• Management and control of proliferative kidney disease (PKD) in a freshwater Atlantic salmon (Salmo salar L.) farm in Ireland: a case history

      Quigley, D.T.G.; McArdle, J.F. (Fish Veterinary Society, 1998)
      During July 1992, an acute clinical outbreak of proliferative kidney disease (PKD) was experienced in two strains (‘Irish’ and ‘Norwegian’) of juvenile (age 0+) Atlantic salmon (Salmo salar L.) held at two adjacent freshwater sites on the River Lee in southern Ireland. Various management strategies (including reduced stocking densities, handling, feeding rates and increased oxygenation), and treatment regimes (involving malachite green and fumagillin DCH) were used to control the disease. A total of 1·3 million juveniles died during the PKD outbreak, representing 61·6% and 54·6% of the Norwegian stock at the two farms respectively. The Irish stock appeared to be more resistant to the disease and only 15·6% died. The weekly prevalence of PKD fluctuated throughout the summer but seemed to disappear by mid-August. Although PKD was detected again during 1993, no clinical outbreak occurred. In conjunction with the management strategies adopted in 1992, seven consecutive weekly prophylactic bath treatments with malachite green (1·6 ppm for 40 minutes) administered prior to mid-July appeared to control the disease. During August 1993, a ten day course of fumagillin (6 mg/kg bodyweight per day) reduced the prevalence of the PKD parasite in a trial batch of juveniles from 24% to zero. The results of this study demonstrated the effectiveness of various management strategies and treatment regimes in controlling PKD.
    • Management of health risks associated with oysters harvested from a norovirus contaminated area, Ireland, February–March 2010

      Doré, B.; Keaveney, S.; Flannery, J.; Rajko-Nenow, P. (European Centre for Disease Prevention and Control, 2010)
      Oysters from a harvesting area responsible for outbreaks of gastroenteritis were relaid at a clean seawater site and subsequently depurated in tanks of purified seawater at elevated temperatures. This combined treatment reduced norovirus levels to those detected prior to the outbreak. On the basis of norovirus monitoring the sale of treated oysters was permitted although the harvest area remained closed for direct sale of oysters. No reports of illness have been associated with the consumption of treated oysters.
    • MATT: Monitoring, Analysis and Toxicity of Toxaphene: improvement of analytical methods

      de Boer, J.; Klungsøyr, J.; Nesje, G.; Meier, S.; McHugh, B.; Nixon, E.; Rimkus, G.G. (1999)
      The European Research Project MATT (Investigation into the Monitoring, Analysis and Toxicity of Toxaphene) started in 1997 and had the objective to provide information on toxicological risks to the consumer of toxaphene residues in fish from European waters. This report includes information on the analytical block of the project, which comprised three studies.
    • Mercury assessment in the marine environment: assessment criteria comparison (EAC/EQS) for mercury

      OSPAR Commission; McHugh, B.; Berbee, R.; Farmer, E.; Fryer, R.; Green, N.; Larsen, M.M.; Webster, L.; Lepom, P.; McGovern, E.; et al. (OSPAR Commission, 2016)
      Mercury is known for its worldwide environmental impact. It is addressed by several existing international agreements addressing atmospheric emissions (CLRTAP), the marine environment (OSPAR, HELCOM, Barcelona, Bucharest), waste (Basel), and export of chemicals (Rotterdam). It can be brought into the biosphere by humans by two different mechanisms: 1) intentional extraction and use, and 2) as a natural constituent in other materials. Mercury is extremely toxic to both man and biota and can be transformed within the aquatic environment into more toxic organic compounds (e.g. methyl mercury). A main pathway of mercury to the sea is atmospheric and it can be carried long distances from its source. The primary risk to the general population is exposure to methylmercury via ingestion of aquatic foods. OSPAR measures and subsequent EU measures regulate the main industrial sources for mercury releases to the environment. A suite of OSPAR measures control mercury emissions, discharges and sources. OSPAR has promoted actions in other international forums, especially the EU, e.g. call for actions to prevent pollution from the disposal of large amounts of pure and waste mercury arising from the closure or conversion of mercury cell chlor-alkali plants and for control measures on the use and marketing of mercury in various products.
    • A Model Compound Study: The ecotoxicological evaluation of five organic contaminants with a battery of marine bioassays

      Macken, A; Giltrap, M; Foley, B; McGovern, E; McHugh, B; Davoren, M (Elsevier, 2008)
      This paper describes the ecotoxicological evaluation of five organic contaminants frequently detected in marine sediments (tributyltin, triphenyltin, benzo[a]pyrene, fluoranthene, and PCB 153) using three marine species (Vibrio fischeri, Tetraselmis suecica, and Tisbe battagliai). The sensitivity of each species varied for all compounds. The triorganotins were consistently the most toxic to all species. The applicability of each test system to assess the acute toxicity of environmental contaminants and their use in Toxicity Identification Evaluation (TIE) is discussed. Suitability of the Microtox and T. battagliai tests for employment in TIE studies were further assessed through spiking experiments with tributyltin. Results demonstrated that the most effective treatment to remove organotin toxicity from the sample was the C18 resin. The results of this study have important implications for risk assessment in estuarine and coastal waters in Ireland, where, at present the monitoring of sediment and water quality is predominantly reliant on chemical analysis alone. Ecotoxicological evaluation of five organic marine sediment contaminants was conducted and the suitability of the test species for marine porewater TIE discussed.
    • Modelling origin and spread of Infectious Pancreatic Necrosis Virus in the Irish salmon farming industry: the role of inputs

      Ruane, N.M.; Murray, A.G.; Geoghegan, F.; Raynard, R.S. (Elsevier, 2009)
      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.
    • Molecular differentiation of infectious pancreatic necrosis virus isolates from farmed and wild salmonids in Ireland

      McCarthy, L; Swords, D; Ruane, N. M. (Wiley-Blackwell, 2009)
      This study investigated the genotypes and sub-groups of infectious pancreatic necrosis virus (IPNV) present in farmed and wild salmonid fish in Ireland. An 1100-bp portion of the VP2 region of segment A from each of 55 IPNV isolates collected over 2003–2007 was amplified by reverse-transcription–polymerase chain reaction and the product directly sequenced. The nucleotide sequences of each isolate were aligned and compared with each other and with the corresponding sequences of a number of reference isolates. All the 55 sequenced isolates belonged to genogroup 5 (Sp serotype) and could be divided into two subgroups. Irish subgroup 1 consisted of isolates from farmed salmon originating from an Irish salmon broodstock. Irish subgroup 2 consisted of isolates from imported farmed stock and all reported clinical outbreaks of IPN were associated with isolates from subgroup 2. Isolates from wild fish were identical to some isolates from subgroup 2, and therefore are believed to have originated from infected farms. These results highlight the importance of import risk analysis for diseases not listed under current legislation.
    • Molecular methods for monitoring harmful algal bloom species

      Keady, E.; Maher, M. (Marine Institute, 2009)
      Shellfish production can be adversely affected by the presence of harmful microalgae (HABs). Toxins produced by Dinophysis, Alexandrium and Pseudo-nitzschia species can accumulate in shellfish and have the potential to cause serious human illness. In order to satisfy EU legislative requirements pertaining to the production and export of shellfish (EC Hygiene Regulations 2004, No. 853/2004 and No. 854/2004, which replaced the EU Shellfish Hygiene Directive 91/492/EEC in January 2006), monitoring the presence of harmful algal species and biotoxins in coastal waters is performed by EU member states. Routine microscopic monitoring methods are unable to identify certain toxic species, in particular, Alexandrium and Pseudo-nitzschia spp. Electron microscopy is required for species identification and this technique cannot be integrated into a routine monitoring programme. Molecular techniques utilise unique sequence signatures within microorganism genomes for species specific identification. Molecular methods applied for the identification and quantification of HAB species include Fluorescent in-situ hybridisation (FISH) and in-vitro amplification based methods, in particular, real-time PCR.
    • Monitoring of Shellfish Growing Areas - 1993

      Nixon, E.; Rowe, A.; Smith, M.; McLoughlin, D.; Silke, J. (Department of the Marine, 1994-08)
      During 1993, water and shellfish from 19 major growing areas were monitored for chemical parameters in accordance with the 1979 Council Directive 79/923/EC. At each site temperature, salinity, pH, dissolved oxygen and suspended solids measurements were taken and shellfish samples were returned to the laboratory for metal, chlorinated hydrocarbon and algal biotoxin determinations. Generally, water quality in all areas was good and conformed to the guidelines of the Directive. The highest levels of metals recorded were: cadmium in Tralee Bay (0.4 to 0.7µg/g) and Carlingford Lough (0.3 to 0.7µg/g) and lead in Wexford Harbour (0.5µg/g). Mercury in all cases was low with the exception of Cromane during November when levels of 0.3µg/g were detected. Chlorinated hydrocarbons levels were extremely low and indicate the clean nature of Irish shellfish, unpolluted by these synthetic organic compounds. Algal biotoxins were not detected in any samples.
    • Monitoring results for trace metals and organohalogens in shellfish (2015) and physicochemical parameters and trace metals in seawater (2016) in accordance with Shellfish Waters Directive. CHEMREP 2018-003

      Marine Institute (Marine Institute, 2018)
      Directive 2006/113/EC on the Quality Required of Shellfish Waters, also referred to as the Shellfish Waters Directive (SWD) requires the monitoring of, inter alia, certain physicochemical parameters including trace metal contaminants in order to assess and protect the quality of shellfish growing waters and the shellfish harvested from them. The SWD is concerned with the quality of shellfish waters and applied waters designated by the Member States as needing protection or improvement in order to support shellfish (bivalve and gastropod molluscs) life and growth and thus to contribute to the high quality of shellfish products directly edible by man. This report details the Marine Institute’s (MI) monitoring results for physicochemical parameters sampled in seawater and shellfish tissue from designated Shellfish Waters and specifically: Dissolved trace metal concentrations and other physiochemical parameters in seawater sampled from Irish Shellfish Waters in 2016 and trace metal and organohalogen concentrations in shellfish sampled in 2015.
    • Monitoring trace metals and organohalogens in shellfish (2014) and physicochemical parameters and trace metals in seawater (2015) under the Shellfish Waters Directive

      Environmental Team, Chemistry Section, Marine Environment & Food Safety Services (Marine Institute, 2017)
      Directive 2006/113/EC on the Quality Required of Shellfish Waters, also referred to as the Shellfish Waters Directive (SWD) requires the monitoring of, inter alia, certain physicochemical parameters including trace metal contaminants in order to assess and protect the quality of shellfish growing waters and the shellfish harvested from them. Sixty-four areas have been designated as Shellfish Waters (SWs) under SI 268 of 2006, SI 55 of 2009 and SI 464 of 2009. The SWD is concerned the quality of shellfish waters and applied waters designated by the Member States as needing protection or improvement in order to support shellfish (bivalve and gastropod molluscs) life and growth and thus to contribute to the high quality of shellfish products directly edible by man. The Marine Institute undertakes a monitoring programme to meet the requirements of the Water Framework Directive (WFD) 2000/60/EC Transitional and Coastal (TraC) Waters and physico-chemical elements of the SWD.
    • Morphological and molecular characterization of the small armoured dinoflagellate Heterocapsa minima (Peridiniales, Dinophyceae)

      Salas, R.; Tillmann, U.; Kavanagh, S. (Taylor and Francis, 2014)
      The dinophycean genus Heterocapsa is of considerable interest as it contains a number of bloom-forming and/or harmful species. Fine structure of organic body scales is regarded as the most important morphological feature for species determination but currently is unknown for the species H. minima described by Pomroy 25 years ago. Availability of a culture of H. minima collected in the south-west of Ireland allowed us to provide important information for this species, including cell size, cell organelle location, thecal plate pattern, body scale fine structure and molecular phylogeny. Light microscopy revealed the presence of one reticulate chloroplast, an elongated centrally located nucleus, and the presence of one pyrenoid surrounded by a starch sheath. Scanning electron microscopy (SEM) of the thecal plate pattern indicated that Pomroy erroneously designated the narrow first cingular plate as a sulcal plate. In addition, SEM revealed as yet unreported details of the apical pore complex and uncommon ornamentations of hypothecal plates. Organic body scales of H. minima were about 400 nm in size, roundish, with a small central hole and one central, six peripheral and three radiating spines. They differ from other body scales described within this genus allowing for positive identification of H. minima. Heterocapsa minima shares gross cell morphological features (hyposome smaller than episome, elongated nucleus in the middle of the cell, one pyrenoid located in the episome on its left side) with H. arctica (both subspecies H. arctica subsp. arctica and H. arctica subsp. frigida), H. lanceolata and H. rotundata. These relationships are reflected in the phylogenetic trees based on LSU and ITS rDNA sequence data, which identified H. arctica (both subspecies), H. rotundata and H. lanceolata as close relatives of H. minima.
    • A multi-year comparison of Spirolide profiles in planktonic field samples from the North Sea and adjacent waters

      Krock, B.; Tillmann, U.; Alpermann, T.; Salas, R.; Cembella, A.D. (Alfred-Wegener-Institut für Polar- und Meeresforschung in der Helmholtz-Gemeinschaft, 2010)
      Alexandrium ostenfeldii isolates from distinct geographical locations showed almost identical profiles, primarily consisting of 20-methyl spirolide G (20-meG). Whereas the Scottish isolate produces only this variant, the Irish isolate additionally yields slight amounts of 13-desmethyl spirolide C (13-desmeC). These profiles were also reflected in the field data, where 20-meG was the most abundant spirolide throughout all samples and years.
    • New insights into the causes of human illness due to consumption of azaspiracid contaminated shellfish

      Chevallier, O.P.; Graham, S.F.; Alonso, E.; Duffy, C.; Silke, J.; Campbell, K.; Botana, L.M.; Elliott, C.T. (Nature Publishing Group, 2015)
      Azaspiracid (AZA) poisoning was unknown until 1995 when shellfish harvested in Ireland caused illness manifesting by vomiting and diarrhoea. Further in vivo/vitro studies showed neurotoxicity linked with AZA exposure. However, the biological target of the toxin which will help explain such potent neurological activity is still unknown. A region of Irish coastline was selected and shellfish were sampled and tested for AZA using mass spectrometry. An outbreak was identified in 2010 and samples collected before and after the contamination episode were compared for their metabolite profile using high resolution mass spectrometry. Twenty eight ions were identified at higher concentration in the contaminated samples. Stringent bioinformatic analysis revealed putative identifications for seven compounds including, glutarylcarnitine, a glutaric acid metabolite. Glutaric acid, the parent compound linked with human neurological manifestations was subjected to toxicological investigations but was found to have no specific effect on the sodium channel (as was the case with AZA). However in combination, glutaric acid (1mM) and azaspiracid (50nM) inhibited the activity of the sodium channel by over 50%. Glutaric acid was subsequently detected in all shellfish employed in the study. For the first time a viable mechanism for how AZA manifests itself as a toxin is presented.
    • Norovirus genotypes present in oysters and in effluent from a wastewater treatment plant during the seasonal peak of infections in Ireland in 2010

      Rajow-Nenow, P.; Waters, A.; Keaveney, S.; Flannery, J.; Tuite, G.; Coughlan, S.; O’Flaherty, V.; Doré, W. (American Society for Microbiology, 2013)
      We determined norovirus (NoV) concentrations in effluent from a wastewater treatment plant and in oysters during the peak period of laboratory-confirmed cases of NoV infection in Ireland in 2010 (January to March). Weekly samples of influent, secondary treated effluent, and oysters were analyzed using real-time quantitative reverse transcription-PCR for NoV genogroup I (GI) and genogroup II (GII). The mean concentration of NoV GII (5.87 104 genome copies 100 ml 1) in influent wastewater was significantly higher than the mean concentration of NoV GI (1.40 104 genome copies 100 ml 1). The highest concentration of NoV GII (2.20 105 genome copies 100 ml 1) was detected in influent wastewater during week 6. Over the study period, a total of 931 laboratory-confirmed cases of NoV GII infection were recorded, with the peak (n 171) occurring in week 7. In comparison, 16 cases of NoV GI-associated illness were reported during the study period. In addition, the NoV capsid N/S domain was molecularly characterized for selected samples. Multiple genotypes of NoV GI (GI.1, GI.4, GI.5, GI.6, and GI.7) and GII (GII.3, GII.4, GII.6, GII.7, GII.12, GII.13, and GII.17), as well as 4 putative recombinant strains, were detected in the environmental samples. The NoV GII.4 variant 2010 was detected in wastewater and oyster samples and was the dominant strain detected in NoV outbreaks at that time. This study demonstrates the diversity of NoV genotypes present in wastewater during a period of high rates of NoV infection in the community and highlights the potential for the environmental spread of multiple NoV genotypes.
    • Novel azaspiracids produced by Amphidomataceae

      Krock, B.; Tillmann, U.; Jeong, H.J.; Potvin, E.; Salas, R.; Kilcoyne, J.; Gu, H. (Alfred-Wegener-Institut für Polar- und Meeresforschung, 2012)
    • Nucleic acid tests for toxic phytoplankton in Irish waters-phytotest: Marine Strategic RTDI project AT/04/02/02 - research update

      Maher, M.; Kavanagh, S.; Brennan, C.; Moran, M.; Salas, R.; Lyons, J.; Silke, J. (Marine Institute, 2007)
      The Phytotest project is a 3 year collaborative project funded through the Marine Strategic Programme in Advanced Technologies as part of the National Development plan 2000-2006. The project partners include the National Diagnostics Centre at NUI Galway and MI. The overall objective of the project is the development of nucleic acid tests (molecular methods) for the identification of key toxic phytoplankton species in Irish waters. In the final year of the programme the aim is to transfer the molecular methods developed in the project into MI to support their monitoring service. Currently, the monitoring for phytoplankton species in Irish waters is performed by light microscopy which can easily identify some plankton species based on distinctive morphological traits. Other species in particular, Pseudonitzschia spp. and Alexandrium spp. cannot be identified to species level by light microscopy. Identification of these species requires more sophisticated microscopic techniques such as scanning electron microscopy (SEM) and transmission electron microscopy (TEM). These techniques cannot easily be integrated into a routine testing environment. Molecular methods utilise unique information contained within an organism’s genome in order to identify it. This genetic information can be exploited in a range of molecular test platforms enabling microorganisms to be identified to species level. Additionally, there has been a major drive towards the development of highly automated platforms to support molecular tests for high-throughput testing in routine laboratory settings.
    • Observations on a bloom of Flagellate "X" in the West of Ireland

      Dunne, T. (ICES, 1984)
      In July 1983 major mortalities of farmed trout and salmon were associated with a bloom of an unidentified organism hitherto unrecorded in Ireland. Three further blooms occurred in 1984, two of which were associated with mortalities. The morphology of this organism (Flagellate "X") as observed in 1983 is described.
    • Observed sequential occurrence of phytoplankton and zooplankton in the Dunkellin Estuary, Galway Bay, Ireland

      Byrne, P.; O'Mahony, J.H.T. (ICES, 1993)
      The Dunkellin is a small tidally-dominated estuary to the south-east of Galway Bay in western Ireland. The plankton of the estuary was studied for 18 months between December 1984 and July 1986. This paper presents results on the variation in the sequential occurrenCe of phytoplankton and zooplankton between the inner and outer estuary. Phytoplankton and microzooplankton occurred in high numbers in the spring to autumn months. Highest abundances of phytoplankton and microzooplankton (non-tintinnid ciliates and tintinnid ciliates) were recorded 10 the Inner estuary, whereas mesozooplankton were predominant in the outer reaches.
    • The occurrence of DSP toxicity in Ireland

      Jackson, D.; Silke, J.; Doyle, J.; Nixon, E.; Taaffe, B. (ICES, 1993)
      The geographical and temporal variations in the occurrence of DSP in Ireland are presented and the implications of the resulting closures on aquaculture operations and fisheries are discussed. Prior to 1992 DSP toxicity had been confined to the southwest and south coasts but in 1992 a protracted occurrence of DSP was recorded in Killary Harbour on the west coast.