Postgraduate Students and Their Projects

• A study of the biological and financial impact of OJD in affected sheep flocks in NSW
• Identification of risk factors for OJD infection-level in sheep flocks
• In vitro survival and dormancy of Mycobacterium paratuberculosis
• Ovine Johne’s disease – investigating mortality rates, disease transmission and control
• Comparison of the S and C strains of Mycobacterium paratuberculosis at genome and proteome levels
• Genomic and phenotypic comparison of isolates of Mycobacterium sp. that contain IS900–like elements
• Apoptosis in sheep with Mycobacterium paratuberculosis infection
• Aspects of the pathogenesis of Mycobacterium paratuberculosis infection in sheep
• Genetic and proteomic differentiation of stages of Mycobacterium paratuberculosis infection
• Detection of Mycobacterium avium. Subsp. pararuberculosis in sheep faeces by direct Quantitative PCR
• The sheep/ Haemonchus contortus relationship
• Investigating role of wildlife and wild canids in transmission of Neospora Caninum
• Biotechnology and epidemiology to control nodavirus in barramundi aquaculture
• Application of molecular diagnostic techniques to epidemiological investigations of Viral Nervous Necrosis (VNN) in barramundi aquaculture
• Specialised management of gilts and their progeny
• Peri-urban regional surveillance for biosecurity for pigs in eastern Australia
• Modelling the emergence of avaian influenza in the Australian poultry industry
• Remote area syndrome surveillance systems for cattle

Mr Russell Bush
Research support: Meat & Livestock Australia.
Supervisors: Dr JA Toribio, Dr P Windsor, Dr S Webster

Debate continues regarding the impact on infected farms of Ovine Johne’s disease (OJD), a chronic enteric disease of sheep caused by the bacterium Mycobacterium paratuberculosis. Accurate estimation of annual mortality rates and the proportion attributable to OJD could provide an insight into the financial significance of this disease. The study quantified OJD mortalities in 12 flocks across four districts of south-eastern NSW, confirming considerable mortality rates (average 6.2%, range 2.1 to 17.5%) contributed to significant financial loss during the 12-month study period. Industry groups can now be provided with accurate figures on direct OJD losses within the endemic area of NSW. The data can be used to justify vaccination programs, and contribute to the development of cost effective strategies for future control and management. Further work on economic modelling will lead to tools being made available to farmers to enable them to optimise disease control programs.

Mr Navneet Kumar Dhand
Research support: University of Sydney International Postgraduate Research Scholarship, Meat & Livestock Australia.
Supervisors: Dr JA Toribio, Professor R Whittington

This project is designed to identify risk factors for the expression of Ovine Johne’s Disease (OJD) in 100 infected flocks through a cross sectional study of 3-4 year old sheep. OJD prevalence estimates will be based on pooled faecal culture. Information about OJD flock history, flock management practices and management of the 3-4 year old cohort will be collected by personal interviews. In addition, soil samples will be collected from the properties for analysis. Statistically significant associations between potential risk factors and OJD infection-level will be identified. The study is particularly focused on identifying risk factors that can be manipulated by farmers to improve on-farm control of OJD.

Mr Sanjeev Gumber
Research support: University of Sydney International Postgraduate Research Scholarship, Meat & Livestock Australia.
Supervisors: Professor R Whittington, Dr D Taylor


Mycobacterium paratuberculosis causes Johne’s disease, an economically significant problem in ruminants in most countries. This organism survives for long periods on pasture and soil, and as the infection is acquired by ingestion, control is difficult. This in-vitro study monitored the survival of the organism (sheep strain) following exposure to different time and temperature combinations. It showed that temperature flux has a more detrimental effect on the survival of M. paratuberculosis than peak temperature. Dormancy was also observed in these experiments. Further work will lead to characterisation of gene and protein expression in the organism during growth and induction of dormancy in experimental models. This knowledge will inform our understanding about the survival of the organism in the environment and also in the host during the development of OJD.

Ms Helen McGregor
Research support: Meat & Livestock Australia, NSW Stud Merino Breeders Association, CSL and proprietors of the study properties
Supervisors: Associate Professor P Windsor, Professor R Whittington


OJD infection in Australian sheep flocks continues to cause significant losses due to an increase in mortality rate but losses in the sub-clinical phase of the disease have not been widely investigated under Australian conditions. Estimations to be made in this study of sub-clinical losses due to reduction in wool growth and retardation in growth rates and the relationship with the development of clinical disease may provide insight into disease pathogenesis. Obtaining an accurate estimation of crude mortality rates and mortality risk in a flock and the proportion of the mortality attributable to OJD will establish the cost of the disease. Determining the contribution of pasture contamination rates and age of sheep, when first exposed to the disease, to incidence of disease in a flock, mortality rate attributable to OJD, the incubation period and the timing of diagnosis will lead to greater understanding of possible strategies for control and monitoring of diseased flocks. Documentation of the effects of whole flock vaccination on faecal excretion rates and mortalities in a high prevalence infected flock will enhance the knowledge and understanding of the benefits of a whole flock vaccination strategy including effects on adult excretion and cyclical pasture contamination.

Mr Ian Marsh
Research support: Meat & Livestock Australia, NSw Department of Primary Industries
Supervisor: Professor R Whittington


Johne’s disease (JD), a chronic and incurable disease affecting many ruminant species, is caused by Mycobacterium avium subsp. paratuberculosis (M. a. paratuberculosis). M. a. paratuberculosis strains can be divided into two groups known as sheep and cattle strains. The host range for the cattle strain is quite broad but the sheep strain primarily affects sheep. S and C strains have different cultural requirements. Little is known about the differences between S and C strains with respect to mechanisms of host specificity and pathogenicity. A greater understanding of these characteristics at the genome level would greatly assist in the control and management of JD both in Australia and abroad. In this study the genomes of S and C strains were compared using representational difference analysis, genome microarray and proteomic techniques. Data are still being analysed but the differences observed thus far are greater than was previously suspected from existing restriction fragment length polymorphism analaysis data, include major genetic deletions and may be related to phenotype.

Mr Martin McLoon
Research support: Meat & Livestock Australia, NSW Department of Primary Industries
Supervisor: Professor R Whittington


Ovine Johne's disease (OJD) is an important economic concern of Australian agriculture. The early diagnosis and implementation of control measures on properties with infected stock is the most effective way in preventing further spread of the disease. Presently a diagnosis of OJD relies on culture of the causal agent, Mycobacterium paratuberculosis, highlighting a mycobactin dependent phenotype in conjunction with PCR for the insertion sequence IS900. Detection of IS900 is included as a confirmatory test, and in some cases, the sole test because it has been shown to be unique to M. paratuberculosis. However, environmental mycobacterial isolates have been discovery which cause a cross reaction in the PCR for IS900 creating a false positive result and indicating the existence of IS900-like insertion sequences. To prevent false positive results a post PCR test was developed. To ensure the validity of this IS900 PCR-REA there is a need to characterise the mycobacterial isolates that possess an IS900-like insertion sequence at both a phenotypic and genotypic level, as well as the individual IS900-like insertion sequences. This analysis will allow a better understanding of the threat they pose to OJD diagnosis and their taxonomic position within the Mycobacterium genus.

Ms Sally Browne
Research support: Meat & Livestock Australia
Supervisors: Dr K de Silva, Associate Professor D Emery

Johne’s disease is a chronic wasting condition of ruminants caused by Mycobacterium avium subsp. paratuberculosis (Mptb). Clinical disease is seen only in adult animals. More knowledge regarding the pathogenesis of this disease, including apoptotic responses during the course of infection, is needed to allow advances towards management and control of Johne’s disease. The aim of this project is to develop assays for detection of apoptosis in sheep then define apoptotic responses in sheep with OJD. In initial experiments Merino sheep aged 7 months were orally dosed with the organism and samples were taken many tissues. At this very early stage in the development of Johne’s disease, there were no significant differences in the percentage of caspase positive cells when lymph node cells were incubated in the presence of medium alone or Mptb antigen. However, at day 6 with Mptb antigen, cells from gut lymph nodes in animals exposed to the highest dosage tended to have a higher percentage of caspase positive cells than the medium controls. Cells from peripheral lymph nodes incubated with Mptb for 6 days had higher apoptotic activity than the medium only controls, regardless of exposure to Mptb. These results suggest that detecting apoptosis in response to Mptb antigen in vitro in lymph node cells may be useful in identifying animals exposed to Mptb. Further studies are being carried out at later time points in the disease.

Mrs Kate Bower
Research support: Meat & Livestock Australia
Supervisors: Professor R Whittington, Dr D Begg, Dr K Bosward

Johne’s disease is characterised by a lengthy incubation period, measured in years. It is well known that cows with severe infections commonly shed the causative organism, Mycobacterium paratuberculosis, into their milk, and may also infect their unborn calf in utero. The organism can be isolated from extra-intestinal sites in such cases. There is a smaller body of evidence for this in sheep, but infection of tissues outside the gut is recognised in advanced cases in rams and ewes. The means by which the organism reaches sites outside the gut is uncertain, but may involve transfer via blood. The aim of this project is to identify extra-intestinal transfer of the organism during experimental and natural Johne’s disease infections in sheep.

Ms Ling Zhong
Research support: Meat & Livestock Australia
Supervisors: Professor R Whittington, Dr D Taylor, Dr L Di Fiore

Johne’s disease is a chronic disease affecting ruminants and other hosts. It is caused by Mycobacterium paratuberculosis (Mptb). The events leading to clinical disease are complex and poorly understood but obvious signs of disease are seen only in adult animals. The genome sequence of the causative organism was recently published and this has triggered a dramatic interest in genomics and proteomics to elucidate mechanisms of disease. During this study a range of genomic and proteomic techniques will be applied to study the early stages of infection of sheep with this organism, and to contrast findings with those occurring later in the disease process. This information will be used to design improved diagnostic tests and disease control strategies.

Ms Satoko Kawaji
Research support: Endeavour Japan Post Graduate Research Scholarship and Meat and Livestock Australia.
Supervisors: Professor Richard Whittington, Dr Deborah Taylor

Satoko’s research is focusing on the detection of Mycobacterium avium subsp. paratuberculosis (MAP) in ovine faeces by direct quantitative PCR. MAP is a causative agent of Johne’s Disease (JD), which is a chronic progressive enteritis of ruminants prevalent worldwide and causes significant economic damage to livestock farming. Although one of the gold standard tests to diagnose JD is isolation of MAP from shedding animals by culture, this organism grows very slowly and often takes several months to form a visible colony on solid media. To develop a new diagnostic method faster and more sensitive than culture, a real-time PCR based test is being validated for use on the detection of MAP DNA in ovine faeces. This tool will be used in basic pathogenic studies in sheep and cattle in the second part of the PhD program.

Ms Kate McMaster
Research support: Meat & Livestock Australia.
Supervisors: Associate Professor N Sangster, Dr K Bosward

Haemonchus contortus is one of the most economically important parasites in the Australian sheep industry. In recent years resistance to parasitic drugs has forced both sheep producers and researchers to look for alternative means of parasite control. A better understanding of the host parasite relationship is an essential step in discovering improved control measures. The balance of the host parasite relationship shifts depending on the status of the host, eg age or reproductive status, and how the parasite responds. Studying the development of the protective immune response of the sheep when infected with Haemonchus will enable a better understanding of the host-parasite relationship and should provide the means to measure the development and mechanisms of immunity and resilience to infection. This will indicate whether we can predict or modulate the response towards protection or test the host’s “resistance status” for selection purposes. It is hoped that this investigation will provide producers with another tool to manage parasitic infections with out resorting to anthelmintic.

Ms Jessica King
Research support: Invasive Animal Cooperative Research Centre
Supervisors: Associate Professor Peter Windsor, Dr John Ellis, Dr Peter Fleming and Dr David Jenkins

Neospora caninum is a cyst-forming coccidian protozoan parasite which was first described as causing fatal neurological disorders in dogs and has since emerged as a major cause of abortion in cattle worldwide. It is estimated to cost the Australian dairy and beef industries up to $30 million per annum. Research in NSW has suggested there is a canine-bovine life cycle involved in bovine neosporosis, with many outbreaks associated with the proximity to bush land, where wild canids are at higher densities. However, data to support the hypothesis that wild canids are a source of infection to cattle is lacking and the possible role of foxes and other carnivores including native animals in bovine neosporosis needs investigation. It is also possible that a sylvatic cycle involving wild canids and wildlife similar to that of hydatidosis prevails in areas where N caninum is endemic, with some preliminary studies suggesting infection may be common in some native wildlife, such as possums.
The aim of this study is to gather evidence to test the hypothesis that there is an association between prevalence of N caninum in wild canids and other wildlife, and that in cattle. Faecal, tissue and blood samples from target animals will be obtained from localities adjacent to cattle herds where reproductive problems due to N caninum have been identified, and examined by diagnostic tests including ELISA or agglutination tests, and PCR’s, in habitats adjacent to farms where endemic bovine neosporosis has been diagnosed. These data will enable spatial epidemiological analysis of the prevalence and distribution of N caninum serovars in wild canid and wildlife populations, potentially enabling modeling of neosporosis risk and assisting management of reproductive failure in cattle.

Mrs Kylie Gore
Research support: Australian Post Graduate Award (Industry),
Australian Research Council Linkage Grant,
Northern Territory Government, Darwin Aquaculture Centre and Berrimah Veterinary Laboratory
Supervisors: Professor R Whittington, Mr G Schipp and Dr D Begg

The barramundi aquaculture industry in Australia has been threatened by a significant new viral infection affecting larvae and juveniles of a number of fish species worldwide. Discovered in the last 20 years, nodavirus causes a disease known as viral nervous necrosis (VNN) which can result in mortalities approaching 100% in hatchery-reared larvae. Knowledge of the epidemiology of nodavirus infection in barramundi is currently limited and control of the disease remains elusive. This is further compounded by the lack of sensitive diagnostic tests available. The University of Sydney has teamed up with industry partners in the Northern Territory to investigate VNN and develop sensitive diagnostic assays. With the development of an enzyme-linked immunosorbent assay (ELISA) to detect (i) the presence of nodavirus and (ii) specific antibodies against nodavirus in the serum, nodavirus-free broodstock can then be selected for aquaculture programs. A comprehensive survey of aquaculture facilities will then provide valuable information on epidemiology of the disease and enable development of an integrated disease control strategy.

Mr Paul Hick
Research support: Australian Post Graduate Award (Industry),
Australian Research Council Linkage Grant,
Northern Territory Government, Darwin Aquaculture Centre and Berrimah Veterinary Laboratory
Supervisors: Professor Richard Whittington, Dr D Taylor and
Dr J Humphrey

A research team based at the University of Sydney with industry partners in the Northern Territory has been established to investigate Viral Nervous Necrosis (VNN), a devastating disease of juvenile fish. Caused by a Betanodavirus, VNN has emerged globally in the previous 20 years in many situations where fish are produced in hatcheries. Within Australia, VNN has proved to be an impediment to the development of the barramundi aquaculture industry as a consequence of unpredictable supply of juvenile fish and concerns regarding the dissemination of the virus into wild fish populations.

Comparison of existing diagnostic techniques to new molecular technologies is expected to provide a refined set of tools for gathering epidemiological information about VNN. Investigation of disease pathogenesis will be will be facilitated by a series of infection trials. A survey of wild barramundi populations will determine disease prevalence based on the existing disease control zones within the Northern Territory whilst a survey of wild fish populations will establish disease prevalence in a variety of fish species.

Ms Yvette Miller
Research support: Australian Pork Ltd
Supervisors: Dr T Holyoake, Dr Alison Collins, Mr R Smits

The aim of the project is to reduce antibiotic use on pig farms to make the pork industry in Australia more globally competitive, and to benefit human health by reducing the risk of amplifying strains of antibiotic-resistant bacteria. The projects seeks to: provide extensive training in pig health and production to provide for succession in the Australian pig industry; improve the pre-weaning growth performance of gilt progeny using supplemental milk; identify risk factors that explain why gilt progeny perform poorly, relative to sow progeny; and, develop management strategies to control the risk factors and hence improve the performance of grower pigs.

Mrs Nicole Schembri
Research support: Australian Biosecurity CRC for Emerging Infectious Disease
Supervisors: Dr Trish Holyoake, Dr Jenny-Ann Toribio

Exotic diseases such as foot and mouth disease may enter Australia through anthropogenic means, most likely closely associated with large urban centres. Pigs in peri-urban settings may be the initial focus of a disease outbreak. This project involves reviewing current pig keeping legislation, educating producers about awareness of abnormal behaviours and clinical signs of disease, reviewing current extension materials and methods, as well as possible alternative animal identification technologies. The information obtained will be used to locate peri-urban pig producers, identify and track pig movements, and improve producer awareness of disease.

Mr Sam Hamilton
Research support: Australian Biosecurity Cooperative Research Centre for Emerging Infectious Disease, Department of Agriculture, Fisheries and Forestry
Supervisors: Dr Jenny-Ann Toribio, Dr Graeme Garner


Highly pathogenic avian influenza (HPAI) poses a serious threat to the Australian poultry industry and potentially also to public health in this country given recent occurrence of human deaths in south-east Asia. Disease modelling, by evaluating the behaviour of this disease under Australian conditions and the effect of alternate control strategies, is recognised as an important tool to support Australia’s preparedness for an incursion of this disease in our poultry population. This project, working with government and industry, will develop a new model of the spread of HPAI within the Australian intensive poultry population to address issues associated with assessing the extent, impact and control of disease outbreaks. This model will be used to enhance national disease planning and will provide technical underpinning for Australia’s outbreak management policy in the event of an outbreak of HPAI.

Mr Richard Shephard
Research support: Meat & Livestock Australia,
Australian Biosecurity CRC
Supervisors: Dr JA Toribio, Dr Peter Thomson,
Dr Angus Cameron, AusVet

Remote extensive cattle grazing regions of Australia are characterised by large herds, long distances between properties and communities, little requirement for veterinary input, sparse veterinary services and inadequate surveillance coverage. This project investigates the potential for syndromic disease information to be captured by lay observers using the disease diagnostic program BOVID, analysed to compare prevalence of symptoms across regions and time periods, and used to determine the relative likelihood of individual disease occurrence. Changes in relative frequencies result in a ‘trigger’, notifying local government veterinary authorities that a given disease syndrome has emerged or changed in frequency, potentially leading to targeted surveillance efforts being focused towards investigation of the syndrome.