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.
Pneumococcal vaccines
Dr Clarke’s principal research projects are the Southampton pneumococcal carriage and disease studies which have been running for more than 10 years, since the introduction of pneumococcal conjugate vaccines in the UK. The Paediatric post pneumococcal conjugate vaccine study with co-investigator Professor Saul Faust takes place at University Hospital Southampton NHS Foundation Trust. It is investigating whether bacteria, in particular Streptococcus pneumoniae and other disease-causing types of bacteria that are carried in the upper airways of children and adults have varied since the introduction of the Prevenar vaccines. The Carriage rates and antibiotic resistance of bacteria in a community study with co-investigator Dr Sarah Williams from Solent NHS Trust samples bacteria from the upper respiratory tract in order to determine community carriage levels of common respiratory pathogens and the prevalence of antibiotic resistance. These studies were the highest recruiting studies in Wessex and sixth in the UK during 2017/18 within the Children and Infection specialties respectively.
Infectious disease epidemiology in South East Asia
Dr Clarke also undertakes world-leading research in South East Asia. In Singapore, he collaborates with Professor Martin Hibberd and Dr Swaine Chen at the A*Star Genome Institute Singapore. Projects focus 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 has numerous collaborations which look at the epidemiology of pathogens causing respiratory infections and healthcare associated infections. These include Professor Victor Lim and Dr Chun Wie Chong at the International Medical University, Kuala Lumpur; Professor Chew Chieng Yeo at the Universiti Sultan Zainal Abidin in Terengganu; Professor Norazmi Bin Mohd Nor at the Universiti Sains Malaysia; Dr Eddy Cheah at the Universiti Tunku Abdul Rahman; Dr Cheng Siang Tan at the Universiti Malaysia Sarawak; and Dr Cindy Teh at the University of Malaya. Some of these were built through a Newton Fund/British Council Institutional Links award. These links have also led to a number of Fundamental Research Grant Scheme grants with the University of Malaya and Universiti Sultan Zainal Abidin.
Genomic epidemiology
Together with Dr David Cleary in the NIHR Southampton Biomedical Research Centre and colleagues at the Wellcome Sanger Institute, Dr Clarke’s research utilises whole genome sequencing to determine the relationships between bacterial species and populations before and during the implementation of new vaccines in the UK. 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.
Clinical biofilm research
Dr Clarke is a key member of the University of Southampton Institute for Life Sciences Biofilm and Microbial Communities Research Group. His main interests lie in understanding the biology of pneumococci and other respiratory pathogens in the single and multi-species biofilm state during pneumococcal conjugate implementation. His main collaborators are Professor Jeremy Webb and Professor Saul Faust.
Chronic Obstructive Pulmonary Disease
In collaboration with a pharmaceutical company, Dr Clarke led 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.
Research investments in Pneumonia
Following funding from the Bill & Melinda Gates Foundation, Dr Clarke was previously the Principal Investigator of the Research Investments in Global Health (ResIn) study. This study investigated infectious disease research investments (in particular pneumonia, and maternal & neonatal infections) across the G20 countries. A report was published in 2018. Co-applicants were Dr 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).
Department(s)
Clinical and Experimental Sciences
Affiliate Department(s)
Infection and Immunity Research group
Dr Stuart ClarkeMolecular Microbiology and Infection Mailpoint 814, Level C, South Block, Southampton General Hospital Southampton SO16 6YD, UK Office 023 8120 6652/ Lab 023 8120 8895 S.C.Clarke@soton.ac.uk
Room Number: SGH/LC86/MP814
