Genomics of Golden Staph: Discovering genomic markers of transmission of Staphylococcus aureus in hospital settings


An opportunity exists for a PhD candidate to undertake work on the molecular epidemiology of Staphylococcus aureus infections in hospitals. Elements of the PhD project may include:
• Development of a rapid genotyping system, which will be used to rapidly detect transmission of S. aureus in the hospital setting.
• Performance of whole genome sequencing on selected isolates
• Analysis of results of whole genome sequencing to confirm chains of transmission
Experience and skills will be gained in molecular diagnostics of highly significant nosocomial pathogens, including next generation sequencing and bioinformatics analysis of whole genome sequencing data.


Dr Matthew O’Sullivan

Research Location

Westmead - Sydney Emerging Infections and Biosecurity Institute

Program Type



The PhD project will be part of a larger, NHMRC funded project commencing in 2014 in which we will modify an existing methicillin-resistant Staphylococcus aureus (MRSA) typing system to make it suitable for the surveillance of methicillin-susceptible S. aureus (MSSA). We will implement this routinely, alongside MRSA typing, at three teaching hospitals with a high incidence of nosocomial S. aureus colonisation and infections. We will compare and contrast the epidemiology of MSSA and MRSA, and determine the burden of MSSA infections, shown to be are due to nosocomial acquisition of clones, which have evolved to thrive and spread in the hospital environment (as opposed to those forming part of an individual's normal skin flora). We will observe the impact, on the rates of hospital infection, of rapid notification of observed clusters of MRSA and MSSA transmission, to clinicians and infection control practitioners on the rates of hospital infection.
We will also employ whole genome sequencing (WGS) of selected isolates, selected from outbreaks identified by binary typing and confirmed by epidemiologic investigation. The WGS data will be examined to determine the microevolution of S. aureus strains during outbreaks and during periods of colonisation in individuals. This will enable us to determine the exact chains of transmission occurring in a given outbreak and to establish guidelines for the interpretation of WGS data when used for the routine surveillance of S. aureus outbreaks.

Additional Information

This research will be undertaken at the Westmead Hospital campus of the University of Sydney, within the Centre for Infectious Diseases and Microbiology and the Marie Bashir Institute for Infectious Diseases and Biosecurity. Westmead Hospital is one of the largest hospitals in Australia, and the Centre for Infectious Diseases and Microbiology includes one of the largest public hospital microbiology reference laboratories in the country.
The successful applicant will join the team of current postgraduate students, postdoctoral researchers and academics. In addition to the listed supervisors, the research team includes A/Prof Vitali Sintchenko, A/Prof Sebastiaan van Hal and Dr Nadine Holmes. This research team has strong track records in public health microbiology, infection control, bioinformatics, whole genome sequencing and molecular epidemiology, with strong links to the Infectious Diseases and Infection Control services at Westmead, Blacktown and Royal Prince Alfred Hospitals.
The successful candidate will be supported by a tax-free scholarship in accordance with the NHMRC postgraduate scholarship stipend rates.

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Infectious diseases, microbiology, Bacteriology, Molecular epidemiology, Molecular diagnostics; Infection Control, Typing, genomics, Whole Genome Sequencing, Bioinformatics, Staphylococcus aureus, MRSA

Opportunity ID

The opportunity ID for this research opportunity is: 1847