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Professor Julian Parkhill - Big beautiful bacterial genomes - 2019

Infectious Talk : An interview with Professor Julian Parkhill, a member of Cambridge Infectious Diseases Interdisciplinary Research Centre. Professor Julian Parkhill left the Sanger Institute in 2019 to become Marks and Spencer Professor of Farm Animal Health, Food Science and Safety, Department of Veterinary Medicine, University of Cambridge. Allyson Walsh, August 2019.

Infectious Talk: Professor Julian Parkhill 

The research of my Group focuses on the evolution of bacterial pathogens; their origin, transmission and adaptation to selective pressure. We primarily use genomic and phylogenetic approaches to address these, and over the last few years the group has used large-scale population genomics to identify the global origin and routes of spread of many human and animal pathogens. Overlaid on the phylogeny, we look for signatures of adaptation to the host, to antibiotics and to vaccine pressure, most recently developing bacterial genome-wide association approaches to identify genetic determinants responsible for this adaptation. In addition to informatics approaches, we develop and apply genome-wide experimental tools, studying interaction with the host and antimicrobial resistance mechanisms. We have an interest in metagenomics, currently studying the microbiota in the gut, the lung, the nasopharynx and the placenta (which doesn’t have one). We often work at an international level, with many collaborations in Low- and Middle-Income countries.

Our work has clear translational benefits for tracking transmission at the hospital level and more broadly. To enable this translation, we have been collaborating with local hospitals, and national and international health-protection agencies, as well as the commercial sector.

 

1. Let's start with your background. How is it exactly that you ended up enthused by bacterial pathogens in the first place, and what big questions you are seeking answers to?

I first got excited by bacterial genetics as an undergraduate. The precision with which you could understand genetic regulatory circuits really fascinated me. After finishing my PhD in this field, I was warned off bacterial genetics, as I was told there was no money for research in the area – everyone was working on eukaryotes. The first bacterial genomes changed that, and opened up the field again. Being able to describe the complete genome of an organism was amazing, and I looked for opportunities to move back into bacterial genetics.

2. You've watched a lot of technology coming through. Which technology excites you the most for the future?

Watching technologies come and go has taught me that it always takes much longer for any particular technology to become practicable than the companies promise. Also that different technologies have different strengths and weaknesses; there is rarely a “killer app” that does everything best. The technology I am most excited for is the one that doesn’t exist yet – a point-of-care sequencer for routine real-time diagnostics and antibiotic resistance prediction. So that next time I go to my doctor he doesn’t say: “I don’t know what you’ve got, or what it’s resistant to, but I’m going to give you this antibiotic based on my best guess”. We’re not there yet, but I’m confident we will get there.

3. You have recently moved from the Wellcome Sanger Institute to take up a new role as Marks and Spencer Professor at University of Cambridge. What key aspirations do you have for your new role? 

I have long been interested in the emergence and spread of drug resistant bacteria. For the most part (and with some honourable exceptions), this is mainly looked at from the separate perspectives of humans or animals. One of the things that attracted me to the Vet School is their focus on One- Health approaches, looking at the interfaces between humans and animals and the environment, and I think there is a lot that can be done in this area. Aside from research, I am looking forward to being more involved in teaching.

4.  Who are the members of your group and what are they each working on?

The group can be quite amorphous, and fuzzy round the edges, but at the core, Andries van Tonder is working on bovine tuberculosis, Marcus de Goffau is working on the microbiota of the gut and placenta (which doesn’t have one), Sebastian Bruchmann is working on Klebsiella interactions with macrophages, Annapaula Correia is working on novel protein antibiotics and Zannah Salter is studying a novel bacterium in the throat (Candidatus Ornithobacterium hominis). Many people in the group are also members of other teams, including Chris Ruis, who is analysing the emergence of Mycobacterium abscessus in the CF community and Aaron Weimann, who is analysing the regulatory circuits of Pseudomonas abscessus, both of whom also work with Andres Floto, and Narender Kumar, who is working on human tuberculosis in India and works with Sharon Peacock. There are also some shared PhD students, including Neil MacAlasdair (Neisseria meningitidis) and Sam Kidman (P. aeruginosa), and others who visit regularly such as Catherine Ludden, Francesc Coll and Kathy Raven, all of whom work with Sharon on various aspects of antibiotic resistance and bacterial genomics.

5. You are a member of Cambridge Infectious Diseases Interdisciplinary Research Centre - what do you think about the value of interdisciplinary research?  Can you share any examples of projects you are working on that involves a mix of disciplines?

Interdisciplinarity is essential to much of our work. The size of the data sets we work with means that collaborations with statisticians and mathematicians are essential, and we work extensively with clinicians to help us understand our data and implement the findings of our research. I believe interdisciplinary research is becoming the norm, and science in Cambridge will be the better for it.

6. Last year you took part in Pint of Science. What at motivated you to give up a valued evening at home to engage with the public?

Fundamentally, the public funds us and our research, and the work we do will have little long-term consequence if it is not translated into societal benefit, which in turn requires understanding and acceptance from the public. Anything we can do to help this is valuable. I also feel that working out how to explain your research to the lay public helps you understand and contextualise it better yourself. Also, you get to talk science and drink beer, which is always good.

7. We’re at a time when truth is at a premium, where facts need to be established and form the basis of public policy debate – can you share any examples of how your research is impacting policy?

At a very practical level, the work we did with Andres Floto demonstrating transmission of M. abscessus between people with CF led to the changing of clinical guidelines on the management of these patients, and fed into the design of the new Royal Papworth Hospital. More broadly our work with Sharon Peacock and others demonstrating that genomics can be used rapidly to predict antibiotic resistance should lead in the longer term to changes in antibiotic prescribing policy and help with antibiotic stewardship.

8. Obviously, you have done a myriad of things. But what are the one or two things that you are most proud of?

My daughters, also known as Thing 1 and Thing 2.

9. How do you take care of your mental and physical well-being – both during the day at work and outside of work?

I try to keep fairly strict separation between work and home: I don’t work at weekends, and I never read e-mail on holiday. It is essential to be able to switch off from work, and if things don’t get done, they don’t get done. Life is more important than work. Physically, I use a standing desk in my office, and I have taken up running, though not very well.

10. I nearly became an archaeologist instead of a biologist. If you had taken a different career pathway- what is the most likely alternative job you would be doing now and why?

If my teachers had had their way, I would have studied medicine. If my career had taken a slightly different route, I suspect I would have gone into computing or perhaps run a pub.