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Q: What is your role at the Doherty Institute and how does it fit in with the work of MDU PHL?

I am a Senior Project Manager working mainly on public health pathogen genomics and its integration into public health surveillance and response. As Victoria’s main genomic public health laboratory, MDU provides microbiological services to identify and investigate pathogens that pose a public health threat. With the introduction of next-generation sequencing technology, the ability to generate the highest-resolution and characterisation of pathogens to better understand their behaviour and transmission has transformed the way we operate as a public health laboratory, enhancing our ability to inform public health surveillance and control.

Transitioning from traditional laboratory methods to pathogen genomics is not a simple task and introduces a raft of new systems and processes that need to be in place to reap the full benefits. MDU has been ahead of the curve, investing early in establishing the technologies and expertise in pathogen genomics making it one of the leading genomics laboratories in Australia. My role is to facilitate the transition of using pathogen genomics as seamless as possible for all stakeholders involved, including technical, government and organisational parties, by coordinating and managing the increasing number of pathogen genomics projects that MDU leads within Victoria and nationally, as the coordinators of the Communicable Diseases Genomics Network, a national network comprised of genomics public health laboratories across all jurisdictions in Australia and New Zealand. 
 

Q: Your work has a focus on public health genomics and improving communicable disease surveillance, response and control. What initially attracted you to this field?

Being able to contribute to protecting the health of others is what attracted me to public health and pathogen genomics is the future in doing this using the best technology available. The revolutionary aspect of the technology and its ability to translate directly for public health benefit was incredibly fascinating to me. Despite not being a scientist, I felt that there was a gap in translating how pathogen genomics has transformed public health microbiology practice and how it could be integrated more broadly into public health policy and systems. Having worked in the Commonwealth Department of Health previously, I wanted to bridge the gap between the technical experts producing ground-breaking work to the policy decision-makers who can invest in implementing this capacity so that is equitable and accessible to the population.
 

Q: Much of your work focuses on pathogen genomics. Can you tell us more about this area and why it’s important?

Pathogen genomics to me, is broken down into three key steps:

1. The genomic sequencing of the sample which happens in the laboratory and provides you with the raw sequence data.
2. The bioinformatics analysis which is the handling, transfer and analysis of the sequence data.
3. The genomic epidemiological interpretation of the analysis for public health purposes including identification and detection of transmission, clusters and outbreaks.

Pathogen genomics is important because it gives insights into the characteristics of the pathogen that enable more precise identification of the pathogen that may be causing a disease and improving the accuracy of the outbreak investigation, it reveals whether the pathogen is resistant to antibiotics that may have been prescribed to treat a patient and for many pathogens, it is more efficient allowing public health responses to be implemented faster, preventing further spread of infection.
 

Q: What projects are you currently working on and does it relate to COVID-19?

At the moment all my projects are somewhat related to COVID-19 but the four main projects I am currently working on include:

1. The development of a microbial genomics service in Victoria, funded by the Victorian Department of Health and Human Services that aims to implement whole-genome sequencing and analysis of key priority bacterial and viral pathogens in MDU and the Victorian Infectious Diseases Reference Laboratory (VIDRL).
2. A Medical Research Future Fund (MRFF) COVID-19 research project to address COVID-19 diagnostics that consists of four streams, each aiming to expand and enhance Australia’s laboratory testing capacity while maintaining high-quality and robust diagnostic results.
3. The national implementation of AusTrakka, a public health laboratory platform developed within MDU and the Communicable Diseases Genomics Network which will facilitate genomics data sharing and analysis between public health laboratories for a broad range of bacterial and viral pathogens of public health significance.
4. Soon another MRFF COVID-19 research grant to track COVID-19 in Australia using genomics, a project consisting of four research questions that each aim to allow a better understanding of the behaviour, spread and evolution of the virus.
    

Q: What do you feel are the biggest challenges in responding to the pandemic?

I feel the biggest challenges in responding to this pandemic have been around communication and time. With so many parties involved and impacted by the pandemic, the communication channels aren’t as clear and this can range from a high-level between experts and decision makers, all the way to having team meetings on Zoom. I mentioned ‘time’ because day in and day out, you can see how hard everyone is working to address this pandemic in the best way possible. Unfortunately, it can be very reactive to address an urgent need without taking or having the time to strategically think through a controlled and measured approach to responding in an effective way. I’ve certainly caught myself in this position many times and am making a conscious effort to think it through.
 

Q: When you’re not working in the laboratory, what are you getting up to in isolation?

I am never really in the lab, unless I am there to pick someone’s brain, but otherwise I am working most nights than not, while listening to records. Though I don’t think I’m alone in this.