvnet SoftwareWritten by Compliance division

The innovative model helps to automate the identification of fish species in Kakadu National Park billabongs. This involves counting and labelling fish from video footage. The challenge is that BRUVNet needs a significant dataset of labelled fish imagery. A large dataset will allow enough accuracy for regular monitoring.

The challenge saw many individuals contribute to labelling the fish. It was Brooke Batham, Brooke from the department’s Innovation Hub who succeeded in labelling the most. A staggering 943 fish!

‘I think it's so important to get involved in citizen science projects. I always love using the skills I learnt from my marine biology background, and I'm so glad I could help out! Brooke said.

‘This gives me the opportunity to use the skills I have learnt to help protect Kakadu without ever leaving Canberra.’

Even though the challenge has ended, you can still help by taking part online. This is an opportunity to contribute to the protection of Kakadu National Park.

We want to hear your innovative ideas to enhance Australia’s national biosecurity system to manage emerging biosecurity challenges and risks, with new project funding now available through the Biosecurity Innovation Program 2021-22!

The challenge

Biosecurity protects Australian livelihoods and is vital to strengthening and supporting our environment and economy, including tourism, trade, and agriculture. It underpins many aspects of our way of life.

The Australian biosecurity landscape is changing quickly and growing in complexity. We are operating in a 24-hour business context, facing increasing volumes of international trade. We are facing increasingly complex global supply chains and changes in the environment, including climate change.

Globalisation, complexity of international supply chains and changes to the Australian operating environment including the COVID-19 pandemic are making biosecurity risk management more challenging.

What we are looking for

Industry plays an essential role in safeguarding Australia’s biosecurity. We want to collaborate with innovators from the business sector, universities, and domestic and international research entities.

Together, we want to identify bold new ideas to support the long-term effectiveness and sustainability of Australia’s biosecurity system.

Tell us your ideas for technologies and approaches that will contribute to a sustainable and effective national Australian biosecurity system, and ways to modernise our current biosecurity risk management practices.

The program will provide financial support for projects that could improve:

• biosecurity screening of goods and passengers
• biosecurity risk detection — for example, drone surveillance, artificial intelligence, robotics, next generation sequencing and new biological controls
• the effectiveness and efficiency of our national biosecurity system in a changing environment.

How to get involved

Applications for 2021-22 financial year funding round opened on 9 November 2020 with submissions closing on 12 February 2021.

Send a short description of your idea to the Biosecurity Innovation Program team (100-300 words) and we will be in touch.

Contact the team early so they can connect you with a project sponsor. The sponsor will champion your idea within the department and work with you to develop your project proposal, including to ensure your idea is aligned to the department’s priorities and the program objectives.

Article written by Compliance Division

Dr. Alejandro collecting dirt samples from vaccum cleaners used by the biosecurity officers responding to the Khapra beetle detection at the Good Guys (Image Courtesy: Dr. Thomas Wallenius, DAWE).

Earlier on The Seed, we reported on the success of using eDNA to detect fish pests in the water. This time we move our focus to land to detect the notorious Khapra beetle from dirt samples.

World-first e-DNA detection

Khapra beetle (Trogoderma granarium) is a listed national priority pest infecting grains, seeds, rice and dried food. It can cause huge losses to our economy if it becomes established. In August 2020, detections were made at two The Good Guys retail outlets in Canberra. This led to a rapid biosecurity eradication response by the department.

Our own entomologist, Dr Thomas Wallenius, teamed up with Dr. Alejandro Trujillo-Gonzalez, the lead researcher in the project. Together, they examined the area for the presence of Kharpa beetle and recovered filters from vacuum cleaners used at the site.

Khapra DNA was identified from the dirt samples taken from the vacuum cleaners, a world first detection using eDNA in biosecurity. The real-time detection was made in under 90 minutes and then validated using the Biomeme Franklin Thermocycler, a portable device that is being tested in the project.

Dr. Uday Divi , one of the project leaders at DAWE, said ‘This is a breakthrough in developing a targeted, portable, cheap and accurate tool for biosecurity officers. It allows them to detect a range of high risk pests, diseases and invasive species that could be entering the country’.

Further applications

While the quest continues for the application of eDNA across a range of biosecurity pest and disease pathways. The enormous potential for the technology across a variety of applications including environment and biodiversity assessments has been realised.

Some of the current project priorities include developing a quick and accurate test to detect exotic invasive ants, myrtle rust, and monitoring for white-nose disease in bats from soil samples. This work is being done in collaboration with the office of the Chief Environmental Biosecurity Officer.

As the project expands, more priority species including honeybees and seed viruses are expected to be added for testing with the technology. The project aims to develop a single and multi-species detection assays for faster, cheaper, and more reliable testing that can be implemented across our biosecurity system.

Progress update

So far, we have shown that this technology works to make rapid and accurate detections in the field. We have made immense progress, but the following questions are still being addressed:

• 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?

Next time on The Seed, we hope to report on its application in Australian biosecurity operations such as container screening and environmental surveillance.

Industry participant wearing the Smartglasses while inspecting underneath a container during a rural tailgate inspection with an Inspection Services officer onsiteImage captionArticle written by Compliance Division

New technology could allow rural tailgate inspections and audits to be conducted remotely.

Smartglasses technology is being tested to see if it is capable of showing biosecurity contaminants. Particularly in areas such as twist locks, tynes and dark crevices of the container.The pilots test the connectivity and usability of the remote technology. Also, whether they are fit for purpose.

The Strategic Risk and Business Improvement Team's Kirsty Creek, Tony Brennan and Amy Mason are leading this work 'For the pilot in rural tailgate inspections, industry participants wore the Smartglasses device. Meanwhile, a biosecurity officer would watch the feed remotely by from their home or office’ Amy said.

‘During the pilot our officers directed the industry participant to different areas around the site. This was done using the device’s audio function.

‘We also had the ability to manage any urgent biosecurity risk matters should they have come up during the activity.

These types of trials and innovation projects help us to redefine how we use our eyes on the ground to enable us to work differently and efficiently. 'They also help address some of our pressing challenges such as increasing trade volumes and the growing spread of diseases,’ Amy said. 'The main focus of these pilots is to test the concept’s applicability to remote inspections and audits. Also to extend into other areas where we could really start to see more benefits.’

Written by Biosecurity Operation division

We are proud to report that our 3D x-ray algorithm project has won Australia’s 2020 Public Sector Innovation Award in the digital and data category.

This ground-breaking trial using 3D x-ray technology helped develop the world’s first algorithm to detect biosecurity risk.

The project began as a proof-of concept trial to try and detect fruit in luggage using algorithms. The technology is now deployed at the Melbourne Airport and Melbourne Gateway Facility.

Since then, continued work means the algorithm can now automatically detect fruit, meat and seafood.

The award judges commented that this was an interesting and unique project that was extremely important for our country. It was evident that it addressed a significant challenge in protecting Australia’s borders, and had a clear and measurable impact.

The socially-distanced award ceremony was held at Questacon in Canberra. The project director, Jessica Mitchell, accepted the award on behalf of the team.

Ms Mitchell thanked the team for their endless enthusiasm and hard work. She also thanked department executives who were willing to support the innovative project.

‘I am really proud of the work we have been able to achieve in 18 months, and excited to see where it goes in the future,’ Ms Mitchell said.

This project was partially funded by the Biosecurity Innovation Program.

Find out more about the technology.