A team of researchers from Malaysia, Australia, New Zealand, Thailand, and the UK is harnessing the power of genome sequencing to help Aquaculture farmers manage fish diseases. Until recently, this was not possible as the technology was not only costly but the genome sequencing process required time and coordination between different specialist labs. But this changed with the invention of MinION from Oxford Nanopore Technologies, a small and easy to use USB device that makes the genomic sequencing cheaper and faster.
The Rapid Genomics Sequencing team is now developing a cloud-based database to get high-resolution information from raw nanopore sequences allowing them to track outbreaks in close to real-time. The information they generate will then be accessed in a user-friendly format via a smartphone, enabling aquaculture inspectors to provide biosecurity advice and management plans to farmers in the palm of their hands. It will also inform local manufacturers what to put into custom vaccines and which farms need it. With real-time data accurately identifying what is killing the fish, local universities and start-ups will be able to produce simple vaccines for aquaculture health practitioners to vaccinate new stocks of fish before dissemination onto farms.
In a demonstration at the WorldFish office, the team created a mock-up scenario of how this portable Lab-in-a-Backpack system works. If a fish farmer experiences a disease outbreak on his farm, local aquaculture inspectors collect samples from diseased fish and send them to a nearby lab where trained operators will be able to process them for whole-genome sequencing, with identification and typing of a bacterial pathogen taking just a few hours.
“Current diagnosis-by-sequencing workflows employ a range of different methods for DNA extraction, sequencing and analysis, and many labs tend to curate their own reference sequence databases in house. This makes it difficult to compare results between laboratories and limits our ability to interpret infection dynamics in a timely manner. Our team is developing a simple and reliable surveillance workflow in which pathogen sequence data is generated on the MinION device and identified in real-time using an intuitive web application. Behind this interface sits a powerful learning algorithm and gold-standard reference sequence database that is continually updated as emergent pathogens are identified.” – said Dr Shaun Wilkinson, of Wilderlab New Zealand.
Tracing of pathogens by molecular epidemiology is extremely powerful. It reveals the fine variations between strains of a particular group of bacteria which helps biosecurity officials to trace the origin of infection and warn farmers or breeders of any problems before moving animals further between regions or countries. For example, a bug’s DNA might show that the strain is new to the fish in country A, but caused an outbreak in a nearby country B a few months earlier.
“Rapid genome sequencing provides all of the information we need to make informed decisions on disease control without the need for pathogen-specific tests and tools that might be very expensive,” said Dr Andrew Barnes of The University of Queensland (UQ), who is part of the team behind the WorldFish-led proposal. “The sequences enable you to infer the origin of a pathogen; see how it is evolving and moving through different environments and across international borders. Most importantly, it allows you to identify possible antimicrobial resistance genes and virulence factors relevant to vaccine formulation. With this kind of knowledge, we can provide very specific advice on how to control and prevent disease outbreaks”.
The research team is sharing and demonstrating their portable Lab-in-a-backpack system with other researchers in Asia and Africa to make rapid genomic sequencing of aquaculture pathogens gradually available. Ultimately, this innovation will enable fish farmers and aquaculture enterprises to track and deal with fish disease in real-time, and thus minimize potential loss of food, incomes and sustainable business.
“We believe this technology will have an incredible impact on the aquaculture industry globally in terms of providing safe, affordable and nutritious fish, especially in developing countries, said Dr Jerome Delamare-Deboutteville, aquaculture scientist with WorldFish.
By gathering information on the latest outbreaks as they happen, the system should pick up valuable epidemiological data, trends in drug resistance or the rise of new bugs that are resistant to current antibiotics. If everything goes well we will have this technology available for aquaculture and fish health experts as well as the data for policymakers to better manage and respond to fish disease outbreaks.”
This research project was undertaken in the framework of the CGIAR Research Program on Fish Agri-Food Systems (FISH) led by WorldFish in collaboration with the University of Queensland and Wilderlab. This project received additional funding by the CGIAR Antimicrobial Resistance Hub on AMR related activities and from the CGIAR Platform for Big Data in Agriculture as part of the 2019 Inspire Challenge prize.
The data in the database were provided as part of two Australian Research Council (ARC) funded projects: Discovery Project DP120102755 Fighting Disease on Farms and Linkage Project LP130100242: A Pan-genome reverse vaccinology approach to streptococcal vaccination in fish. Some bacterial DNA samples and viral amplicon products for sequencing were kindly provided by researchers from Centex/Mahidol University/BIOTEC. Viral PCR amplicon sequences were analysed by a researcher from Kasetsart University. Researchers from the University of Exeter and the Centre for Environment Fisheries and Aquaculture Science (Cefas) provided their support on analyses of viral sequences extracted from cell cultures.
Source: The World Fish Center