The Univeristy of Melbourne The Royal Melbourne Hopspital

A joint venture between The University of Melbourne and The Royal Melbourne Hospital


04 Sep 2020

Meet the team: Dr Danielle Ingle advances microbial genomics research

Dr Danielle Ingle, Australian National University and University of Melbourne

Can you introduce yourself and your role at the Doherty Institute?

I am an early career researcher working in microbial genomics. I am currently appointed at The Australian National University (ANU) and hold an honorary appointment at the University of Melbourne, where I work closely with the Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL) at the Doherty Institute.

I will be formally moving to the Department of Microbiology and Immunology at the Doherty Institute at the start of 2021 to begin my NHMRC Emerging Leadership Fellowship.

What are you currently working on?

Enteric bacterial pathogens have long represented a significant global public health threat. Compounding this problem is the emergence of widespread multidrug resistance to standard antimicrobial therapies. My research focuses on understanding the evolution, epidemiology and virulence dynamics of these pathogens, which include pathotypes of Escherichia coli, Shigella species and serovars of Salmonella enterica. My program of research integrates rapidly advancing genomic analyses with population modelling, molecular microbiology and epidemiology. This will provide novel conceptual frameworks to better understand these pathogens, and to open up avenues to translate these findings into public health spaces.

What initially attracted you to the field of science your area of expertise?

Microbial genomics sits at the interface of microbiology and computational biology and has revolutionised basic research and public health of bacterial pathogens. During my PhD at the University of Melbourne, supervised by Professor Roy Robins-Browne and Professor Kathryn Holt, my project took an unexpected but excellent twist. Taking advantage of new sequencing technologies, my PhD became largely computational. This was a great opportunity and, while it did involve a steep learning curve, I really enjoyed the scale at which big research questions could be posed that underpin the evolutionary dynamics within bacterial populations that were previously not possible.

How does this contribute to Australia and the field of science?

In the past decade, microbial genomics has fundamentally altered both research and public health surveillance of enteric bacteria. In my current role, with ANU and the University of Melbourne, I am embedded at MDU PHL, led by Professor Benjamin Howden and Professor Deborah Williamson, and investigate the changing epidemiology and outbreak dynamics of enteric bacteria. My work has had significant translational outcomes for public health. These includes providing evidence for public health advisories for cases of shigellosis in Victoria due to changing outbreak patterns. Additionally, I have led the development and implementation of a sequence-based typing scheme for E. coli that replaces traditional wet lab approaches at MDU PHL, which is an international leader in the translation and implementation of public health genomics.

What do you see as the biggest scientific challenges in your area of work?

There remains much we do not understand about enteric bacteria. These pathogens constantly evolve and adapt, evidenced by the widespread emergence of antimicrobial resistance. This requires novel paradigms and new investigative tools. Sequencing technologies have opened up a realm of new research avenues, and to explore these questions requires the new methods to be developed that provides for the synthesis and analysis of extremely large scale and increasingly complex datasets. While this represents one of the biggest challenges, it is an equally exciting research space; the field is fast-paced and highly collaborative, and has impacts in basic research, clinical and public