Clear insights for healthy fish: Rapid genomic detection of aquaculture pathogens

Abstract

We are Jerome Delamare-Deboutteville and Andy Barnes and we represent the bid for Inspire Challenge 2019 support by World fish, The University of Queensland and our analytics partner Wilderlab New Zealand to provide clear insights for farm fish health and welfare. According to the united Nations, food security is achieved if adequate food in terms of quantity, quality, safety and socio-cultural acceptability is available and accessible for, and satisfactorily utilised by, all individuals at all times to live a happy and healthy life. Fish address the quality and utilisation targets of this goal particularly well. Not only is fish a good source of high quality, well-utilised protein, fish is also rich in micronutrients that are essential to good nutrition. Fish is high in iron, vitamin A and iodine that are critical in childhood development and have been identified as deficient in many staple foods. As fisheries are mostly fished to capacity, the increasing demand for quality seafood is being met by aquaculture. Production from capture fisheries has remained static since the 1980s, yet farming of fish has seen remarkable growth. Indeed, 54.1 million tonnes of finish were produced via aquaculture in 2018. IN addition to contribution to food supply, aquaculture has many social and economic benefits with annual revenue estimated at 138.5 billion US dollars in 2018 and an estimated 19.3 million people directly in finfish aquaculture production, the majority of these in developing countries. Alongside the rapid expansion in farming of aquatic animals came a rapid increase in losses to infectious diseases. While it is hard to place figures on global losses, the significance of the problem was clear at the meeting of the FAO Committee on Fisheries/ Sub-committee on Aquaculture (COFI/SAC) in Trondheim Norway in August this year. Losses to infectious disease in aquaculture in China alone were estimated at 5.3 billion US dollars in 2017, up 1.2 billion from 2016. Accumulated losses add-up substantially. For example in Thailand between 2010 and 2017 more than 12 billion US dollars were lost, both directly and through export restrictions, due to a single disease agent in the shrimp industry. Global losses to disease have serious implications for local economies, food security and animal welfare In most developing countries, mitigation of disease includes overstocking to offset the losses, and antibiotic treatments. Neither of these approaches is satisfactory as the former makes the problem worse through overcrowding, water quality degradation, and increased operating cost. Use of antibiotics is often not evidence-based, ineffective and leads to antimicrobial resistance. There are 67 antimicrobials reportedly used in aquaculture in the 11 major producing countries. Moreover, recent research shows that resistance mechanisms in fish pathogenic bacteria are similar to those in terrestrial farm animals and humans, contributing to the global pool of resistance and underscoring the importance of a One Health approach. But this is not a new problem - restricted development coupled with high antibiotic use happened in the salmon industry nearly 40 years ago. This chart shows antibiotic use in blue and salmon production in red in Norway during the 1980s and 90s. You can see that in the late 1980s almost 50,000 kilograms of antibiotics were used in aquaculture - 50% more than was used human and terrestrial animal medicine combined at the time. Growth in production was also restricted by disease. So what changed in the early 1990s? How did we get from here to here (point), with almost zero antibiotics being used (point) at the same time as industry expansion resumed (point)? It was the introduction and adoption of simple killed oil-emulsion vaccines. It revolutionised the industry in terms of management of bacterial diseases. So there is a path to follow. There are some challenges to getting vaccination into developing tropical and subtropical aquaculture where they are most needed. Firstly the market is fragmented amongst tens of thousands of small and medium enterprises, there are many farmed species of low economic value, and warm water fish ponds are hotbeds of microbial diversity and evolution leading to many different, rapidly changing pathogens. But it is possible and we do it successfully in a number of countries using locally produced autogenous vaccines. These work extremely well but need accurate typing information quickly in order to formulate and deploy them effectively. In cases of disease, local aquaculture inspectors collect samples from the farm; these two are from An Giang Province in Viet Nam. Our proposal adds a genome sequencing stage to the routine diagnostics. Until recently this was not possible as it was costly, required expensive equipment and specially equipped labs. This changed with the invention of nanopore sequencing. These small devices are cheap to buy, simple to operate and don’t require specialist lab facilities - it is feasible to operate them locally connected via a mobile data network. But the data that these devices generate in real time is “fuzzy” - it is not possible to get epidemiologically relevant information directly from raw reads. Our innovation adds cloud-based machine learning via our partner Wilderlab’s Aphid package. Using training datasets developed by UQ and World Fish partners…we enable accurate, epidemiologically-relevant strain typing. This forms the hub of our Inspire proposal this year. The information and metadata can be then be accessed in a user-friendly format via a smartphone, enabling the fisheries officers to advise the farmer on the ground and for custom vaccines to be formulated and deployed, produced by local fermentation capability. These are not technically challenging vaccines to produce. They can be used to vaccinate new stock on farms that have the same strain types…thereby securing the output of the next crop and preventing further spread between farms. It will also reduce or remove the need for antibiotics. These big-data informed, but locally targeted and implemented solutions, align well with the recently proposed Progressive Management Pathway for Improving Aquaculture Biosecurity. Our Inspire project will provide readily accessible real-time, useable information that can be employed directly in biosecurity risk definition, systems implementation, preparedness and, off course, sustainable health management through vaccination. This will deliver real advances in local economy, nutrition security, human health and importantly, animal welfare