Projects

We are accepting postgraduate, honours, and short-term project students.


Please visit or contact Ruiting Lan to discuss your opportunities.


You are also welcome to contact any of our current members.


Projects on the respiratory tract pathogen Bordetella pertussis

Pertussis, commonly known as whooping cough, is an acute respiratory disease caused by B. pertussis . Despite widespread vaccination, pertussis remains a public health burden. Australia is currently experiencing a prolonged pertussis epidemic, with nearly 40,000 cases at its peak in 2011.



Project 1: Proteomic analysis of B. pertussis during in vivo attachment to human respiratory epithelial cells
The current resurgence of pertussis has spurned renewed interest in understanding the pathogenesis of B. pertussis infections. Currently, most proteomic studies have been performed under in vitro conditions which may not reflect the proteomic changes of the bacterium during infection. The aim of this project is to elucidate key proteomic changes which contribute to colonisation when B. pertussis cells are co-cultured with human respiratory epithelial cells. This project involves proteomics, mass spectrometry, tissue culture and bioinformatics analysis.


Project 2: Elucidating essential genes in B. pertussis under infection relevant conditions
To combat the global re-emergence of pertussis, an improved pertussis vaccine is required to better target current strains. The simplest strategy to improve the vaccine is the addition of new antigens. Essentials genes required for infection would be ideal targets to prevent adaptation as these genes cannot be inactivated. This project will use TraDIS to elucidate the essential genes in B. pertussis under different infection relevant conditions. TraDIS is a technique that combines transposon mutagenesis and genome sequencing to determine the essentiality and function of every gene under specific conditions.


Projects on genomic methods studying bacterial pathogens

In the past decade Next generation sequencing (NGS) has provided unprecedented amounts of genomic data for many pathogenic bacterial species. NGS has been increasingly employed to prospectively identify and track outbreaks as well as to define and examine large scale population structures and trends. NGS has major advantages over other pathogen typing methods as it promises a standardised universal solution for high-resolution typing. We have developed new bacterial typing methods that utilise whole genome sequencing data to cluster bacterial strains into groups of related isolates.


Project 3: Applying new genomic methods to Neisseria gonorrhoeae, an important sexually transmitted infection.
N. gonorrhoeae causes the sexually transmitted infection, gonorrhoea and infected an estimated 87 million people in 2018. The number of isolates with whole genome sequencing data available has grown to over 13,000 and is increasing rapidly. This project will develop the previously described typing methods for this species with an aim to provide insights into the spread of antimicrobial resistance and an overview of N. gonorrhoeae population structure.


Project 4: Applying new genomic methods to Staphylococcus aureus typing.
S. aureus, commonly known as golden staph, is normally a commensal bacteria that can cause a range of infections from skin lesions to severe bacteraemia and is especially common in hospital acquired infections. Methicillin resistance S. aureus (MRSA) is a major threat to global health due to its high resistant to drugs normally used to treat the bacterium. There are nearly 60,000 S. aureus isolates with NGS data publicly available. This project will use these data to develop the previously described genomic methods to create a standardised system for examining the population structure of S. aureus and the spread of antimicrobial resistance.