24 February 2015

Behind enemy lines: a medic goes native among the scientists (Part Three)

Professor Mark Pallen

In my previous post, I talked about how I entered the world of laboratory medicine, first as a clinical academic gaining my MD at Barts, and then doing my PhD at Imperial College.

In this, my final piece, I'll talk about my focus on basic research, the challenges faced by clinical academics and how advances in technology eventually led me back to translational research.

Making a living from basic research

In late 1998, my fellowship finished and I returned to my old job at Barts. The first year back was very exciting, as I got stuck into analysing bacterial genome sequences that were being sequenced at the UK’s new genome sequencing centre, the Sanger Centre.

Through my interactions with the BMJ, I had gotten to know a bright tech-savvy 18-year old, Nick Loman, who was doing a gap year while attempting to get into medical school. I recruited him to work for me for most of that year and together we both gained our exciting first taste of bioinformatics in the genomics era. This culminated in co-authorship of a Nature paper for me and entry on to the MBChB programme at Barts-London for Nick.

Learning point:

The following year my mentor Soad Tabaqchali was forced to retire and my friend Brendan Wren left Barts for a chair at the London School of Hygiene, so I began to feel restless. I said to my wife that I would start looking for a chair in medical microbiology and that we might have to move to any one of the UK’s two dozen or so medical schools. We both agreed that Aberdeen and Belfast might be just a bit too far to go…

The first chair in medical microbiology to be advertised was, of course, in Belfast and complete with another one of those offers one cannot refuse, I took up a chair at Queen’s University Belfast in late 1999. Having achieved the lofty status of “prof”, I moved back to England a couple of years later, to take up a chair in microbial genomics at the University of Birmingham.

Learning point:

  • You will probably have to move jobs to get promoted. If you want to move fast up the ladder, you may have to move far away. But once you made it up to the next rung, you can move back closer to home.

In the decade that followed, I largely stayed true to my commitment to do basic rather than translational research, developing a grant-funded research programme that spanned genomics, bioinformatics and lab-based research, with a focus on E. coli and a specific bacterial protein secretion system known as type III secretion.

Learning point:

  • Even if you like to work on lots of things, it is good to have one or two in which you are recognised as an expert.

Alongside the academic career, for well over a decade after I had achieved consultant status, I managed to keep first a foothold and then a toehold in clinical practice, just enough to maintain my status as a clinical academic.

However, on both sides of the job there was a creeping tendency to formalise the employer’s expectations of the clinical academic. Clinical governance, the new consultant contract with its formal job plans and revalidation took hold in the NHS, while academic life was governed more and more by the need to get grant money in and high-impact papers out for the Research Assessment Exercise and to improve the student experience for the NSS.

When the new consultant contract finally caught up with me, I was told I was no longer doing enough clinical work to merit clinical academic status under the new scheme, so I would either have to do more clinical work, or I could become a non-clinical academic. I chose the latter option, in the hope of maintaining my competitive research credentials.

Learning point:

  • The powers that be need to put more effort into making it possible for clinical academics to survive in the modern workplace. Universities should recognise their unique contribution and the challenges they face

Back to my roots?

Ironically, just as I was abandoning my clinical academic status, a new development that would lead me back into translational research was setting the world of genomics alight — the arrival of high-throughput sequencing, that is sequencing technologies that made it possible for research groups outside of major sequencing centres to sequence bacterial genomes. I was a keen early-adopter of the new high-throughput sequencing technology for microbial applications, but in the process tracked a path back to my roots in translational research.

In parallel with several others in the field, I showed that bacterial genome sequencing could be used to investigate the epidemiology and evolution of bacterial pathogens, particularly within outbreaks. We focused our efforts on hospital outbreaks caused by antibiotic-resistant Gram-negative pathogens, such as Pseudomonas aeruginosa and Acinetobacter baumannii.

Learning point:

  • Can you become an ex-medic? Or is this a badge you carry for life?

I managed to recruit Nick Loman back into working for me and together we explored the potential of social media in academic life. This led to our involvement in a pioneering crowd-sourced analysis of the genome of an E. coli strain causing a devastating outbreak in Germany, which resulted in a paper in the high-profile New England Journal of Medicine.

The team at Warwick Medical School
We were also early adopters of the new smaller, faster benchtop sequencing platforms—a pioneering comparison of three new benchtop platforms led to a highly cited paper in Nature Biotechnology. And then a second collaboration with a group in Germany allowed us to reconstruct the genome of the E. coli outbreak strain just by sequencing and analysing faecal samples from the outbreak, without having to culture the strain.

I moved to Warwick in April 2013 and shortly afterwards this work appeared in the high-impact journal JAMA. And since I have been here, I have sponsored research projects for two academic clinical fellows.

So here I am in Warwick Medical School, in the Division of Translational and Systems Medicine. But have I moved entirely back to translational clinical work? No, not all!

One of the most promising directions in my recent research concerns the study of ancient DNA. This has involved recovering pathogen genomes from hundreds of years ago, from which one can spin a translational narrative — it really is shedding light on the epidemiology and diagnosis of contemporary infection. However, with Robin Allaby in the School of Life Sciences, we have also been sequencing ancient DNA from 8000-year-old submerged sediment cores to investigate the spread of domesticated plants to the British Isles and it is impossible to call that translational medical research.

Learning points:

  • Am I pleased that I stayed a medical student and a medic in my early career. Yes!
  • Would I recommend a career as a clinical academic? Yes!
  • Is it possible for medics to become scientists too? Yes!
  • And do you make your own luck in this life? Yes!

If you want to know more about my academic journey, take a look at my inaugural lecture on the WMS website or on Storify.

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