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Student research projects

Farm Animal Health PhD research
A summary of the current research projects being undertaken by our PhD students.

Current PhD projects

Crystal Espinoza

The Use of Topical Analgesia for Improving the Welfare of Livestock Following Invasive Husbandry Procedures

Supervisors: Professor P Windsor and Dr G Cronin

Animal husbandry procedures such as castration, tail-docking and dehorning are routinely performed on millions of animals worldwide each year. Such procedures are performed for varying reasons including animal health, for facilitating management and for the safety of farm workers. While the conduct of these surgical procedures are important in commercial animal production, the procedures cause pain and distress and are traditionally performed without anaesthesia or analgesia. The main limitation to currently available pain relief options is that they involve too much time, expense and labour and thus are not be economically viable for commercial production.

An alternative solution may be the use of topical local analgesia in the form of a liquid substance containing local anaesthetics, which is applied during or immediately after a surgical procedure. Topical analgesia is more practical and affordable than current options and has the potential to be fast-acting and highly effective. Topical analgesia has recently been found to alleviate the pain associated with castration and tail-docking in lambs and calves, and mulesing in lambs.

It is hypothesised that its application can be successfully expanded to surgical procedures applied to other production species. Findings from this research have the potential to improve the welfare of production animals, which has become a critical issue in modern society.

Iridoviruses of ornamental fish and implications for Australian marine species

Jeffrey Go

Research Support: Australian Post Graduate Award and Vice Chancellor’s Research Scholarship
Supervisor: Professor R Whittington

Iridoviruses, particularly those of the genus Megalocytivirus, have been associated with mass mortalities in a range of cultured finfish species throughout Asia. Additionally, this group of viruses have been reported from a range of fish species in the ornamental fish trade. In 2003, a Megalocytivirus associated disease outbreak occurred in a Victorian Murray cod farm.

This represented the first occurrence of this viral group in Australian aquaculture, although the outbreak was contained and the disease subsequently eradicated from the facility. The extremely close genetic relationship between the viral isolate involved in this outbreak, and Megalocytivirus isolates from ornamental fish suggests that the ornamental fish trade was the most likely origin of this virus. Recent research also suggests that marine fish may be susceptible to infection with Megalocytivirus isolates from the ornamental fish trade, which could have severe implications for Australian marine ecosystems and emerging Australian marine aquaculture industries.

A research project is currently underway to further characterise the nature of Megalocytivirus infections and to test the susceptibility of a number of Australian marine finfish using material originating from the ornamental fish trade. The project will also aim to develop improved diagnostic tests for this group of viruses including in situ hybridisation, and serological tests such as enzyme linked immunosorbent assay.

Understanding the risks of Foot-and-mouth disease to Australia: modelling disease spread in feral and domestic animal populations

Katherine Negus

Research support: University of Arizona
Supervisor: Professor M Ward

Our ability to detect and appropriately respond to emerging and exotic diseases is critical for Australia’s biosecurity. However, there remain large gaps in our knowledge of the potential spread and areas of greatest risk for such disease occurrences, thus limiting our preparedness. Considerable effort, particularly recently, has been applied to modelling animal disease spread via livestock movements. However, the disease threat from wild animal (feral and native) and unfenced livestock populations that might form disease reservoirs has received comparatively little attention; such uncontrolled animal populations can represent a considerable proportion of the entire susceptible animal population for a variety of diseases. These populations can exacerbate outbreaks, form reservoirs of disease, and might allow novel diseases to become endemic.

Specific key outcomes – improve our understanding of the potential spread of FMD in Australia by using a spatial disease spread model within a geographic information system framework; and identify critical risk factors that predict the outcome of FMD incursions, in order to improve surveillance and control strategies. Research components – disease risks maps will be developed to illustrate criticality of locations to incursions of FMD by performing a semi-quantitative risk analysis; population surfaces for susceptible animal populations will be developed; a series of targeted simulations will be run to identify the possible spread from likely disease initiation points; those conditions (environmental and population) that can lead to larger outbreaks of disease will be characterized and the model used to evaluate different management strategies to mitigate disease spread.

John Stratton

Cambodian field veterinary services and bovine health, with an emphasis on improved FMD control

Research support: Australian Biosecurity Cooperative Research Centre for Emerging Infectious Disease, Australian Centre for International Agricultural Research
Supervisor: Professor Peter Windsor

The descriptive component comprises visiting Cambodian village animal health workers who are semi-skilled para-veterinarians responsible for delivering village veterinary services. Also involves analysing information on village animal health-worker training, their contact with farmers and the government, and their knowledge and experiences of the two most important diseases of Cambodian cattle and buffalo, haemorrhagic septicaemia and FMD, both of which are endemic by utilising village animal health workers to field trial FMD vaccination in the face of outbreaks.

Ms Diana Jaramillo Martinez

Host response of Australian native fish species to Nervous Necrosis Virus

Research support: Fisheries Research & Development Corporation, ALA AusAID Scholarship
Supervisors: Professor R Whittington, Dr P Hick

Viral Nervous Necrosis (VNN) has become one of the most important health challenges facing marine fish farming. This disease, seen worldwide, causes high mortalities of up to 100% in young populations when outbreaks occur. In Australia, barramundi farms have been particularly affected by the condition as supply of fingerlings has become uncertain and the cost of biosecurity measures is impacting the profits of the sector. Since the agent was reported for the first time in 1989, the virus has been well described and studied.

However, our understanding of the epidemiology and pathogenesis of the disease is still very limited.This is compounded by the various international research groups focusing on different strains of the virus and species of fish, making it difficult to draw conclusions out of the results that could be applicable for the local situation. Addressing the importance of an integral understanding of the disease, this research project is focused on studying the host response of native Australian fish species affected by the virus.

Specific aspects include transmission, immunology and diagnosis. Thus, the outcomes of the research are expected to contribute to the construction of more informed biosecurity policies and more effective disease control and prevention measures.

Ms Olivia Evans

Transmission factors of Ostreid Herpesvirus-1 in the Pacific Oyster (Crassostrea gigas)

Research support: Australian Postgraduate Award and Fisheries Research and Development Corporation Scholarship
Supervisors: Professor R Whittington, Dr I Paul-Pont, Dr P Hick

Pacific oyster mortality syndrome (POMS) is a complex, multi-factorial disease arising from the interaction of oysters, pathogens and environmental parameters. POMS, as the name suggests, causes severe mortality in the Pacific oyster (Crassostrea gigas), affecting predominantly oyster spat and juveniles with mortalities of 100% and 40-100% respectively. Ostreid herpesvirus 1 (OsHV-1), the sole member of the family Malacoherpesviridae within the order Herpesvirales, has been identified in Australia and abroad as one of the key pathogens causing POMS.

The disease, which first appeared in Australia in the Georges River in November 2010, has been documented and investigated in a range of countries worldwide including France, New Zealand, Spain, the United Kingdom and the Republic of Ireland. POMS poses a serious threat to the Australian C. gigas industry (2007-08: $53 million), with a potential to cause dramatic economic loss to producers nationwide. Within the current literature there exists a significant degree of research on crucial OsHV-1 diagnostic methodologies, however very little information exists surrounding the issue of OsHV-1 transmission factors. Little is understood about where this virus actually exists in the environment surrounding commercially produced C. gigas, how the virus infects a host and what environmental parameters trigger these outbreaks. Thorough investigation into where, when, and how this virus operates is crucial to understanding the disease cycle of POMS and vital to creating practical and economically viable recommendations for producers on how to deal with future POMS outbreaks, so as to limit the economic loss to industry associated with the disease.

Ms Viki Brookes

A risk assessment and simulation modeling framework for exotic disease prioritisation in the Australian pig industry

Research support: Australian Pork Limited
Supervisors: Professor M Ward, Dr M Hernandez-Jover,
Dr B Cowled, Dr T Holyoake

The domestic pig population in Australia is free from over thirty diseases that can adversely affect pig production, the production of other livestock species (such as foot and mouth disease), or human health (such as Nipah virus). Although Australia’s geographic isolation and biosecurity practices protect from disease incursions, the entry of equine influenza in 2007 highlighted that protection from risk cannot be complete.

The aim of this project is to enhance exotic disease preparedness, response and recovery in the case of an incursion, for the three highest priority diseases for the Australian pig industry. Multi-criteria decision analysis was used as a decision aid to determine the highest priority diseases according to potential disease impact and stakeholder opinion regarding the importance of areas of impact. Stakeholders selected African swine fever, porcine reproductive and respiratory syndrome (highly pathogenic strain), and Japanese encephalitis. Further investigation of these diseases will include quantitative risk analysis and spatial disease modeling.

Ms Lechelle van Breda

A comprehensive risk factor analysis of E.coli disease in the piggery environment

Research Support: Pork CRC
Supervisors: Professor M Ward, Dr O Dhungyel

The project has the potential to reduce E.coli disease occurrence by allowing producers to change management in the disease pathway prior to clinical disease incidents. Reduced disease incidence will improve animal welfare standards (reduced number of deaths, reduced morbidity, reduced runts and reduced treatments). Removing (or lessening) gastrointestinal disease will improve live weight gains and potentially reproductive efficiency. A successful disease scoring system will also lead to less medication and therefore less antimicrobial resistance pressure within herds, therefore leading to a healthier product and reduction in public health risk.

Mrs Karen Williams

Shiga Toxin producing E. coli

Research Support: Meat & Livestock Australia
Supervisors: Professor M Ward, Dr O Dhungyel, Dr K Plain, Professor R Whittington

Cattle are a reservoir of the human pathogen E coli O157 which ‘colonises’ the intestinal tract of the animal and is shed in the faeces. The nature of this shedding is heterogeneous with regards both level and duration of shedding. This variation between animals and more specifically the phenomenon of super-shedding is poorly understood with significant public health implications.

This project involves a longitudinal study of cattle to monitor the levels of O157 excreted by cattle over time in the course of natural infection. This will provide a clearer picture of shedding levels and variability. The project will be looking at the patterns from an epidemiological point of view and aiming to identify risk factors that affect the level or duration of shedding.

In vitro studies to assess the nature of bacterial attachment to the bovine gastro-intestinal tract (GIT) will further investigate the nature of differential shedding. The use of primary bovine cells isolated from the GIT will be used as a model for adhesion trials.

Mr Matt Van der Saag

Bluetongue Viruses and biting midges

Research Support: NSW Centre for Animal and Plant Biosecurity
Supervisors: Professor M Ward, Dr A Nicholas and Dr P Kirkland

Bluetongue viruses (BTVs) are a group of economically important, insect borne viruses that affect ruminants such as sheep and cattle. BTVs are endemic in Northern parts of Australia and Northern NSW is the farthest south that BTVs have been known to occur. Certain species of biting midges, belonging to the genus Culicoides (Diptera: Ceratopogonidae) are the vectors of BTVs, and, the main focus of this project. Specifically, our main aim is to develop a suite of tools that can be used to study the vector capacity of any given biting midge for BTVs. This includes the development of a laboratory blood feeding system that facilitates the infection of wild caught midges with BTVs. Other areas of research include the development and application of rapid diagnostic qPCR assays for the identification of vector midge species and their blood feeding habits. At the conclusion of this project it is hoped that the tools and methods developed will be applicable and relevant for the surveillance of BTVs and their vectors in Australia.

Mr Sonevilay Nampanya

Foot and Mouth Disease (FMD) and Biosecurity in northern Lao PDR

Research Support: John Alwright Fellowship, AusAID
Supervisor: Professor P Windsor

Foot and Mouth Disease (FMD) is endemic in the Mekong region of SE Asia and a SEACFMD roadmap (South East Asia and China FMD) for possible control and eradication of the disease has been developed by the OIE (world organisation for animal health) office in Bangkok that aims to coordinate FMD activities of countries in the region.

However little is known of the epidemiology of disease transmission or the socioeconomic impact of FMD and farmer, trader and extension worker knowledge of the role of vaccination and biosecurity in disease management is severely deficient in Lao PDR. Sonevilay is conducting a range of studies that address these questions in addition to cattle productivity research that explores whether sustainable FMD vaccination and biosecurity can be incorporated into village-level smallholder systems.


Mr Jim Young BVSc MVPHMgt

Evaluation of financial and social impacts of large ruminant transboundary diseases in developing countries in the Greater Mekong Subregion

Supervisors: Professor P Windsor, Dr R Bush

Within the Mekong region changes in population demographics including the rising middle class (particularly Vietnam and China) are driving higher beef prices in turn creating an opportunity for smallholder farmers to meet this demand. Cattle and buffalo remain an important component of smallholder mixed farm systems in Cambodia and Laos, and improving productivity offers a pathway for higher incomes, poverty alleviation and improved food security. However largely uncontrolled transboundary animal diseases including foot-and-mouth disease and haemorrhagic septicaemia are endemic within the region and cause significant impacts on both rural livelihoods and the public good. Jim’s project takes a systems approach to seek greater understanding of both local and community impacts of large ruminant TADs to identify sustainable methods and motivation for improved biosecurity and disease control.