18 results

Aquatic Animal Health Training Scheme 2019-2022

Project number: 2019-148
Project Status:
Completed
Budget expenditure: $131,250.00
Principal Investigator: Nicholas J. Moody
Organisation: CSIRO Australian Animal Health Laboratory
Project start/end date: 6 Feb 2020 - 30 Aug 2022
Contact:
FRDC

Need

While the AAHTS has been in operation for 9 years, there remains a need for the continual education and training of aquatic animal health professionals to enhance their skills across a range of specialist disciplines. Based on the significant outcomes from the previous nine years of the AAHTS, the Department of Agriculture has contributed $75,000.00 (less $7,500.00 (10%) management fee, cash contribution to FRDC) to ensure that the AAHTS continues to be implemented for a further 3-year period (2019/20-2021/22) with matching funding anticipated from the FRDC Aquatic Animal Health and Biosecurity Subprogram. Thus, an application is needed to generate an agreement between CSIRO-AAHL and FRDC for continuation of AAHTS which would be administered as previously, i.e., by CSIRO-AAHL (rather than FRDC) through the FRDC Aquatic Animal Health and Biosecurity Subprogram.

Objectives

1. To improve the knowledge and skills in aquatic animal health management to support Australia’s fishing and aquaculture industry, including the aquarium sector
Industry
PROJECT NUMBER • 2021-129
PROJECT STATUS:
COMPLETED

Understanding of spatial extent, infection window and potential alternative hosts for the oyster disease QX in Port Stephens

This report details an investigation by the NSW Department of Primary Industries into QX disease in Sydney Rock Oysters (Saccostrea glomerata; SROs) in Port Stephens during the 2022. This followed from the first incursion of this disease in this estuary in August of 2021. QX disease has...
ORGANISATION:
Department of Primary Industries and Regional Development (NSW)

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
PROJECT NUMBER • 2019-095
PROJECT STATUS:
COMPLETED

Update of AQUAVETPLAN Disease Strategy Manual, White Spot Disease

This disease strategy for the control and eradication of white spot disease (WSD) is an integral part of the Australian Aquatic Veterinary Emergency Plan (AQUAVETPLAN). AQUAVETPLAN disease strategy manuals are response manuals and do not include information about preventing the introduction of...
ORGANISATION:
DigsFish Services Pty Ltd
Environment
PROJECT NUMBER • 2017-054
PROJECT STATUS:
COMPLETED

NCCP: Social, economic, and ecological risk assessment for use of Cyprinid herpesvirus 3 (CyHV-3) for carp biocontrol in Australia

The ecological and social risk assessment detailed in the three volumes of this report was one of the projects funded through the NCCP. The ecological component of the assessment was undertaken in two parts: (a) A compilation of the science and epidemiology of CyHV-3 and an assessment of...
ORGANISATION:
CSIRO Health and Biosecurity
Environment
PROJECT NUMBER • 2017-215
PROJECT STATUS:
COMPLETED

Storm Bay Biogeochemical Modelling & Information System Supporting sustainable aquaculture expansion in Tasmania

This project delivers a hindcast and near real time Storm Bay Modelling and Information System that is fit for the purpose of simulating water quality and characterising nutrients in Storm Bay from ocean currents, sediment resuspension, river and anthropogenic (including fish farm) inputs. The...
ORGANISATION:
CSIRO Oceans and Atmosphere Hobart
Environment
PROJECT NUMBER • 2004-201
PROJECT STATUS:
COMPLETED

Innovative Solutions For Aquaculture: planning and management - addressing seal interactions in the finfish aquaculture industry

The broad aims of this study were to provide information on the foraging zones of seals, and the location of breeding colonies and haulout locations in the Eyre Peninsula region of South Australia, to assist in the zoning, appropriate placement and management of future finfish aquaculture...
ORGANISATION:
SARDI Food Safety and Innovation