Timothy Walker

Graduate Research Prize Winners Spring 2014

Timoty Walker

I read Politics, Philosophy and Economics at Oxford before studying medicine in London, and eventually migrating back to Oxford where I am a specialist registrar in Infectious Diseases and Microbiology. I am in the final year of the DPhil in Clinical Medicine looking into the application of whole genome sequencing for the diagnosis and control of tuberculosis.

The main aim of my research has been to understand how whole genome sequencing data can be used to detect transmission of tuberculosis in a community and thereby better direct public health interventions. By analysing the genetic distances between tuberculosis genomes from historical outbreaks, I devised a metric for identifying transmission between future cases. The results have already played a significant role in helping Public Health England decide to adopt the method on a national level to improve routine diseases surveillance.

I have since applied the method to a population study of Oxfordshire – the first of its kind using whole genome sequencing technology. Assessing all patients over a 6 year period I was able address one of the key questions Public Health England have – the relative contribution of overseas born patients to local transmission. I found that whilst most patients diagnosed in Oxfordshire were born in an endemic country, a greater proportion of patients born in the UK were involved in local transmission. I am currently repeating the study in Birmingham, a city with more tuberculosis cases and transmission than Oxfordshire.

The success of these studies has allowed me to go on to look at the potential of whole genome sequencing technology in a routine diagnostic setting, both for pathogen identification as well as the prediction of drug resistance. With sequencing technologies rapidly advancing, the knowledge-base this research is contributing to has the potential to form the basis for tuberculosis diagnostics in the future, not just in the UK, but also in countries where the burden of disease is far higher.


Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007-12, with whole pathogen genome sequences: an observational study. Timothy M Walker, Maeve K Lalor, Agnieszka Broda et. al.. Lancet Respiratory Medicine, early online publication 4 March 2014.

Genomics and outbreak investigation: from sequence to consequence. Esther R Robinson, Timothy M Walker, and Mark J Pallen. Genome Medicine 5:36, 2013

Contact investigations for outbreaks of Mycobacterium tuberculosis: advances through whole genome sequencing. T M Walker, P Monk, E G Smith and TEA Peto, Clinical Microbiology and Infection Sep; 19(9):796-802, 2013

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Timothy M Walker, Camilla LC Ip, Ruth H Harrell et. al.. Lancet Infectious Diseases 13:137-46, 2013

A whole-genome sequencing approach to targeting Mycobacterium tuberculosis outbreak management. Timothy Walker, Camilla Ip, Ruth Harrell et. al.. The Lancet, Volume 380, Page S77, 23 November 2012

Risk factors for recurrence after staphylococcus aureus bacteraemia. A retrospective matched case-control study. Timothy M Walker, Ian CJW Bowler and Philip Bejon.
Journal of Infection 58 (2009), pp. 411-416

Ethical dilemmas – should scientists, God or lawyers decide? Timothy Walker. Clinical Medicine – The Journal of the Royal College of Physicians of London, 2001; 1:383-4