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The Marine Institute carries out monitoring of chemical residues in aquaculture in accordance with Council Directive 96/23/EC of 29 April 1996, on measures to monitor certain substances and residues thereof in animals and animal products, also known as the Residues Directive. This is carried out on behalf of the Department of Agriculture, Food and the Marine (DAFM). For the aquaculture sector, the Sea Fisheries Protection Authority (SFPA) with technical support from the Institute is responsible for residue controls on farmed finfish on behalf of the national residue monitoring plan. Annually, the National Residues Control Plan (NRCP) for Aquaculture is prepared by the Institute and this sets out the monitoring requirements for residues in animal products in required by the directive. The main objectives of the National Residue Control Plan for Aquaculture is to ensure farmed fish are fit for human consumption; to provide a body of data showing that Irish farmed fish is of high quality; to promote good practices in aquaculture; and to comply with EU Directive 96/23/EC. Based on production tonnage, the following species for the period of 2012 to 2014 were sampled and tested: Atlantic salmon (Salmo salar), freshwater and sea reared trout (Oncorhynchus mykiss & Salmo trutta). In excess of 2,141 tests and a total of 4,972 residue measurements were carried out over this three year period. Tests were carried out for banned substances such as growth promoters and other unauthorised substances such as malachite green, which should not be present. Harvest fish were also tested for authorised veterinary treatments such as antibiotics and sea lice treatments, environmental contaminants such as trace metals, polychlorinated biphenyls and organochlorine pesticides, to check for compliance with Maximum Residue Levels (MRL) where available. As in previous years, no non-compliant results were reported in the surveillance monitoring programme for farmed finfish during the period 2012 to 2014. Overall, in recent years the outcome for aquaculture remains one of consistently low occurrence of residues in farmed finfish, with 0.23% non-compliant results from routine targeted monitoring in 2004, 0.09% in 2005 and one of full compliance with 0% non-compliant target residue results for the period 2006-2014.

Lead partner: Marine Institute, Oranmore, Co. Galway. Project Partners: Vet Aqua International, Oranmore, Co. Galway., Global Trust Certification Ltd., Dundalk, Co. Louth. Project duration: 01/10/2008 to 31/10/2011, The AquaPlan project brought together key stakeholders from the finfish aquaculture industry and state agencies with the aim of drafting and implementing a national strategic plan for fish health in Ireland. Many countries already have well established comprehensive strategies for managing aquatic animal health which are deemed necessary for the sustainable development of the industry. A range of deliverables were produced by the project which are all essential components of the strategic plan for fish health management., Funder: Ireland's EU structural funds programme 2007-2013, co-funded by the Irish government and the European Union- European Regional Development Fund, Marine Institute. Grant-Aid agreement no. PBA/AF/08/003(01)

Lead Partner: Marine Institute, Rinville, Oranmore, Co. Galway. Project Partners: Vet-Aqua International, Oranmore, Co. Galway. Coastal & Marine Research Centre (CMRC), University College Cork. Veterinary Sciences Division, Agri-Food & Biosciences Institute (AFBI), Belfast., The aims of the GILPAT project were to take a multidisciplinary approach in order to further understand the underlying causes of gill disease in Irish farmed fish. A specific aim was to establish a pilot zooplankton monitoring programme and use training workshops to enable fish farmers to upskill in areas such as zooplankton sampling and basic identification of the main zooplankton/jellyfish species common to Irish waters. Complimenting this was the development of a number of molecular diagnostic methods for the detection of potential pathogens suspected of being involved in the development of the condition. Together with a comprehensive literature review, epidemiological study, and experimental challenge studies, the project aimed to bring all these elements together with the objective of outlining potential mitigation measures and identifying areas for future research., This project (Grant-Aid Agreement No. PBA/AF/08/002(01)) was carried out under the Sea Change strategy with the support of the Marine Institute and the Marine Research Sub-Programme of the National Development Plan 2007–2013, co-financed under the European Regional Development Fund., Funder: Marine Institute

NOTICE: this is the author’s version of a work that was accepted for publication in Cells Tissues Organs. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. The Copyright for this material belongs to Karger. A definitive version was subsequently Cells Tissues Organs, [Issue 197, (November 2012)] (DOI: 10.1159/000343291), http://content.karger.com/ProdukteDB/produkte.asp?Doi=343291, peer-reviewed, Sparc (Osteonectin) is a multifunctional matricellular glycoprotein expressed by many differentiated cells. Members of this family mediate cell-matrix interactions rather than acting as structural components of the extracellular matrix and therefore can influence many remodelling events, including haematopoiesis. We have investigated the role of sparc in embryonic haematopoiesis, using a morpholino antisense oligonucleotidebased knockdown approach. Knockdown of sparc function resulted in specific erythroid progenitor cell differentiation defects that were highlighted by changes in gene expression and morphology, which could be rescued by injection of sparc mRNA. Furthermore, a comparison of blood phenotypes of sparc and fgfs knockdowns with similar defects and the sparc rescue of fgf21 blood phenotype places sparc downstream of fgf21 in the genetic network regulating haematopoiesis in zebrafish. These results establish a role for an extracellular matrix protein (Sparc) as an important regulator of embryonic haematopoiesis during early development in zebrafish.

Peer-reviewed.Released with a Creative Commons Attribution Non-Commercial No Derivatives License, Observed emergence of IPNV in farmed Irish salmon is simulated using a model originally developed to analyse the spread of the virus in Scotland [Murray, A.G., 2006a. A model of the spread of infectious pancreatic necrosis virus in Scottish salmon farms 1996–2003. Ecol. Model. 199, 64–72]. IPNV appears to have become established relatively recently in Ireland and the model is altered to explicitly simulate the origin of the spread of the virus. Input to freshwater farms was key to initiation of infection, but modelling suggests that endogenous spread was responsible for much of the subsequent increase in prevalence of IPNV. From the modelling, it is unlikely that direct imports accounted for most IPNV cases. If this is the case, cessation of imports, without a substantial improvement in biosecurity, would be likely to be of only limited effect in controlling IPNV. Marine IPNV prevalence appears to be insensitive to direct interventions in the marine environment (as in the Scottish model). A multi-element control strategy, targeting both endogenous spread and external input of infection and prioritising freshwater sites, but extending to marine sites, would probably now be required to eradicate IPNV from Ireland.

This publication constitutes the final report for the research project ST/05/01 “Site investigations and disease management of the pancreas disease virus in Irish farmed salmon”, funded under the NDP Marine RTDI Programme. Work undertaken within the project included longitudinal studies of rainbow trout and Atlantic salmon at sea following the course of infection, testing for vectors and reservoirs of the virus, molecular studies of the virus and an epidemiological investigation of pancreas disease in Ireland. Results have shown that although pancreas disease is endemic in marine farmed Atlantic salmon, no evidence of infection in rainbow trout farmed at sea was found. Serological and molecular based diagnostic methods were shown to be suitable for the screening of fish stocks for the presence of the virus. For the confirmation of clinical outbreaks, farm data and histopathological results should be included. The results also suggest that horizontal transmission of the virus may be the main route of infection between sites. The project also involved the technology transfer of molecular and serological diagnostic methods for pancreas disease between partners and the final chapter includes practical information on management of, and mitigation against, pancreas disease. Pathologies such as pancreas disease, heart and skeletal muscle inflammation and cardiomyopathy syndrome, pose a serious threat to salmonid farming in Ireland, Scotland and Norway. Most significant among this group of diseases is pancreas disease, a viral disease affecting Atlantic salmon during the marine stage of the production cycle. From the first description of pancreas disease in farmed Atlantic salmon from Scotland in 1976 the disease has now become endemic in Ireland and parts of Norway and continues to be significant in Scotland. The causal agent of pancreas disease, a salmonid alphavirus, has now been characterised and a closely related subtype of the virus is known to cause sleeping disease in farmed rainbow trout on continental Europe and in the United Kingdom. The Irish salmon farming industry has estimated that pancreas disease has resulted in a total loss of turnover of €35 million with €12 million loss of profit in the years 2003-2004. The economic impacts are estimated to be in the range of €100 million per year in Norway. In Scotland, pancreas disease and related pathologies are increasingly responsible for significant losses in marine salmon farms but these have yet to be quantified., Funder: Marine Institute

Infectious pancreatic necrosis (IPN) is an economically significant viral disease of salmonid fish worldwide. Infectious pancreatic necrosis is categorised as a List III disease under Annex A of EU Council Directive 91/67/EEC. List III diseases are present within the EU and up to 2004 were regulated under national control programmes within each member state. The disease was first described in freshwater trout in North America in the 1950’s (Wood et al., 1955) and has been reported in Europe since the early 1970’s (Ball et al., 1971). Initially, IPN was regarded as a serious disease affecting rainbow trout fry and fingerlings (Roberts & Pearson, 2005). However as the salmon farming industry began to expand during the 1970’s, incidence of IPN disease in salmon also increased with the result that IPN is now widespread in the salmon farming industry in both Norway and Scotland. The economic loss due to the disease is large and outbreaks may occur in Atlantic salmon juveniles in fresh-water and in post-smolts after transfer to sea-water. Historically in Ireland, isolations of the IPN virus have been rare and occasional outbreaks have occurred in both rainbow trout and Atlantic salmon facilities. The Marine Institute and its predecessor, the Fisheries Research Centre, have been testing farmed and wild fish for disease pathogens since the mid 1980’s. The first reported clinical outbreak of IPN in Atlantic salmon occurred in 2003. However in 2006 severe outbreaks in a number of freshwater salmon hatcheries occurred which were all linked to imports from a specific single source. To date, clinical outbreaks of IPN in Ireland have been associated with imports of infected ova and their subsequent movement within the country. This report reviews the prevalence of the IPN virus in the Irish salmon farming industry and also in wild fish from selected rivers. It describes the steps taken by the industry to control the disease in 2006 and aims to provide some practical solutions to reduce the prevalence of the virus in farmed and wild fish and to prevent future outbreaks of the disease., Funder: Marine Institute

Pancreas Disease is the most significant single infectious disease affecting marine salmon farms in Ireland. The first epidemiological studies of Pancreas Disease (PD) in Ireland in the early 1990’s indicated that significant losses occurred in farmed Atlantic salmon in their first year at sea on some individual farms (Menzies et al., 1996). A serological survey for the presence of Salmon Pancreas Disease Virus (SPDV) antibody in 1996 revealed that 53% of Irish sites were positive, but that not all positive sites had recognised clinical signs of PD. This indicated a relatively low incidence and severity of PD at that time (McLoughlin et al., 1998) and this pattern persisted throughout the remainder of the 1990’s. In 2002, a serious increase in both the incidence and severity of PD was reported on farmed Atlantic salmon marine sites in Ireland. An epidemiological survey of Irish sites for 2002 revealed that 59% of sites reported an outbreak of PD, with mortalities averaging 12% (range 1 – 42%; McLoughlin et al., 2003). A recent study using data collected for 2003 and 2004 indicated that PD occurred in 62% and 86% of sites respectively. The average mortality due to PD on affected farms was 18.8% in 2003 and 14.8% in 2004. In response to these significant losses due to PD a range of research initiatives was launched in Ireland and was supported by the Marine Institute. This document gives an overview of the most recent findings from the current projects, carried out in 2004/2005 and also provides an overview of the various actions in Scotland and Norway, where PD has also become a disease of economic significance in salmon aquaculture., Funder: Marine Institute

Peer-reviewed, This report described the first detections of koi herpesvirus (KHV) in the Republic of Ireland in imported koi carp. In both cases the KHV suspicions were confirmed by molecular diagnosis and the infected stocks culled., Funder: Marine Institute