Integrated commercial data to empower salmon industry

This project represented an integrated programme of applied epidemiological research into Salmon Rickettsial Syndrome (SRS) and Caligus in the Chilean aquaculture industry. The research sought to address many knowledge gaps about the causes of disease and the effectiveness of control measures. Ultimately, the goal is to improve the health, profitability and sustainability of the Chilean aquaculture industry, for the benefit of the Chilean environment, economy and people.

Currently, diseases such as SRS and Caligus contribute substantially to the costs of salmonid fish production in Chile. In addition, concerns about product quality and antimicrobial usage decrease the price of Chilean salmon in international markets. There is a strong desire on the part of the industry and Chilean Government to improve the control of diseases in the aquaculture industry.

This project aimed to identify and describe risk factors for SRS and Caligus in the Chilean aquaculture industry and assess the effectiveness of specified interventions. It was applied research, focussed on providing innovative, feasible and practical solutions that will aid in the management of these and other diseases.

The project consisted of four interrelated components:

1. A retrospective study of risk factors, based primarily on existing regulatory data
2. The establishment of a secure web-based research platform to integrate company-generated data relevant to epidemiological research
3. A prospective study of risk factors and the effectiveness of interventions, based on analysis of company data across the salmon industry
4. Stakeholder engagement and collaboration.

The retrospective study identified and quantified risk and protective factors for SRS and Caligus based on existing data. It used regulatory data available in the SIFA and INFA databases, a substantial but underutilised resource which had already been collected by Sernapesca on behalf of industry.

The research platform developed was a highly secure, powerful, web-based platform used to integrate all relevant company and other data. It included analytical capability to support the prospective study, as well as providing a resource for future research by other authorised researchers. The research platform was built using the Omnisyan data integration and analysis framework and provided high levels of confidentiality and security, and was based on an existing framework already used in other countries and industries. It provided a highly efficient means of acquiring the data necessary to address numerous research questions.

The prospective study provided the opportunity to assess the efficacy of various interventions (treatment and management) for SRS and Caligus, and refine our understanding of risk and protective factors. It took advantage of detailed, disaggregated, cage-level data and other risk factor data not available in the regulatory databases. This was achieved by using comprehensive whole-of-industry data managed by the integrated research platform.

Partnership with aquaculture companies and collaboration with other researchers was an essential part of this project. Through consultations and workshops, stakeholders had the opportunity to be involved at every stage of the project: from refining the research questions to be addressed, to approaches to data analysis and interpretation of results. Meetings, newsletters and publications facilitated coordination and promoted dissemination of the research findings.

This project included some innovative approaches to applied epidemiological research that have been used elsewhere but may be novel in the Chilean aquaculture industry. These include:

• Use of population data instead of samples—efficient and inexpensive capture of industry data so analyses are based on the whole population
• Remove the need for controlled trials—industry-wide observational data may be used to evaluate the impact of various interventions (vaccines, management practices, etc.) that differ between times, places and companies
• Capture all relevant data—efficient and highly secure information systems to provide data necessary to address multiple research questions and provide ongoing, real-time analysis
• Reduce the costs of data collection—establishment of automatic data flows to minimise costs of data collection and management
• Maximise benefit for the industry and other researchers—establishing a valuable data resource to support research, disease control and risk management.

The outcomes of this research programme included;

• baseline descriptions of SRS and Caligus disease impact, estimation and standardisation of key biological parameters
• identification of risk and protective factors for Caligus and SRS
• risk models that allow the impact of different interventions or management strategies to be evaluated, taking all other identified factors into account
• analysis of spatial and neighbourhood factors that may provide a basis for the refinement of barrio boundaries and re-development of synchronised treatment strategies
• evaluation of the effectiveness of three specific interventions.

In addition, the research platform had the potential to provide a valuable and sustainable resource for applied research and the benefit of the industry.