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Dr David W Cleary BSc, PhD

Senior Research Fellow in Microbial Sciences

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Dr Cleary is a Senior Research Fellow in Microbial Sciences in Medicine and the Southampton NIHR Biomedical Research Centre.

Microbiomes are clearly important in human health, yet how these consortia function and interact with the each other and the host is still not fully understood. My research seeks to understand these host-bacteria interactions and the consequences for respiratory disease.

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 elucidate the community-host interactions that underpin colonisation and progression to disease.
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.

Qualifications

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

Appointments

Senior Research 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 emphasis of my research is the application of genomics to investigate intra- and inter-host bacterial pathogen dynamics. Central to this is our increased understanding of the intricate and balanced relationship with our microbiome(s). Shifts in this balance may arise as a result of environmental pressures, clinical interventions, the changing epidemiology of carriage, infection, or indeed simply colonisation with new ‘types’ or strains of pathogens. Broad research interests include:

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 the 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 dysbiosis that enables outgrowth of a particular pathogen or alteration in host responses to microbial encounters in the lower airways.

Current projects include:

  • Characterising the respiratory microbiome of Orang Asli villagers in Malaysia (Collaboration with Prof. Yeo Chew Chieng, UniSZA Malaysia)
  • Describing alterations in gut microbiomes in those with Asthma (Collaboration with Dr Gemma Walton, University of Reading)
  • Seasonal and age-stratified analysis of upper respiratory tract microbiomes from a cross-sectional community carriage study.

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 PhD Projects

  • Pneumococcal carriage and disease during the implementation of PCV13: 2006 to 2016 (PhD, co-supervisor)
  • Multispecies biofilm formation by Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis and their interaction with nasopharyngeal microbiota and probiotic species (PhD, co-supervisor)
  • 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)

Department(s)

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 Teaching Responsibilities

MSc Genomic Medicine

1. Assistant Academic Module Lead -  Applications of Genomics to Infectious Disease. Lectures on Bacterial Genomics, Bacterial Diversity and Future Diagnostics.

2. Omics Module – Lecture: Next-Generation Sequencing Strategies in Infectious Disease.

BM5 Year 1 Microbiology

Lectures on Bacterial Colonisation and Infection, Toxins and Immunisation

Past Teaching 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

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
Email: d.w.cleary@soton.ac.uk

Room Number: SGH/LC86/MP814

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