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Dr David W Cleary BSc, PhD

Career Track Post-Doctoral Fellow

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Dr Cleary is a Career Track Post-Doctoral Fellow in the Faculty of Medicine and the Southampton NIHR Biomedical Research Centre.

His research focuses on the application of computational biology approaches to understand the epidemiology and pathogenicity of infectious disease, primarily of those pathogens that can be carried in the human respiratory tract such as Streptococcus pneumoniae and Non-typeable Haemophilus influenzae. In addition, his research involves characterising respiratory tract microbiomes to determine the community-host interactions that underpin colonisation and progression to disease.

As a microbial ecologist I’m interested in the microbiome of the respiratory tract - how it functions, the interactions of the different members of these communities, the response of the host and ultimately the impact of all these factors on health.

Dr Cleary graduated in Medical Microbiology from the University of Surrey in 2002. He went on to complete his PhD with the University of Warwick in 2013 whilst employed as a microbiologist at the Defence Science and Technology Laboratories (DSTL), Porton Down. His PhD research investigated the impacts of gene abundance, horizontal gene transfer (HGT) and environmental persistence of DNA in relation to the detection of microbial taxa in complex communities, specifically pathogenic species of the genus Burkholderia.

Prior to his current appointment, he was a Senior Scientist and Technical Lead for Genomics within the Biological Sciences Group at the DSTL, Porton Down. He led a number of research programmes including those investigating the environmental and ecological interactions of highly pathogenic bacteria, quasispecies of RNA viruses, detection of pathogens within bio-aerosols, aerobiological responses of select agents and the design and development of analytical techniques for pathogen detection.


BSc (HONS) Microbiology (Medical), University of Surrey (2002)
PhD, University of Warwick (2013)


Career Track Post-Doctoral Fellow, Microbial Sciences, Southampton NIHR Biomedical Research Centre and University of Southampton (2017 – Present)

Research Fellow, Microbial Genomics, University of Southampton (2014 – 2017)

Senior Scientist, Molecular Biology Team, Defence Science and Technology Laboratory Porton Down (2009 – 2014)

Scientist, Molecular Biology Team, Defence Science and Technology Laboratory Porton Down (2002 – 2009)

Research Assistant, Microbiology and Virology Research and Advice Team, Centre for Environment, Fisheries and Aquaculture Science (CEFAS) (2000 – 2001)

Research interests

The focus of my research is to understand the role of the upper respiratory tract microbiome in airways disease. This includes examining the genomic epidemiology of specific bacterial pathogens, the interaction of these with commensals, host-pathogen interactions and how shifts in microbiota composition impact infection/health.  

1. Genomic Epidemiology of Respiratory Pathogens

Respiratory tract infections remain a significant contributor to global morbidity and mortality, particularly in the very young and old. In collaboration with the group of Dr Stuart Clarke (UoS) his ongoing carriage studies allow us to examine the changing epidemiology of respiratory microbiota in the context of changes in national vaccine schedules, for example the swap of pneumococcal vaccine from PCV7 to PCV13.

2. Non-typeable Haemophilus influenzae (NTHi)

NTHi is a Gram-negative, human nasopharyngeal bacterium. It is recognised to cause severe invasive infections such as meningitis and septicemia, although historically this was predominantly caused by capsulated H. influenzae, in particular serotype B, (Hib).  The burden of the latter has been reduced by vaccination, but a vaccine against NTHi remains elusive and global mortality and morbidity remains significant.

NTHi can be associated with acute otitis media (AOM) and in exacerbations of chronic lung conditions such cystic fibrosis and chronic obstructive pulmonary disease. NTHi is the leading cause of invasive H. influenzae disease with the burden highest in infants and those ≥60 years of age. The former burden is due to a concerning increase in neonatal disease notification.

My research examines the genomic epidemiology of this important pathogen in terms of carriage in paediatric populations, as the cause of non-invasive infections and in those with chronic respiratory disease.

3. Microbiomes

Humans play host to both a staggering number and variety of microorganisms with whom we have co-evolved over millennia. The study of these microbiomes, being the communities of bacteria, archaea, viruses and fungi found on or within our bodies, has expanded considerably over the last decade. My research focusses on the microbiome of the respiratory tract and the opportunistic commensal bacteria (pathobionts) that reside there. These communities can have considerable impact on chronic conditions, such as asthma, COPD and cystic fibrosis, through for example, ecological shifts that enable outgrowth of a particular pathogen or alteration in host responses to microbial encounters in the lower airways.

4. Interactions between bacterial members of the respiratory tract microbiome

Current work is exploring the interactions between those bacteria commonly thought of as opportunistic pathogens and other commensals of the respiratory tract such as Dolosigranulum and Corynebacterium sp.

Current projects (as PI):

  • Transcriptomics of host-microbiota interactions using direct dual-RNA-sequencing (Funding: Wessex Medical Research, Innovation Award)
  • Characterising the respiratory microbiome of Orang Asli villagers in Malaysia (Collaboration with Prof. Yeo Chew Chieng, UniSZA Malaysia)
  • Seasonal and age-stratified analysis of upper respiratory tract microbiomes from a cross-sectional community carriage study (Funding: Rosetrees Trust)
  • Application of phylogenomic analyses to understand the epidemiology of Haemophilus influenzae in Hong Kong (Collaboration with Prof. Margaret Ip, Chinese University of Hong Kong. Funding: Worldwide Universities Network)
  • Impact of Bordetella pertussis colonisation on the upper respiratory tract microbiome (Collaboration with Dr Andy Preston, University of Bath and Prof. Andrew Gorringe PHE. Funding: HIC-Vac)

Current PhD Projects

  • Molecular epidemiology of Streptococcus pneumoniae isolates causing pneumococcal disease in Singapore (PhD, co-supervisor)
  • Skin microbiota associations in inflammatory skin disease (PhD, co-supervisor)
  • Epidemiology of M. catarrhalis in community-based carriage studies (PhD, co-supervisor)
  • Functional and interpretive analysis of the microbiome and assessment of ileal transcriptome and genetic interactions in paediatric Crohn's disease (PhD, co-supervisor)
  • Interaction of respiratory bacterial and viral infections on host inflammation in the asthmatic airway (PhD, co-supervisor)
  • Breathomics in severe asthma (PhD, co-supervisor)
  • The regulation of obesity and metabolic disorder by gut microbiome (PhD, co-supervisor)
  • A single gene deficiency (TIMP3) affects the regulation of metabolism and nutrition – harnessing the gut microbiome (PhD, co-supervisor)
  • Characterisation of Primary Ciliary Dyskinesia epithelial responses to non-typeable Haemophilus influenzae biofilm infection (PhD, co-supervisor)


Clinical and Experimental Sciences

Affiliate Department(s)

Infection and Immunity Research group

Dr Cleary’s research supports activities in the, Southampton NIHR Biomedical Research Centre and the Wessex Investigational Sciences Hub (WISH) based at University Hospital Southampton.

He has international research links with laboratories in SE Asia, Australia, France, Norway and the USA. He is a local point of contact for engagements with the Defence Science and Technology Laboratory, Porton Down.

Dr Cleary is a member of the Microbiology Society, the European Respiratory Society (ERS) the British Association for Lung Research (BALR), the European Society for Clinical Microbiology and Infectious Disease (ESCMID) and the Society for Molecular Biology and Evolution (SMBE).

Dr Cleary is a STEM Ambassador and has led engagement activities for a Biomedical Science Summer School for A Level students in Jersey and for Hampshire primary school science days.

Dr Cleary co-supervises a number of students working towards their PhDs and has co-supervised two to completion.

Internal MPhil/PhD examiner, external PhD examiner.

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Current Responsibilities

MSc Public Health

MEDI6068: Communicable Disease Control – Module Co-lead

MSc Genomic Medicine

MEDI6245: Communicable Disease Control with Genomics – Module Co-lead

MEDI6234: Genomics Guided Treatments = lecturer

MSc Allergy

1. Allergic Airways Diseases. Lecture: Airway Microbiome and Asthma

BM5 Year 1 Microbiology

1. Lectures: Bacterial Colonisation and Infection, Bacterial Toxins

Past Responsibilities

Integrated PhD, Infection and Immunity Pathway – small tutorial group teaching on Bacterial Infection in the Airways

MSc Genomic Medicine (2017) Deputy Module Lead: Dissertation and lecturer on Applications of Genomics to Infectious Disease module. Lectures: Bacterial Genomics, Bacterial Diversity and Future Diagnostics.


Dr David W Cleary
Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Room LC95, Mailpoint 814, Level C, Sir Henry Wellcome Laboratories South Block, University Hospital Southampton Foundation NHS Trust, Tremona Road, Southampton SO16 6YD Tel: +44 (0)2381 206652

Room Number: SGH/LC86/MP814

Telephone:(023) 8120 8895

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