The University of Southampton

Dr Stuart Clarke MSc, DLSHTM, PhD, FFPH, FRCPath

Associate Professor in Infectious Disease Epidemiology

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Dr Stuart Clarke is an Associate Professor in Infectious Disease Epidemiology in the Faculty of Medicine at the University of Southampton.

Dr Clarke has a major interest in the epidemiology of infectious diseases, particularly in relation to vaccine development and the evaluation of new vaccines. He works mostly with Streptococcus pneumoniae and Haemophilus influenzae.

Dr Clarke initially trained in medical microbiology in Berkshire, gaining a MSc in Medical Microbiology from the University of Surrey, before studying for a PhD in Molecular Microbiology at the University of Leicester. He was Director of the Scottish Meningococcus and Pneumococcus Reference Laboratory in Glasgow between 1998 and 2004. He then took up specialist training in public health in Hampshire and was awarded an MSc in Public Health from the London School of Hygiene and Tropical Medicine in 2005. He became a Fellow of the Royal College of Pathologists and a Fellow of the Faculty of Public Health of the Royal Colleges of Physicians of the United Kingdom in 2007.

In 2009, Dr Clarke won the Bupa Foundation's award of ‘best emerging medical researcher in the UK’ for his work on the molecular epidemiology of pneumococcal infection around the introduction of pneumococcal conjugate vaccines.






Research interests

Dr Clarke developed his independent research career in 1999 when he was Director of the Scottish Meningococcus and Pneumococcus Reference Laboratory. His research focuses on the molecular epidemiology of Streptococcus pneumoniae and other vaccine-preventable bacterial infections, particularly in relation to polysaccharide conjugate vaccines. Dr Clarke was involved in the national meningococcal carriage study, led by Professors Martin Maiden and James Stuart, which was mainly funded by the Wellcome Trust. His laboratory led on the Scottish component of the study jointly with Health Protection Scotland. His laboratory was the first to introduce automated methods for multi-locus sequence typing (MLST) and was also the first reference laboratory in the world to introduce the method as a routine clinical service. He has since been involved in various pneumococcal and MenB carriage studies. The Southampton paediatric pneumococcal carriage study has been running for 10 years, since the introduction of pneumococcal conjugate vaccines in the UK.

In collaboration with a pharmaceutical company, Dr Clarke leads the microbiology component of a 5 year programme of work which aims to generate epidemiological data to further explore determinants of Chronic Obstructive Pulmonary Disease (COPD) and the contribution of bacterial and viral pathogens to Acute Exacerbation of COPD (AECOPD) episodes.

Following funding from the Bill & Melinda Gates Foundation, Dr Clarke is also the Principal Investigator of the Research Investments in Global Health (ResIn) study. This will investigate infectious disease research investments (in particular pneumonia, and maternal & neonatal infections) across the G20 countries. Co-applicants are Michael Head (University of Southampton), Dr Joseph Fitchett (Harvard School of Public Health), Professor Rifat Atun (Harvard School of Public Health), Professor Marie-Louise Newell (University of Southampton), and Professor Anthony Scott (London School of Hygiene and Tropical Medicine).

Dr Clarke has many other international collaborations, mostly in South East Asia. In Singapore, he collaborates with Professor Martin Hibberd and Dr Swaine Chen at the A*Star Genome Institute Singapore and also with colleagues in the Department of Microbiology at the National University of Singapore where he holds an Adjunct Associate Professor position. Research in Singapore focuses on the genomic epidemiology of S. pneumoniae and the prevention of urinary tract infections via an improved understanding of biofilm-derived variation of E. coli. In Malaysia, he collaborates with Professor Shamala Devi at the University of Malaya Medical School; with Professor Victor Lim, Dr Chun Wie Chong and Dr Ivan Yap at the International Medical University; with Professor Norazmi Bin Mohd Nor at the Universiti Sains Malaysia; with Associate Professor Mohd Nasir Mohd Desa at University Putra Malaysia; with Associate Professor Zaini Mohd Zain at Universiti Teknologi MARA; with Dr Cheng Siang Tan at the Universiti Malaysia Sarawak; and with Professor Chew Chieng Yeo at the Universiti Sultan Zainal Abidin. Many of these collaborations are part of a Newton Fund/British Council Institutional Links award. He is a Visiting Professor in the Faculty of Medicine at Universiti Teknologi MARA in Kuala Lumpur.

Dr Clarke is also a partner in the Global Pneumococcal Sequencing Project. This study aims to examine the effect of the rollout of pneumococcal conjugate vaccine on pneumococcal strains escaping the vaccine in developing countries through the sequencing and comparison of whole genome sequences of the species before and after vaccination.


Academic unit(s)

Clinical and Experimental Sciences Academic Units

Affiliate academic unit(s)

Infection and Immunity Research group

Dr Clarke heads a large multidisciplinary research group undertaking infectious disease epidemiology and molecular microbiology research with a translational focus. The group comprises postdoctoral research fellows, biomedical scientists, research technicians, research facilitators, and PhD students. The PhD students are based in various locations including Southampton, Singapore, and Sydney. He also hosts undergraduate medical students during their MMedSci projects.

He is a Member of the American Society of Microbiology and the Society for General Microbiology. He is a member of the editorial boards for the Journal of Clinical Microbiology (2003-date) and Journal of Medical Microbiology (2005-date). He was a member of the editorial boards for Molecular Biotechnology (2001-2007) and British Journal of Biomedical Science (2001-2007).

Dr Clarke was invited to be a Member of the Clinical Microbiology Group of the Society for General Microbiology between 2003 and 2006, as a Member of the Institute of Biomedical Sciences (IBMS) Advisory Committee for Medical Microbiology between 2001 and 2004, and as a Member of the IBMS Advanced Practice Working Group during 2003. Between 2010 and 2011, he was a Member of the HPA’s Next Generation Sequencing and Bioinformatics Working Group. He is currently Chair of the management group for an Institutional Links Award in Malaysia which is funded by the Newton Fund/British Council.




Book Chapters

Dr Clarke has teaching experience at the Universities of Glasgow, Edinburgh, Leicester and Southampton. To date, he has supervised nine PhD students to completion. He has chaired sessions at international conferences and given numerous national/international lectures. He has acted as an external examiner for the University of Malaya, Monash University, the National University of Singapore, and the Chinese University of Hong Kong.

Dr Stuart Clarke
Molecular Microbiology and Infection Mailpoint 814, Level C, South Block, Southampton General Hospital Southampton SO16 6YD, UK Office 023 8120 6652/ Lab 023 8120 8895

Room Number:SGH/LC86/MP814

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