Infectious Disease Genomics
Introduction
We are a multi-disciplinary group using cutting-edge genomics techniques to address some of the most pressing problems in Infectious Diseases. This encompasses a variety of pathogens ranging from the most problematic bacteria encountered in clinical settings globallyto viral pathogens such as SARS-CoV-2, and an end-to-end approach from fundamental discoveries to translation and clinical implementation.
We are ideally positioned within the Department of Infectious Diseases, Alfred Health and Central Clinical School, Monash University with laboratory facilities on-site, including robotic sample handling and a wide range of sequencing equipment, and have close integration with the clinical activities of the Department. This allows us to work ‘bench-to-bedside’ by ensuring scientific developments translate into clinical practice, but also ‘bedside-to-bench’ where unmet clinical needs are identified through our daily practices, guiding our research activities to potential solutions.
Antimicrobial resistance (AMR) is a core interest for our group. While it is often identified as a global health crisis, we experience it on a daily basis in the care of our patients within the hospital system. We are therefore passionate about applying genomic tools to better understand AMR epidemiology and mechanisms of AMR spread, with the ultimate goal of developing new tools and interventions to address this critical health challenge.
We are also excited about leveraging new technologies in our work. Our group has a particular focus on the advancements in long-read (eg. Oxford Nanopore) sequencing and its clinical application in a hospital context, as well as population level genome-scale metabolic modelling. These interests have led to development of new computational methods. Artificial intelligence is also a key interest, particularly in how we can use genomic data in combination with proteomic and clinical data to improve our predictions regarding phenotypes and clinical outcomes. We are actively studying innovative techniques such as direct from sample sequencing and metagenomics.
Find out more:
Programs and services
Fundamental Microbial Genomics Program
Our fundamental science projects generate the knowledge that underpins our translational research and informs the design of effective pathogen control strategies. From the application of genomic epidemiology and evolutionary analyses to understand how bacterial pathogens and AMR spread in the hospital setting; to the use of statistical and machine learning approaches to identify genomic virulence markers. We leverage bacterial and viral isolate collections from the Alfred Hospital to explore local pathogen dynamics and tailor our research to the most salient problems.
Translational Microbial Genomics Program
Our translational projects are a bridge between fundamental research and application in the clinical setting. These projects address issues such as genomic epidemiology and understanding AMR mechanisms, with a view to ultimately impacting clinical practice. We identify and address key roadblocks; develop and test streamlined protocols and computational methods; and generate evidence to demonstrate the value of these approaches for our clinical partners.
Clinical Infectious Diseases Genomics Service
We are working to implement genomics approaches into our standard clinical practice, whether this is in the management of individual patients or for shaping our approaches to infection prevention and control. This work leverages the knowledge and approaches developed in our Fundamental and Translational Microbial Genomics Programs to help develop robust workflows and practices for the clinical space, including in outbreak investigation, pathogen surveillance and personalising infectious diseases therapies.
Meet the team
Principal Investigators
Computational Biologists
Other staff and students
ID Genomics Staff Scientists
- Jess Wisniewski (Senior Scientist/Laboratory Manager)
- Taylor Harshegyi
- Matthew Parker
- Quynh Doan
- Tiffany Hong
PhD students
- Helena Cooper
- Hugh Cottingham
- Andy Nguyen
- Kalani Paranagama
- Yashpal Ramakrishnaiah
Flagship projects
SuperbugAI
This MRFF-funded project aims to develop the necessary tools to transform genomic and healthcare data into systems that help fight the rise of AMR in our hospitals. This will be done through development of an integrated genomics, digital health and machine learning system for the rapid diagnosis and precise treatment of AMR infections, as well as for powering a real-time AMR infection prevention response platform.
Clinical metagenomics: MetaGP
We are a key site for this project, which focuses on the development of wet and dry-lab protocols for detecting a pathogen directly from a patient sample. This would drastically reduce the turnaround time for diagnosis of infectious diseases from days to hours. This work is being performed in collaboration with multiple sites across Australia as an MRFF-funded project led by the University of Melbourne. Our aim for this research program is to have fully accredited metagenomics workflows to be embedded directly in our clinical workflows.
Clinical applications of long-read sequencing
Through this research program, we aim to transform the way we track and respond to AMR infections and prevent their spread in healthcare. We have developed a technical pipeline focusing on Oxford Nanopore sequencing for detecting bacterial resistance determinants and isolate relatedness, which will allow us to diagnose AMR infections early and also understand if outbreaks are occurring in the hospital setting.
Unravelling Clinical Carbapenem Resistance in an Australian Setting
We are using innovative genomic technologies to dissect the rise and spread of carbapenemase-producing organisms in the Australian hospital setting. Using a collection of bacterial isolates dating back >15 years and ongoing surveillance, we study how carbapenem resistance has evolved, in particular through use of long-read approaches to perform analysis of mobile genetic element dynamics and interspecies spread.
Genomic surveillance of Klebsiella pneumoniae to inform vaccine design
We are developing genomic tools to predict Klebsiella surface antigens, and apply these tools to large genome datasets in order to inform the design of novel vaccines targeting K. pneumoniae.
SARS-CoV-2 Genomics in Hospital Clinical Settings
There is an urgent need to integrate the insights of SARS-CoV-2 genomics into patient care and outbreak response pathways. We are developing and implementing an on-site sequencing platform to inform individual patient management in real-time through rapid detection of SARS-CoV-2 variants-of-concern, detection of in-host SARS-CoV-2 evolution and outbreak detection.