Pathogen-host interactions and resilience on-farm.


This project forms part of an integrated new program on resilience to endemic disease. The project aims to (i) investigate host-pathogen interactions and pathogen evolution for an intestinal bacterial pathogen and an intestinal parasite, (ii) examine how pathogen stains are evolving, the effect this may have on on-farm infection and disease rates, and the potential drivers and risk for the industry into the future.


Dr Karren Plain

Research Location

Sydney School of Veterinary Science - Generic

Program Type



Animal production industries confront a range of constraints to productivity, such as endemic infections, parasitic onslaughts and mixed infections. Pathogen genomics is an integral aspect of the holistic approach to disease control. Pathogens have evolved over time with their respective hosts, leading to ‘success’ in establishing a host niche and preferences. Advances in pathogen genomics can enable more ‘in depth’ interrogation of genetic shifts and diversity within the pathogen.This project aims to investigate host-pathogen interactions and pathogen evolution for the intestinal pathogen, Mycobacterium avium subspecies paratuberculosis (MAP) and the parasite Haemonchus contortus, utillising recent advances in sequencing approaches and increased availability of genomic information. This will enable improved knowledge of how pathogen stains are evolving, the effect this may have on on-farm infection and disease rates, and the potential drivers and risk for the Australian livestock industry into the future. It will also enable a greater understanding of population-level heterogeneity, with the potential to impact decisions regarding disease management at regional and farm levels.

Additional Information

A PhD scholarship valued at $25,000 per annum (tax exempt) is available to an Australian citizen/permanent resident or a New Zealand citizen enrolled full-time for 3 years to participate in this project. However, students are encouraged to apply for Research Training Program (RTP) Stipend and University of Sydney Postgraduate Awards (UPA). International students should apply for RTP for international students. The applicant must be a veterinary, agriculture or science graduate with interest in infectious diseases of animals. The successful applicant will be based at the Camden campus of the University of Sydney, with interactions through existing collaborations with other major research institutes, including the Westmead Institute for Medical Research mycobacterial whole genome sequencing node.This project is part of an integrated new research program aimed at understanding key factors involved in host resilience in the face of endemic infection, linking environmental, pathogen and host interactions. The successful candidate will work within a large multidisciplinary and supportive team.

HDR Inherent Requirements
In addition to the academic requirements set out in the Science Postgraduate Handbook, you may be required to satisfy a number of inherent requirements to complete this degree. Example of inherent requirement may include:

- Confidential disclosure and registration of a disability that may hinder your performance in your degree;
- Confidential disclosure of a pre-existing or current medical condition that may hinder your performance in your degree (e.g. heart disease, pace-maker, significant immune suppression, diabetes, vertigo, etc.);
- Ability to perform independently and/or with minimal supervision;
- Ability to undertake certain physical tasks (e.g. heavy lifting);
- Ability to undertake observatory, sensory and communication tasks;
- Ability to spend time at remote sites (e.g. One Tree Island, Narrabri and Camden);
- Ability to work in confined spaces or at heights;
- Ability to operate heavy machinery (e.g. farming equipment);
- Hold or acquire an Australian driver’s licence;
- Hold a current scuba diving license;
- Hold a current Working with Children Check;
- Meet initial and ongoing immunisation requirements (e.g. Q-Fever, Vaccinia virus, Hepatitis, etc.)

You must consult with your nominated supervisor regarding any identified inherent requirements before completing your application.

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Pathogens, mycobacteria, Parasites, genomics, Infectious diseases, veterinary, animal health, farm animals, Infectious Disease

Opportunity ID

The opportunity ID for this research opportunity is: 2210