WGS-aqua: Capacity building for the widespread adoption of whole genome sequencing (WGS) for the molecular epidemiology of aquaculture pathogens.

The rapidly increasing global population, combined with mounting environmental pressures and resource limitation, means that the sustainable production and distribution of adequate quantities of healthy, safe food for everyone is set to become one of mankind's biggest challenges. Due to poor global regulation and management, many of our natural resources have been hopelessly over-exploited, particularly so over the last few decades. The fishing industry is a perfect example, where catastrophic collapses of whole fisheries have resulted from decades of short-termism. This has inevitably resulted in an increasing reliance on farming (aquaculture), and this industry globally now accounts for more seafood (fish and shellfish) consumed than the capture sector.

A major cause of commercial losses in aquaculture is infectious disease, and intensive farming practices in particular will increase the risk. Rearing stressed animals at high densities greatly increases the probability of disease outbreaks on a farm, and pathogens may spread to other farms or even to wild fish. Moreover, the international trade in eggs and live fish increases the likelihood of global disease spread, and the introduction of exotic pathogens into vulnerable native species. In addition to parasites such as lice, serious diseases are also caused by microbes such as bacteria and viruses. In order to detect and manage these infections more efficiently, we urgently require more data on the genetics of the pathogens, why they cause outbreaks when they do, and how they can transmit geographically or between different species of fish.

Many of these challenges are analogous to human diseases, and public health infectious disease epidemiologists are faced with understanding why a new strain of a "superbug" (such as MRSA) has emerged, and how likely it is to spread. Fortunately, the last few years have witnessed a huge technological advance which provides to means to address these problems with much more confidence. This technology makes it possible to decode the entire genetic content (genome) of different strains of bacteria and viruses very quickly and relatively cheaply. Tiny variations in the genome makes it possible to track the transmission of these pathogens, and by being able to identify all the genes present in the genome it is possible to predict whether a given strain will be highly virulent, or difficult to treat due to antibiotic resistance.

This project will exploit the advances in the generation and analysis of genome data for human pathogens, and will apply the same, or similar, techniques to aquaculture pathogens. By doing so, it is hoped that other academics, stakeholders and companies will recognize the benefits of the approach and it will become widely adopted. One of the major challenges with the new sequencing technology is that the vast amounts of data quickly become unwieldy and difficult to manage and analyse efficiently. To address this, a major focus of the project will be the modification of intuitive software tools developed for the genome data for public health pathogens. In order to make sure the system is as useful as possible, we will first hold a workshop which will bring together experts in different fields, both public health and aquaculture, in order to identify the key requirements of such a system. It is very important that such an easy to use, yet powerful, system like this is developed now, so that data from different studies can be combined efficiently, and we can have a truly global picture of the emergence and spread of different strains. Once we have optimized the software, we will illustrate its usefulness by generating genome data for three serious aquaculture pathogens (two bacterial species and one virus) and uploading the data to the system. This will show the relationships between the different strains, where they are distributed on a map, and which disease and resistance genes they contain.

Recent years have seen a rapidly increasing reliance on aquaculture as a global food source. Significant challenges need to be overcome in order to ensure this means of food production is sustainable. Infectious disease management represents one such challenge. International trade in eggs and live fish increase the risk of pathogen spread, and there is a danger of disease spillover from farmed to wild stocks. Whilst antibiotics might be effective in the short-term but, as with human pathogens, resistance quickly emerges. The advent of next-generation whole genome sequencing (WGS) of pathogens has greatly advanced our understanding of disease emergence and spread, and much of the methodology is transferable from public health to aquaculture. The adoption of WGS for targeted studies and, ultimately, routine surveillance of aquaculture pathogens, would represent a critical turning point in ensuring the long-term sustainability of aquaculture as a global food source.

The over-arching aim of this project is to facilitate the widespread adoption of WGS for aquaculture disease management. This will be achieved by optimizing and implementing community-oriented WGS database infrastructure and software tools designed for intuitive data management and visualization of pathogen spread, and housing these resources under a single site, wgs-aqua.net. The project will bring together bioinformaticians, modellers, statisticians and population genomicists working at the forefront of infectious disease epidemiology in the public health arena, with key stakeholders and academics in the aquaculture sector. We will demonstrate the broad utility of WGS, and of our software, by sequencing a total of ~250 genomes of Flavobacterium psychrophilum, Vibrio anguillarum and Koi Herpes Virus as exemplars of commercially important pathogens. These data will shed light on transmission, host adaptation, resistance and virulence.

A key deliverable of this project is the development and provision of a web-based platform for the intuitive storage, sharing and visualization of whole genome sequence (WGS) data for aquaculture pathogens. Taking a strong lead from work carried out for public health pathogens, this system will provide the means for efficient epidemiological surveillance and detailed molecular, evolutionary and ecological analysis and modelling. This will have a wide range of benefits both for disease management and for basic bioscience. Key beneficiaries will include researcher in the academic and industrial sector working on novel intervention and containment strategies for aquaculture disease, such as the development of vaccines, novel treatment options (eg phage therapy), and diagnostic kits. The surveillance tools will also provide important data informing on the spread of pathogens that have acquired resistance to antibiotics, thus informing on optimal stewardship strategies. Researchers working on basic bioscience questions, for example relating to pathogenesis or genome dynamics, will also find the databases invaluable for gene mining and understanding spatial patterns of diversification.

The provision of a central surveillance system will allow key stakeholders (eg Cefas) and industry to identify and provide early warning of novel pathogen variants that may be particularly virulent or transmissible. Moreover, the data may also provide evidence concerning management options (eg through identification of resistance genes), or evidence that spread is linked to a potential control point in the rearing process. Developments are ongoing to link pathogen databases (eg wgsa.net; developed by DA, a Co-I on the project) with collection of metadata in the field via a smartphone app (www.epicollect.net). The linking of genome sequence data, with extensive metadata in a central resource will make it possible to develop detailed models of pathogen emergence and spread, and the evaluation of potential intervention strategies in biological (evolutionary and ecological) and economic contexts. Such advances will ultimately benefit policy makers in re-evaluating guidelines for disease control measures.

This project has a strong emphasis on community engagement including academics, stakeholders (Cefas, Defra), and industry. Broad academic support is highlighted elsewhere, we also have key support from three major industrial partners, Novartis, Ridgeway Biologicals and Dawnfresh farming, who highlight the importance of pathogen tracking and in utilizing the WGS data for vaccine development (see letters of support). As stated by Spencer Russell, research manager at Novartis in his letter of support

"Bacterial and viral diseases will be a general and on-going problem in aquaculture and the need to develop methods for tracking the spread of current and emerging diseases using advanced molecular epidemiological methods is critical to the future of aquaculture disease management"

We will seek further industrial participation, primarily through the workshop at the start of the project, and will provide additional community benefits through resources housed on our portal site, wgs-aqua.net.

Aquaculture is the fastest growing food-producing sector in the world, and the societal benefits of improved disease management for sustainable aquaculture are profound. Given pressing challenges facing global food security and the increasing reliance on aquaculture, the development of measures to ensure fish health and protect against disease spread is of paramount importance. Aquaculture is set to play a central role in maintaining the world's food supply, but the risks and losses due to infectious disease will increase and the sector expands and becomes even more globalized. The development of the infrastructure required for central surveillance and WGS data storage is therefore critical and timely.