Diagnostic Detection Of Aquatic Pathogens Using Real-time Next Generation Sequencing
Funder
Fisheries Research and Development Corporation
Funding Amount
$216,000.00
Summary
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 diag ....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. Read moreRead less
Building Industry Capacity To Lead Co-management Initiatives Within The Bass Strait Central Zone Scallop Fishery: Training Industry To Conduct Biomass Estimate Surveys
Funder
Fisheries Research and Development Corporation
Funding Amount
$90,462.00
Summary
There is a need to develop capacity within industry in order to progress future co-management initiatives in the Bass Strait Central Zone Scallop Fishery (BSCZSF). Central to future co-management initiatives will be industry’s ability to collect data in a systematic and scientific manner that is robust and reliable to inform management decision making. Industry needs to be trained to coordinate and collect data. This data may also deliver cost savings when compared to the current pre-season biom ....There is a need to develop capacity within industry in order to progress future co-management initiatives in the Bass Strait Central Zone Scallop Fishery (BSCZSF). Central to future co-management initiatives will be industry’s ability to collect data in a systematic and scientific manner that is robust and reliable to inform management decision making. Industry needs to be trained to coordinate and collect data. This data may also deliver cost savings when compared to the current pre-season biomass surveys.
The unprecedented impacts of the COVID-19 pandemic have forced industry and management to review existing research and management processes to ensure the on-going viability Australia’s fishing industry. Whilst the scallop fishery has to date been largely shielded from the impacts (a seasonal effect) there is tremendous uncertainty about the coming fishing year and markets. There is now a need to re-think the data collection processes for this fishery and provide the industry with the opportunity and capacity, under a co-management approach, to cost-effectively collect data to inform management decisions.
The coming season provides the perfect opportunity for the first steps into a new co-management paradigm. The biomass in western Bass Strait waters are significant, with many in the industry saying it’s the highest in over 40 years of fishing. Based on the 2019 TAC, the maximum harvest fraction last season was less than 9% of the surveyed biomass, noting it was even lower, as the TAC remained under-caught. Furthermore AFMA have recently announced that the formal pre-season biomass estimation survey will not proceed in 2020 due the uncertainties surrounding the impacts of COVID-19.
This project will investigate industry’s capacity to coordinate in-season biomass surveys and provide the opportunity for industry to understand the requirements to undertake formal scientific studies.
Objectives: 1. Build industry capacity to lead and participate in fishery data collection projects 2. Industry coordinated data collection to inform biomass estimation of the fishery 3. Industry coordinated data collection and data analysis to inform decision making and develop co-management arrangements Read moreRead less
Discovery Early Career Researcher Award - Grant ID: DE230100085
Funder
Australian Research Council
Funding Amount
$440,954.00
Summary
Forensic genomic toolkit for tracking the illegal wildlife trade. This project aims to analyse the illegal parrot trade by utilising conservation genomic approaches. The project will reveal wildlife trade routes in South-east Asia by developing cutting-edge forensic genomic techniques and criminological methods. Expected outcomes of this project include new field-deployable sequencing technology to provide in-situ genetic information for identifying the taxonomy and provenance of confiscated spe ....Forensic genomic toolkit for tracking the illegal wildlife trade. This project aims to analyse the illegal parrot trade by utilising conservation genomic approaches. The project will reveal wildlife trade routes in South-east Asia by developing cutting-edge forensic genomic techniques and criminological methods. Expected outcomes of this project include new field-deployable sequencing technology to provide in-situ genetic information for identifying the taxonomy and provenance of confiscated specimens, and a first ever genetic database of traded wildlife. The project will facilitate important countermeasures to the illegal wildlife trade including confiscation, reintroduction, improved law enforcement, and education for better biodiversity outcomes in our region.Read moreRead less
Toxigenic Vibrio Baselines And Optimum Storage, Transport And Shelf-life Conditions To Inform Cold Supply Chains In The North Australian Tropical Rock Oyster Industry
Funder
Fisheries Research and Development Corporation
Funding Amount
$199,300.00
Summary
Internationally, Tropical Rock Oysters have a poor safety reputation with Vibrio at the top of the list. While a pro-active not reactive approach to vibrio food safety is essential for product assurance and branding, effort needs to be proportional to risk. And risk assessment also needs to be informed by real data. There are certainly knowledge gaps for north Australia, but we know seawater contains up to 42 Vibrio spp. including several known toxigenic species in addition to the human pathogen ....Internationally, Tropical Rock Oysters have a poor safety reputation with Vibrio at the top of the list. While a pro-active not reactive approach to vibrio food safety is essential for product assurance and branding, effort needs to be proportional to risk. And risk assessment also needs to be informed by real data. There are certainly knowledge gaps for north Australia, but we know seawater contains up to 42 Vibrio spp. including several known toxigenic species in addition to the human pathogens Vibrio parahaemolyticus (Vp) and V. vulnificus (Vv). We know Vp responds to temperature but Vv does not. And we know Vv concentrations in seawater are higher in the wet season compared to the dry, and more shellfish are Vp and Vv positive in the wet season. So if vibrio diversity and abundance in TRO is seasonal (as shown elsewhere), it is likely that Vibrio spp. infections in humans will also follow a seasonal trend which has implications for risk management. A major bottleneck is that we don’t know how vibrios respond to storage and transport temperatures in TRO. We know that the Pacific and Sydney Rocks respond differently so it is not ‘one size fits all’ and it is certain TROs will be different again. In addition to identifying vibrio baselines in TRO and developing tests for toxigenic species, we will identify the best post-harvest storage and transport temperatures and assess TRO shelf life at realistic storage temperatures. This will provide fundamental information to inform cold supply chains that will support farmers, wholesalers and retailers of TROs from north Australia. We can also use this information to prepare an appropriate and regionally relevant vibrio risk profile for TRO in northern Australia to assist initial risk management activities. This information will provide the developing TRO industry with the knowledge needed to ensure an exemplary reputation, thus giving access to premium markets.
Objectives: 1. Measure vibrio baseline in Tropical Rock Oysters and develop tests to vibrio species that are toxigenic to oysters and humans 2. Identify optimum storage and transport temperatures to inform post-harvest cold supply chains 3. Assess TRO shelf life at realistic storage temperatures to maximise product quality and inform cold supply chains 4. Use objective 1-3 outcomes to produce a risk profile for vibrio in north Australian TRO that will support the industry as it seeks to deliver a safe, premium product Read moreRead less
Trusted business processes. This project aims to use conceptual design, process modelling and co-design approaches to create a structured approach for the management of trust. With a focus on business processes, it is intended to develop research- informed methods in order to (1) identify and specify trust concerns and opportunities, (2) model these within a common process modelling language and (3) propose patterns for how to mitigate trust concerns and how to benefit from opportunities. If suc ....Trusted business processes. This project aims to use conceptual design, process modelling and co-design approaches to create a structured approach for the management of trust. With a focus on business processes, it is intended to develop research- informed methods in order to (1) identify and specify trust concerns and opportunities, (2) model these within a common process modelling language and (3) propose patterns for how to mitigate trust concerns and how to benefit from opportunities. If successful, this would lead to an operational, and world first, detailed trust methodology for organisations in all sectors. As a result, Australian customers would engage with business processes with reduced trust concerns and experience increased integrity and benevolence.Read moreRead less
Faecal Microbiota Transplantation And Other Novel Therapeutic Microbial Manipulation Strategies In Inflammatory Bowel Disease
Funder
National Health and Medical Research Council
Funding Amount
$645,205.00
Summary
There is growing interest in the role of microbial-based strategies including faecal microbiota transplantation (FMT) for the treatment of inflammatory bowel disease. This project will develop such strategies into valid treatment options through a combination of clinical & basic science work including (1) characterising viral & fungal factors of importance, (2) evaluation of novel orally-delivered formulations of FMT, and (3) development of better defined, more reproducible microbial treatments.
The WRL industry needs to adopt new digital technology to benefit from the digital economy and ensure industry is efficient, highly productive and world-leading in all its management practices and policies. This is fundamental to achieving the WRL Strategic Plan objectives and aims to develop the western rock lobster industry’s competitiveness in digital technologies and ensure that the industry can draw the full benefits from digital innovation.
Discussions on 2017/18 research prioriti ....The WRL industry needs to adopt new digital technology to benefit from the digital economy and ensure industry is efficient, highly productive and world-leading in all its management practices and policies. This is fundamental to achieving the WRL Strategic Plan objectives and aims to develop the western rock lobster industry’s competitiveness in digital technologies and ensure that the industry can draw the full benefits from digital innovation.
Discussions on 2017/18 research priorities and potential areas for collaboration were discussed extensively at the FRDC Annual Stakeholder Workshop in August 2017 with digital technology a commonality across all groups, including scoping data collecting and analysis innovations for policy, management and operations; New apps for commercial recreational catch, management, markets and effort; and Monitoring and sensor (environment to consumers).
There is a need for the WRL to seek expertise to create a new digital platform that will be capable of adding new modules and applications in to the future as required as well as interoperability with other systems. Industry wants to generate and manage its own data (noting that it will make every effort to be compatible with a national industry data management project) and supply the requested data to government when it is required and in the appropriate form. This will require trust but industry needs to accept this responsibility if it wants to act fast and make the most of opportunities in the digital economy. Industry can't rely on government to achieve this.
The WRL needs to identify and implement new digital applications that will improve process efficiency and assist fishers, managers, scientists, regulators and key stakeholders to make more informed and better decisions.
The WRL needs to scope what other fisheries and non-fishing industries are doing nationally and internationally with collecting data and using it in new and innovative ways to improve operations, management, policy, science and decision making.
This program needs to make provision for extension areas such as a new on-line OH&S standards and automatic reporting, digitised traceability from catch to plate, new auto entry catch application, and new monitoring and sensor technologies. Objectives: 1. Scope national and international data collection and analysis innovation to assist policy development and fisheries management 2. Develop and extend a fully digitised database to achieve at least three management objectives 3. Expand database to meet non-managment objectives. Read moreRead less
Leadership diversity through relational intersectionality in Australia. This project aims to investigate leadership in contexts characterized by the complex intersection of cultural and gender differences - what is called here ‘relational intersectionality'. The expected outcomes will contribute to the development of new theory on leadership diversity, and a means through which that theory can be leveraged through leadership practice and education. The project will inform methods to better man ....Leadership diversity through relational intersectionality in Australia. This project aims to investigate leadership in contexts characterized by the complex intersection of cultural and gender differences - what is called here ‘relational intersectionality'. The expected outcomes will contribute to the development of new theory on leadership diversity, and a means through which that theory can be leveraged through leadership practice and education. The project will inform methods to better manage the increasing diversity of the Australian workforce and enable improved leadership performance.Read moreRead less
Exploring The Occurrence And Potential Associated Risk Factors For Pilchard Orthomyxovirus (POMV) In Tasmanian Farmed Atlantic Salmon
Funder
Fisheries Research and Development Corporation
Funding Amount
$209,295.62
Summary
Following basic epidemiology principles, no infectious disease occurs ‘randomly’ and its occurrence follow logical and predictable patterns. The presence of an infectious agent is unlikely sufficient to explain these patterns and most aquatic diseases result from the complex interaction between the agent, the host and its environment. Therefore, the targeted outcome for a POMV control plan is threefold: 1. Decrease transmission between infected and susceptible fish groups – this requires ide ....Following basic epidemiology principles, no infectious disease occurs ‘randomly’ and its occurrence follow logical and predictable patterns. The presence of an infectious agent is unlikely sufficient to explain these patterns and most aquatic diseases result from the complex interaction between the agent, the host and its environment. Therefore, the targeted outcome for a POMV control plan is threefold: 1. Decrease transmission between infected and susceptible fish groups – this requires identifying risk factors associated with the introduction, spread, and maintenance of the pathogen within the industry; 2. Decrease the number of susceptible fish – this mainly requires identifying risk factors associated with the susceptibility of the host (e.g. husbandry-related stress) and the development of a safe and effective prophylaxis; 3. Decrease the amount of virus in the environment - this requires detecting infected fish cage(s) early to implement timely control strategies. Diagnostic capacity to confirmed POMV outbreak has been developed and is currently used in routine by the industry. A vaccine against POMV is currently under development at the Tasmanian Aquatic Animal Health and Vaccines Centre of Excellence and will be available in the future. However, little is known about risk factors specific to POMV and about its full economic impact. We define as a ‘risk factor’ any attribute of the agent, the host or its environment that increases the risk and intensity of a disease outbreak. Most of the environmental risk factors (including farming practices) facilitate the introduction, transmission, or maintenance of the pathogen; while the host risk factors affect the susceptibility of the host and its capacity to become diseased. Like the closely related ISAv, the magnitude and occurrence of POMV outbreaks appeared to be highly variable. This supports the existence of additional factors other than the POMV infection that contribute to the intensity of an outbreak. It is anticipated that by identifying and intervening on some of the manageable risk factors, the frequency and the severity of POMV outbreaks can be reduced. Objectives: 1. Describe the occurrence of POMV outbreaks in the Tasmanian salmon industry 2. Quantify the direct financial impact of POMV mortality to the Tasmanian salmon industry 3. Identify potential management, environmental and stock risk factors directly or indirectly increasing the risk and intensity of a POMV outbreaks Read moreRead less
Exploring the role and outcomes of employee voice in a hospital setting. This project aims to identify ways to improve patient care and enhance employee wellbeing of healthcare workers through better utilisation of employee voice practices that enable employees to speak up. We aim to do this by identifying and distinguishing between the types of practices used by these workers to speak up on issues concerning working conditions and patient care concerns. The project will identify the determinant ....Exploring the role and outcomes of employee voice in a hospital setting. This project aims to identify ways to improve patient care and enhance employee wellbeing of healthcare workers through better utilisation of employee voice practices that enable employees to speak up. We aim to do this by identifying and distinguishing between the types of practices used by these workers to speak up on issues concerning working conditions and patient care concerns. The project will identify the determinants of speaking up in healthcare and the consequences this voice has for quality of patient care and worker wellbeing. This will have significant benefits for hospital stakeholders, including improved patient care, employee satisfaction and retention, and hospital efficiencies.Read moreRead less