Boosting pathogen genomics in Australia

The immense benefits of including pathogen genomics into public health strategy have never been as clear as they are now during the COVID-19 pandemic response. Two significant Doherty Institute projects intend to keep that momentum going.

Professor Deborah Williamson working in office

A national approach to preventing and controlling infectious diseases and antimicrobial resistance (AMR) through the use of whole genome sequencing will be a gamechanger for the field of pathogen genomics and public health in Australia.

Through genomic sequencing, we can see how pathogens are changing and spreading through mapping even single changes in the genetic code.

In October 2020, the Commonwealth Government’s Medical Research Future Fund backed two projects at the Doherty Institute with a total of $17 million for the prevention and control of infectious diseases and AMR.

The Australian Pathogen Genomics Program (AusPathoGen) (approximately $10 million) will implement and evaluate a nationally synchronised approach to public health pathogen genomics with a real-time genomic analysis and reporting platform to facilitate rapid and coordinated responses to infectious disease.

This program will be led by University of Melbourne Professor Benjamin Howden, Director of the Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL).

Professor Howden says AusPathoGen would integrate genomics practices and information sharing across all states and territories across four areas of national need – respiratory and vaccine preventable diseases, foodborne diseases, sexually-transmitted infections and AMR.

“Through AusPathoGen, health departments across Australia and Commonwealth communicable diseases control agencies will have access to cost-effective genomic technologies across a unified platform that will enable them to rapidly identify, communicate and prevent the spread of infectious diseases and AMR,” he says.

“The program will ensure harmonised and equitable public health responses across jurisdictions including regions traditionally lacking access to emerging technologies.”

The second program, META-GP, will be led by University of Melbourne Professor Deborah Williamson, Director of Microbiology at The Royal Melbourne Hospital and Deputy Director of MDU PHL at the Doherty Institute, and will deliver a clinical metagenomics platform for Australia.

Clinical metagenomic next-generation sequencing (mNGS) is a transformative approach in microbial diagnostics and patient care, because it can be used to detect and characterise all known pathogens – bacterial, viral, fungal, parasitic – in one single test.

The META-GP program will develop and implement clinical metagenomic diagnostics for infectious diseases in Australia.

Professor Williamson explains that metagenomic next-generation sequencing is an emerging technology that enables detection of pathogen genetic material directly from clinical specimens in real time.

“By the end of the META-GP program, Australia will have the first accredited, nationally-accessible network of laboratories that can apply metagenomic approaches in patient care,” she says.

Professor Ben Howden and his genomics team
Professor Deborah Williamson
Professor Deborah Williamson working in office

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