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Adoption
PROJECT NUMBER • 1997-336
PROJECT STATUS:
COMPLETED

Symposium on parasitic diseases of aquatic animals: 10th International Congress of Protozoology

A symposium on protozoan diseases of aquatic animals was planned as a feature of the 10th International Congress of Protozoology. Speakers invited for the symposium were: Dr Mike Hine, NIWA, NZ, an expert on oyster and fish diseases, Prof. Tim Flegel, Mahidol University, Bangkok, an expert on prawn...
ORGANISATION:
University of Queensland (UQ)

Diagnostic detection of aquatic pathogens using real-time next generation sequencing

Project number: 2018-147
Project Status:
Current
Budget expenditure: $216,000.00
Principal Investigator: David Cummins
Organisation: CSIRO Australian Animal Health Laboratory
Project start/end date: 30 Jun 2019 - 28 Oct 2021
Contact:
FRDC

Need

Current diagnostic programs generally rely on highly -specific assays for pathogen detection. While these techniques are invaluable, they are one dimensional and do not provide detailed information critical to a disease investigation. These gaps include the inability to detect unknown pathogens and potential variants of know pathogens and provide no additional genomic or transcriptomic data. Moreover, samples must be shipped to trained personnel in a laboratory, further delaying the time to diagnosis. The MinION, on the other hand, can theoretically detect any pathogen and can potentially be deployed to the field. Moreover, the MinION can rapidly generate full-length genomes, allowing for epidemiological tracking of viral or bacterial strains in near real-time. Such rapid data, which cannot be obtained as quickly using existing methods, are vital if the intention is to intervene in an outbreak and reduce impacts on the productivity and profitability of aquaculture facilities. For example, a rapid, early diagnosis may allow mitigating actions to be taken on-farm, such as the diversion of intake water, movement restrictions of stock and the isolation of infected ponds.
These qualities make the MinION an attractive complimentary platform to fill several gaps in the data obtained during disease outbreak investigations, or routine diagnostics, and potentially for use in the field. However, results from the misuse or lack of understanding of the technology could also have adverse regulatory implications for aquaculture industries. For example, without appropriate guidelines, an inexperienced diagnostician may misinterpret a distant DNA match in a pathogen database as a significant result, this may create unwanted attention to industry and potential stock destruction or changes to disease status that are unjustified. Thus, it is critical that the MinION is evaluated at the Australian Animal Health Laboratory, and guidelines and procedures are developed for accurate diagnostic evaluations. The activities detailed in this application will establish the feasibility of using the MinION for diagnostic applications, and ensure that the data is reliably generated and interpreted appropriately.

Objectives

1. Evaluate if MinION data meets or exceeds the data obtained using established laboratory-based NGS platforms. Objectives (1) and (2) align with Methods section (1).The first objective of this project is to demonstrate if the MinION can obtain quality genome assemblies of known pathogens, such as WSSV, AHPND, OsHV-1 and HaHV that have been created using existing NGS technology. Moreover, determine if the MinION is capable of producing a diagnostic result more rapidly and with greater confidence than traditional techniques. STOP/GO POINT: If MinION data does not produce reliable genome assemblies, no improvement in genome quality, or is significantly more laborious to set-up/run or analyse than existing NGS technologies, do not proceed with objective 2.
2. Evaluate the performance of the MinION using existing diagnostic extraction techniques and produce robust methods and protocols for sample preparation, sequencing and data analysis. This objective will optimise MinION protocols for sample pre-processing, optimal sequencing conditions, and data post-processing. We will then evaluate the MinION data produced from a range of aquatic organisms against data produced using traditional techniques from the same samples. STOP/GO POINT: If after these optimisations, the MinION cannot detect pathogens as reliably as traditional techniques, do not proceed with objective 3.
3. Compare the applicability of MinION to standard molecular assays for identification of pathogens in diagnostic samples. Objective (3) is aligned with Methods section (2).In this objective, diagnostic samples will be tested using existing diagnostics tools (qPCR, cPCR) and MinION sequencing. Analysis between the methods will be detailed, including time to result, pathogen identity and genomic information. This objective will not only provide an insight into real-time sequencing for diagnostics, but in addition the feasibility of MinION technology for field application in the future.
Environment

Selective breeding for disease resistance and fast growth in Sydney rock oysters

Project number: 1996-357
Project Status:
Completed
Budget expenditure: $332,308.00
Principal Investigator: John Nell
Organisation: Department of Primary Industries and Regional Development (NSW)
Project start/end date: 27 Feb 1997 - 18 Mar 2004
Contact:
FRDC

Need

The NSW oyster industry has suffered from QX disease and winter mortality for a very long time. It has responded to these disease challenges by vacating affected leases seasonally or in the case of Georges River by abondoning the infested part of the estuary. The history of inter-estuary transfer of oysters for on-growing has not allowed the development of resistant strains in NSW. However, if resistant strains of oysters are not developed, the industry will have no better management tool available in future than that used in the past, ie moving or selling oysters before a disease outbreak is expected or abondoning oyster leases.

If the opportunity for breeding QX disease resistance in Sydney rock oysters is not taken up, a unique opportunity will be lost, to use breeding lines previously selected for fast growth in the selection for disease resistance. It is important that breeding for QX resistance begins now, before another estuary is infested with this parasite. In Georges River, the industry responded to the QX outbreak by abandoning affected leases.

Growth rates in Sydney rock oysters have been improved by an average of 4% for the first generation of selection in Port Stephens. Now the initial progress has been made and four breeding lines are established, it is important that the momentum is maintained and selective breeding for fast growth is continued. The growth rate of the Port Stephens selection lines can be increased by 4% for each successive generation.

Growth rates in Sydney rock oysters can be improved by both selective breeding (an average of 4% faster growth for the first generation of selection) and triploidy (30-40% faster growth). However, triploids have not previously been produced from improved breeding lines. It is important to determine if improvements in growth rates by these two methods are additive. For example with triploids produced from improved breeding lines, a 30% increase in growth rate with triploidy plus another 8% for two generations of selective breeding may increase growth rates of oysters by 38%.

Objectives

1. Evaluation of the resistance of fourth selected generation Georges River oysters to QX disease and winter mortality against controls
2. Evaluation of the growth rate of fourth selected generation Port Stephens selection line diploids and triploids against non-selected diploid and triploid controls
Environment
PROJECT NUMBER • 2004-217
PROJECT STATUS:
COMPLETED

Aquafin CRC - Atlantic Salmon Aquaculture Subprogram: development of an AGD vaccine: phase II

Amoebic gill disease (AGD) is considered to be the most significant health problem for farmed Atlantic salmon in Tasmania, costing the industry an estimated $15-20 million pa. It is caused by the presence of Neoparamoeba spp. on the gills and if untreated can lead to death. Although some control of...
ORGANISATION:
CSIRO Australian Animal Health Laboratory
People
PROJECT NUMBER • 2002-665
PROJECT STATUS:
COMPLETED

Aquatic Animal Health Subprogram: enhancement of the emergency disease management capability in Victoria - adapting the AQUAVETPLAN control centre management manual

In the past 20 years, many fisheries and aquaculture industries around the world have suffered major production losses through the impact of disease epidemics. To date, Australia has avoided many of these epidemics and retains a favourable disease status, which facilitates international trade and...
ORGANISATION:
Agriculture Victoria
Environment
PROJECT NUMBER • 2001-245
PROJECT STATUS:
COMPLETED

Aquafin CRC - Atlantic Salmon Aquaculture Subprogram: model development for epidemiology of Amoebic Gill Disease

Amoebic Gill Disease (AGD) is the main health problem affecting salmon industry in Southern Tasmania. To improve management of fish with AGD on the farms, the industry needs better understanding of AGD epidemiology. This will provide a basis on which to develop strategies for new...
ORGANISATION:
University of Tasmania (UTAS)
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