PhD Research Students
COMPLETED PROJECTS
Application of molecular diagnostic techniques to epidemiological investigations of Viral Nervous Necrosis (VNN) in barramundi aquaculture
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 R Whittington, Dr D Taylor and Dr J Humphrey
Completed: March 2010
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.
Studies of the Epidemiology and Risk Factors Involved in the Pathogenesis of Acorn Calf Disease in Australia
Peter White
Research Support: Australian Post Graduate Award, Meat and Livestock Australia
Supervisors: Dr J-A Toribio and Professor P Windsor
Completed: March 2010
Acorn calf disease is a congenital chondrodystrophy that has recently caused significant losses to many producers in southern NSW and northern Victoria. Affected calves are born with a range of skeletal deformities and are often stillborn or die soon after birth. Australian outbreaks appear to be associated with years of drought. Similar outbreaks have occurred worldwide, but a cause has never been established.
The University of Sydney, in collaboration with state Departments of Primary Industry and the NSW Rural Lands Protections Boards, and with support from Meat and Livestock Australia, will conduct research into identifying the risk factors for Acorn Calf Disease. A survey of rural veterinarians will assist in establishing the distribution of the syndrome, which it is believed is under reported. A case-control study will be undertaken to identify the risk factors for the disease in Australia, with the aim of providing producers advice to reduce the occurrence of Acorn calves.
Investigating role of wildlife and wild canids in transmission of Neospora Caninum
Jessica King
Research support: Invasive Animal Cooperative Research Centre
Supervisors: Professor P Windsor, Dr J Ellis, Dr P Fleming and Dr D Jenkins
Completed: 2010
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.
Modelling the emergence of avian influenza in the Australian poultry industry
Sam Hamilton
Research support: Australian Biosecurity CRC for Emerging Infectious Disease,
Department of Agriculture, Fisheries and Forestry
Supervisors: Dr J-A Toribio, Dr G Garner
Completed: 2009
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.
Reducing antibiotic usage in pig herds: controlling Lawsonia intracellularis by vaccination, housing and hygiene.
Meg Donahoo
Research Support: Australian Research Council Linkage Grant, NSW Department of Primary Industry, Boehringer Ingelheim
Supervisors: Assoc Prof D Emery, Dr T Holyoake, Dr A Collins.
Completed: 2009
Proliferative enteritis (PE) is an intestinal disease of pigs caused by the intracellular bacteria Lawsonia intracellularis. It is a major profit-limiting disease for pig producers globally and affected herds suffer from reduced growth, diarrhoea and increased mortalities. A new vaccine, Enterisol Ileitis® is now registered for commercial use in Australia as an alternative to antibiotics to control PE in pig herds. The immunology section of this project involves undertaking experiments focussed on improving the efficacy of the Enterisol Ileitis® vaccine under Australian pig management systems and to induce immunity to Australian field isolates of L. intracellularis. Approaches include determining the protective efficacy of the vaccine before weaning, identifying immune correlates associated with vaccine protection and determining an optimal medication-free window for vaccination.
Detection of Mycobacterium avium. Subsp. paratuberculosis in sheep faeces by direct Quantitative PCR
Satoko Kawaji
Research support: Endeavour Japan Post Graduate Research Scholarship, University of Sydney, International Post Graduate Research Scholarship and Meat and Livestock Australia.
Supervisors: Professor R Whittington, Dr D Taylor
Completed: December 2009
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.
Peri-urban regional surveillance for biosecurity for pigs in eastern Australia
Nicole Schembri
Research support: Australian Biosecurity CRC for Emerging Infectious Disease
Supervisors: Dr T Holyoake, Dr J-A Toribio
Completed: 2009
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.
Specialised management of gilts and their progeny
Yvette Miller
Research support: Australian Pork Ltd
Supervisors: Dr T Holyoake, Dr A Collins, Mr R Smits
Completed: 2008
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.
Ovine Johne’s disease – investigating mortality rates, disease transmission and control
Helen McGregor
Research support: Meat & Livestock Australia, NSW Stud Merino Breeders Association, CSL
and proprietors of the study properties
Supervisors: Professor P Windsor, Professor R Whittington
Completed: 2008
OJD infection in Australian sheep flocks continues to cause significant losses due to mortality but losses in the sub-clinical phase of the disease have not been widely investigated under Australian conditions. Estimates to be made in this study of sub-clinical losses include reduction in wool growth and retardation in growth rates and their relationship with the development of clinical disease. This may provide insight into disease pathogenesis. Obtaining an accurate estimate 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.
Genetic and proteomic differentiation of stages of Mycobacterium paratuberculosis infection
Ling Zhong
Research support: Meat & Livestock Australia
Supervisors: Professor R Whittington, Dr D Taylor, Dr L Di Fiore
Completed: December 2008
Johne’s disease is a chronic disease affecting ruminants and other hosts. It is caused by Mycobacterium paratuberculosis. 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 were 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.
Genomic and phenotypic comparison of isolates of Mycobacterium sp. that contain IS900–like elements
Martin McLoon
Research support: Meat and Livestock Australia, NSW Department of Primary Industries
Supervisor: Professor R Whittington
Completed: December 2007
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 discovered 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.
Identification of risk factors for OJD infection-level in sheep flocks
Navneet Kumar Dhand
Research support: University of Sydney International Postgraduate Research Scholarship, Meat and Livestock Australia.
Supervisors: Dr J-A Toribio, Professor R Whittington
Completed: 2007
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.
In vitro survival and dormancy of Mycobacterium paratuberculosis
Sanjeev Gumber
Research support: University of Sydney International Postgraduate
Research Scholarship and Meat and Livestock Australia.
Supervisors: Professor R Whittington, Dr D Taylor
Completed: December 2006
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.
Remote area syndrome surveillance systems for cattle
Richard Shephard
Research support: Meat and Livestock Australia, Australian Biosecurity CRC
Supervisors: Dr JA Toribio, Dr Peter Thomson, Dr Angus Cameron
Completed: November 2006
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.
Comparison of the S and C strains of Mycobacterium paratuberculosis at genome and proteome levels
Ian Marsh
Research support: Meat and Livestock Australia, NSW Department of Primary Industries
Supervisor: Professor R Whittington
Completed: March 2006
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. The differences observed thus far are greater than were previously suspected from existing restriction fragment length polymorphism analysis data, include major genetic deletions, and may be related to phenotype.
A study of the biological and financial impact of OJD in affected sheep flocks in NSW
Russell Bush
Research support: Meat and Livestock Australia.
Supervisors: Dr JA Toribio, Dr P Windsor, Dr S Webster
Completed: December 2005
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.