30 April 2024

Professor Ben Howden, from the University of Melbourne at the Doherty Institute, is a renowned clinician researcher whose dedicated focus on public health microbiology, genomics and antimicrobial resistance (AMR) has impacted thousands of lives.

Genomics—technology to sequence the whole genome of an organism—has been Professor Howden’s forte. During his PhD in the early 2000s, he was the first to sequence Staphylococcus aureus genomes in Australia.

His work since has not only revolutionised the way we understand and combat bacterial pathogens but has also played a pivotal role in shaping public health surveillance and response strategies around the world.

This story is part of our 10 of the Best -Fifteenth edition. 10 of the Best is an annual NHMRC publication, showcasing 10 NHMRC-funded health and medical research projects. See more 10 of the Best.

‘We’re seeing significantly increased antibiotic resistance around the world and in Australia. Genomic technologies allow us to deeply understand how bacteria are becoming resistant to antibiotics and how those resistant bacteria are spreading, for example, in hospital settings,’ said Professor Howden. 

In 2016, he began a NHMRC Practitioner Fellowship to improve prevention, tracking and treatment of major human bacterial pathogens. He pioneered the use of genomics in public health microbiology to address crucial knowledge gaps and drive innovation in disease surveillance and outbreak management. 

As a result of the work conducted in the Fellowship, Professor Howden helped change public health microbiology practice in Australia, enabling the country to be much better prepared for the COVID-19 pandemic.

‘I think what we've seen now through the pandemic is that the use of genomic technologies has become mainstream,’ said Professor Howden.

‘We've really revolutionised the use of pathogen genomic technologies in Australia now. We've helped government agencies build national systems for integrating genomic data from all the public health laboratories around the country to better spot and understand outbreaks for key public health pathogens, including COVID-19.’

‘We also supported 8 countries in the Pacific region with their COVID-19 response through analysing their samples and I’m proud of that,’ he said.

What’s the impact? Fewer infections, fewer people having their lives affected (or lost) and saved taxpayer money as health management costs have been reduced.

Achieving success wasn’t a straightforward process, according to Professor Howden who said he’s fundamentally changed the way he does research.

‘I had to change my mindset around the way I did my research from just being in a lab and thinking about things at the laboratory level to implementation, partnerships, data governance and evaluation. So, it's been a big transition,’ he said.

‘The fact that we had a strong foundation of this research on genomics allowed us to take a leadership role on the COVID-19 genomics for Victoria and Australia. The timing meant we were “ready to go” in Australia. We had one of the best responses to COVID-19, from a genomic point of view, in the world because of that,’ he said.

‘This type of research is only possible when you've got great partnerships locally, nationally, internationally, and also with end users, like our public health units, particularly the Victorian Department of Health.’

Next steps

Professor Howden and his collaborators have established the Centre for Pathogen Genomics at the University of Melbourne (Doherty Institute) with a focus on international partnerships. Appropriate sharing of data and the implementation of cutting-edge technologies will play a crucial role in disease surveillance and response in the future.

‘We're taking that next step of working internationally to foster relationships with other labs in the public health environment to implement genomic technologies and understand how we use it in a meaningful and cost-effective way,’ he said.

Chief Investigator (CIA)

Professor Ben Howden

Administering Institution

University of Melbourne

Research title

Improving prevention, tracking and treatment of major human bacterial pathogens 


Associate Professor Torsten Seemann

Associate Professor Norelle Sherry

Dr Stefano Giulieri

Dr Claire Gorrie

Dr Romain Guerillot

Dr Glen Carter

Dr Patiyan Andersson

Ms Courtney Lane

Dr Jason Kwong

Dr Sarah Baines

Dr Anders Gonçalves da Silva

Ms Chantel Lin

Ms Tuyet Hoang

Dr Danielle Ingle

Dr Jean Lee

Dr Angeline Ferdinand

Ms Ashleigh Hayes

Ms Adrianna Turner

Ms Lucy Li

Dr Susan Ballard

Ms Marion Easton

Dr Wei Gao

Dr Charlie Higgs

Grant information



Practitioner Fellowships