Q&A: Dr Tim Walker

Tim WalkerTomorrow, at the Federation of Infection Societies (FIS) 2015 conference, Dr Tim Walker will be giving the British Infection Association’s Barnett Christie lecture about his work on the genome sequencing of Mycobacterium tuberculosis. We asked him about his career and his research.

How would you describe a typical day at work?

At the moment I’ve got a job that is half-academic and half-clinical, so it really depends what day it is.

I’m a medical doctor, a Registrar in a clinical microbiology laboratory in the John Radcliffe Hospital, Oxford, training in microbiology and infectious diseases. Any clinical sample from the patients in our Trust comes to our lab and I act as the interface between the scientists and the clinicians.

In parallel, I’m carving out an academic career; I’ve done a PhD and am part of a large research group at the University of Oxford. I’m either in the laboratory working with TB strains, or at a computer looking at whole genome sequences.

Your first degree was in Politics, Philosophy and Economics. Why did you change fields?

I was very focused on humanities at school and wasn’t particularly interested in science – it was only after finishing my degree that I had to have a think about what I wanted to do for the rest of my life. On the one hand, I would have loved to have been a political philosopher, but I’m not sure I would have made much difference to anyone. I wanted to do something socially useful and medicine seemed like a reasonable way of achieving this. I was extremely fortunate; I got a place in medical school three weeks after deciding it was what I wanted to do – it was a bit of a whirlwind.

At what point did you decide to lean more towards science?

After I’d qualified and done three years of clinical work, I started to think that maybe research was the way forward. I still enjoy clinical work, but I wanted something more.  Being able to jump from one to the other was a very attractive balance and it’s turned out to be a good thing.

What’s your field of TB research?

The unifying factor with all the work we do is Whole Genome Sequencing. We’re taking advantage of new technologies that allow us to sequence large amounts of pathogen genomes rapidly and cheaply.

The initial focus of our work was to use these technologies to better identify person-to-person TB transmission and translate that knowledge into improved public health interventions.

How will Whole Genome Sequencing make a difference in patient treatment? Where do you see this new technology leading?

I think we’re at one of the most important times in microbiology since we first started identifying and cultivating bacteria. We’re now starting to transition away from culture and base most, if not all, of our diagnostic efforts on molecular and sequencing data. TB is leading this field for a number of reasons, not least because it is a relatively slow-growing organism, so culturing creates long delays to obtaining useful clinical data.

We’re working towards a future where we’ll be able to obtain all the information needed to treat a patient and control a disease in a community from a single genomic sequence, rather than from a group of tests that each give out fragments of information.

Once we’ve achieved that it’s not hard to imagine the clinical possibilities. Genome sequencers are getting smaller and cheaper, and the software is getting faster – these can be run from a laptop, which could itself be run by a solar panel. You could take this combination and run it in a low resource setting – where most TB is – and have a point-of-care test that rapidly gives you all the results you want.

Has your medical job helped your scientific one, and vice versa?

Very much so. Because the research we do is so translational the two naturally feed into each other. As a scientist, you want to know what the clinician needs, in order to design something that is user-friendly and that will be used. You also want to create something that people are comfortable using; otherwise they’ll revert to what they’re used to.

As a clinician, your day-to-day activity throws up new questions, which you might want to address through research. If you’re completely detached from clinical medicine it can be difficult to focus on what matters.

What will you be talking about in your lecture tomorrow?

I’m going to present the work my colleagues and I have done over the last five years and how we’ve used sequencing to learn about TB transmission, species identification and drug resistance. The title of my talk is Whole Genome Sequencing of M. tuberculosis: how big a revolution? – given that I’ve said it’s possibly the biggest change in 130 years, I’d say the answer is very!

What does being invited to give this lecture mean to you?

It’s very flattering, but this work is not an individual effort; you can only do it with a large group of collaborators. We’ve got a multidisciplinary team in Oxford, but we also work with researchers elsewhere in the UK and internationally. All the research is a synthesis of thought and effort from many people.

Benjamin Thompson

Image credit: Tim Walker
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Microbes: Martian miners of the future?

ISSIn the world of ‘Emerging Tech’, asteroid mining is an idea that won’t go away. As we whittle away our resources here on Earth, many companies are looking to the orbiting lumps of rock in our Solar System as the next source of valuable metals and minerals. This isn’t as far-fetched as it might seem; for example, NASA is planning a mission to bring back a piece of asteroid and have it orbit the moon in the near future.

Rather than sending a Bruce Willis-esque miner into space to do the extracting, most of these future-gazers are envisioning robots, satellites and lasers to do the work. But might there be another way?

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Arsenic in drinking water: Detecting a silent killer

Today at the Society’s Focused Meeting on Industrial Applications of Metal–Microbe Interactions, Dr Joanne Santini spoke about her group’s research into biosensors for arsenic contamination.

In the3132110060_0a47f6733e_z 1970s, the United Nations (UN) and the World Bank led a movement to improve the quality of drinking water in Bangladesh. At the time, pathogens in dirty surface water were infecting and killing huge numbers of the country’s population, many of them children. The solution was simple – by digging down into underground sources of water and drawing it up through a tube, communities could be given access to clean, safe water. Tube wells were a cheap and effective way to prevent diseases like cholera and dysentery, and would save thousands of lives. Or so people thought.

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The JAM was packed…

CroppedLast month, the Institute for Microbiology and Infection hosted the first Junior Award for Microbiology event, organised to give early-career researchers a forum to talk about their research and network with their peers. In this post, Dr Amanda Rossiter – a Sir Henry Wellcome Postdoctoral Fellow at the University of Birmingham – tells us about the event.

Nearly every academic institution runs a seminar programme, which invites academics from across the world to present their latest research. While this is a very successful model, these programmes are predominantly aimed at senior academics. At the Institute for Microbiology and Infection (IMI), within the University of Birmingham, many junior academics recognised the lack of networking events that were aimed solely at junior academics. To help resolve this issue, I have been working with a group of microbe-lovers at the IMI on a shared vision to revolutionise the way early-career researchers interact. The vision was simple: create an event that motivates early-career researchers to network with their peers. Emphasis was placed on creating a relaxed environment, which would encourage junior microbiologists to let their ‘scientific mojos’ flow, without the intimidating presence of Professors who often, let’s face it, dominate Q&A sessions. Continue reading

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Microbe Talk Extra: Swallowed by a whale

12422148723_4522577c36_bBaleen whales are some of the largest creatures on Earth, but they feed on some of the smallest – tiny ocean-dwelling crustaceans called krill and copepods.

Smaller still are the microscopic organisms that help the whales to digest this vast quantity of prey.

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New to science: October 2015

Each month, the Microbiology Society publishes the International Journal of Systematic and Evolutionary Microbiology, which details newly discovered species of bacteria, fungi and protists. Here are a few of the new species that have been discovered and the places they’ve been found. The full papers are available to journal subscribers, but the abstracts are free to read.

Anarctic-penguin2Microbes! Microbes! Get your newly discovered microbes!

In Tunisia, a team of researchers has identified a new species of Geodermatophilus – hardy bacteria that can withstand things like ultraviolet (UV) radiation, heavy metals and extremely dry environments. Geodermatophilus sabuli is a gamma radiation-resistant Actinobacterium isolated from limestone in the Sahara desert.

Antarctic penguins were the source of another novel species, Planococcus faecalis. As the name suggests, it was isolated from faeces, which were collected from penguin colonies on King George Island. Continue reading

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Microbe Talk: October 2015

6897598788_ca62d442fc_zThis month’s podcast is all about microbes in remote and hostile environments.

Ben spoke to Dr Lewis Dartnell, an astrobiologist from the University of Leicester, about NASA’s recent announcement that there is liquid water on Mars. Lewis told us more about the discovery, and how microbes might be able to survive in this extremely salty Martian environment.

We also hear from Dr Kevin Newsham of the British Antarctic Survey. Kevin spoke to us about his expeditions to the maritime Antarctic, and the impact of climate change on soil fungi and the ecosystems found there.

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