Dr David Cleary

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

Dr Cleary graduated in Medical Microbiology from the University of Surrey in 2002. His degree included a placement with the Centre of Environment, Fisheries, and Aquaculture Science (CEFAS) where he used molecular methods to screen bivalve molluscs for noroviruses.

After graduating he joined the Defence Science and Technology Laboratory (DSTL), Porton Down. It was during this period that he undertook a PhD with the University of Warwick, completing those studies in 2013. The topic of his PhD was the impact of gene abundance, horizontal gene transfer and environmental persistence of DNA in relation to the detection of microbial taxa in complex communities, specifically pathogenic species of the genus Burkholderia.

At the end of his twelve years at DSTL he was a Senior Scientist and Technical Lead for Genomics within the Biological Sciences Group. He led several research programmes to investigate the environmental and ecological interactions of highly pathogenic bacteria, the detection and responses of pathogens within bio-aerosols and the development of analytical techniques for pathogen detection.

In 2014 he moved to the University of Southampton to join the Infectious Disease Epidemiology Group led by Professor Stuart Clarke. This was followed by five years as a Career-track Post Doctoral Fellow in the NIHR Southampton Biomedical Research Centre where he worked across several research programmes including those involving controlled human infection models using Neisseria lactamica and Bordetella pertussis.  

Dr Cleary joined the Institute of Microbiology and Infection in 2022 as an Assistant Professor in Microbial Genomics.

Dr Cleary leads the Analysing Microbial Genomic Data (AMGD) CPD which also forms part of the MRes in Microbial Genomics.

Dr Cleary also supports teaching in the Institute through lectures, small group teaching, and practical sessions for the following programmes:

• Biomedical Sciences – Immunity and Infection
• Biomedical Sciences – Bacterial Threats and Defence
• Pharmacy – Health, Disease and Therapeutics
• MSc Genomic Medicine - Applied Genomics and Infectious Disease

Dr Cleary co-supervises several students working towards their PhDs and has co-supervised ten to completion.

Prospective self-funded students can find details here or are welcome to contact Dr Cleary directly. The general topic of the lab is genomic characterization of human respiratory tract pathobionts and commensals in order to

1. determine strain diversity and epidemiology in different populations and disease backgrounds
2. elucidate microbial community compositions,
3. examine longitudinal genomic stability during prolonged carriage, and 4) identify putative interactions both within and between species/strains that may be exploited as potential therapeutic interventions. 

Dr Cleary’s research interests fall into four broad areas:

Genomic Epidemiology of Streptococcus pneumoniae

This involves collaboration with the group of Prof. Stuart Clarke (University of Southampton) and his ongoing paediatric pneumococcal carriage study as well as international partners in South-east Asia, particularly Malaysia.

Non-typeable Haemophilus influenzae (NTHi)

Specifically, epidemiology in paediatric carriage, as the cause of non-invasive infections and in those with chronic respiratory disease such as COPD. This includes collaboration with Prof. Margaret Ip (Chinese University of Hong Kong).

Upper Respiratory Tract Microbiomes

Research focussing on ecological shifts that enable outgrowth of a particular pathogen(s) or alteration in host responses to microbial encounters. Also includes an exploration of interactions between opportunistic pathogens and commensals such as Dolosigranulum and Corynebacterium sp.

Controlled Human Infection Models (CHIM)

Dr Cleary remains involved with Controlled Human Infection Model (CHIM) research with the University of Southampton. Here he studies genomic stability of bacterial inocula during challenge as well as the impact on resident microflora.

Editorial Boards

• Editor Microbial Genomics 2022-present
• Editor Pneumonia 2021-present
• Editor mSystems 2017-present

Membership of Scientific Societies

• Microbiology Society
• European Society for Clinical Microbiology and Infectious Diseases (ESCMID)
• European Respiratory Society (ERS)
• British Association of Lung Research (BALR)
• Society for Molecular Biology and Evolution (SMBE).

Former International Committee Memberships

• Anglo-France, DSTL-DRG, Biological Detection Research Working Group (2012-2014)  
• UK MoD Representative for the Anglo-Netherlands-Norway and Germany (ANNG) Collaboration Panel II-8 on Detection, Diagnostics and Medical Countermeasures to Biological Threat Agents (2009-2014)