Stefan Rooke

Research Project

The emergence and spread of clinically relevant antibiotic resistance is a truly global healthcare challenge, with antibiotic-resistant infections, and in particular those caused by multi-drug resistant and extensively resistant strains becoming an increasingly common occurrence.  The reality of this problem is that antibiotic resistant organisms, and the mechanisms of horizontal gene transfer have existed long before humans devised methods to harness antimicrobial compounds. Thus it is incumbent upon us to accept the inevitability of adaptation by bacteria, and strive to understand the dynamics that shape the evolutionarily driven challenges which we face - in the hopes that we can manage both their emergence and persistence.

The primary means by which we can achieve this is front-line surveillance of resistant, and pathogenic bacteria. My PhD project aims to evaluate the use of portable long read sequencing (Oxford Nanopore, MinION) as a tool within a more traditional integrated surveillance system in rural Western Kenya, enabling a more decentralised means of genome-level surveillance. By taking a hybrid approach, merging cheaper traditional methods of antibiotic resistance surveillance augmented with strategically-targeted sequencing it is hoped that we can describe the dynamics of antibiotic resistance determinant sharing across host organisms, in a relatively low-resource environment.

It is our hope that this degree of resolution, when applied on a larger scale might enable a surveillance system within which traditional methods and novel technologies might work together to answer important questions about trends in resistance for policy-makers, with relatively limited resources that would simply not be possible by the classical methods of surveillance.

My project forms a part of the wider Zoonotic and Emerging Diseases (ZED) group project: Zoonoses in Livestock in Kenya (ZooLinK). The goal of ZooLinK is to enable Kenya to develop an effective zoonotic disease surveillance programme, which by its design integrates both the human and animal health sectors - .


Currently I am a PhD student under the joint supervision of Prof. Mark Woolhouse, Dr Till Bachmann and Prof. Ross Fitzgerald, funded as part of a joint MRC funded Edinburgh-Glasgow doctoral training partnership in Precision Medicine.

My undergraduate study was broadly based in biological sciences, with particular leaning towards evolution, ecology and genetics.

Following this I completed an MSc degree in Post-Genomic Sciences, at the University of Liverpool.  My research project studied the microbiome of the built-environment of hospitals. Specifically,  I undertook a metagenomic sequencing approach the the study of the bacterial communities present within the atrium area of the newly built Alder Hey Children's Hospital.

At present, I am interested in how selective pressures from antibiotic usage affect the diversity and spatial spread of antibiotic resistance determinants; especially with regards to how these processes play out on larger-scales. The nature of surveillance strategies, and their effective implementation especially in low-middle income countries is of specific interest to me - as these elements have a crucial role in our increasingly global economies.


  • PhD Precision Medicine, University of Edinburgh (2016 - Current)
  • MSc Post-Genomic Sciences , University of Liverpool (2015 - 2016)
  • BSc Biology (Hons) 1st, University of Hull (2012 - 2015)

Contact details


138 Ashworth Labs,
King's Buildings

Phone 0131 651 7112 (Ext 505445)