Dr David Cleary

Dr David Cleary

Institute of Microbiology and Infection
Assistant Professor in Microbial Genomics

Contact details

University of Birmingham
B15 2TT

Dr David Cleary is a microbiologist and microbial bioinformatician whose research interests relate to bacterial pathogens of the human airways. Topics include population genomic epidemiology and intra-host evolution, as well as the roles of these pathogens in acute or chronic respiratory diseases, and general function within the airway microbiome.


  • 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

Postgraduate supervision

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.

Other activities

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)


Recent publications


Das, S, Pandey, AK, Morris, DE, Anderson, R, Lim, V, Wie, CC, Yap, IKS, Alattraqchi, AG, Simin, H, Abdullah, R, Yeo, CC, Clarke, SC & Cleary, DW 2024, 'Respiratory carriage of hypervirulent Klebsiella pneumoniae by indigenous populations of Malaysia', BMC Genomics, vol. 25, no. 1, 381. https://doi.org/10.1186/s12864-024-10276-4

Cleary, DW, Lo, SW, Kumar, N, Bentley, SD, Faust, SN & Clarke, SC 2023, 'Comparative genomic epidemiology of serotype 3 IPD and carriage isolates from Southampton, UK between 2005 and 2017', Microbial Genomics, vol. 9, no. 3, 000945. https://doi.org/10.1099/mgen.0.000945

Woodall, CA, Hammond, A, Cleary, D, Preston, A, Muir, P, Pascoe, B, Sheppard, SK & Hay, AD 2023, 'Oral and gut microbial biomarkers of susceptibility to respiratory tract infection in adults: A feasibility study', Heliyon, vol. 9, no. 8, e18610. https://doi.org/10.1016/j.heliyon.2023.e18610

Christodoulides, M, de Oliveira, D, Cleary, DW, Humbert, MV, Machado-de-Ávila, RA & La Ragione, RM 2022, 'An in silico reverse vaccinology study of Brachyspira pilosicoli, the causative organism of intestinal spirochaetosis, to identify putative vaccine candidates', Process Biochemistry, vol. 122, pp. 128-148. https://doi.org/10.1016/j.procbio.2022.08.014

O'Neill, CE, Skilton, RJ, Forster, J, Cleary, DW, Pearson, SA, Lampe, DJ, Thomson, NR & Clarke, IN 2022, 'An inducible transposon mutagenesis approach for the intracellular human pathogen Chlamydia trachomatis', Wellcome Open Research, vol. 6, 312. https://doi.org/10.12688/wellcomeopenres.16068.1

Cleary, DW, Jones, J, Gladstone, RA, Osman, KL, Devine, VT, Jefferies, JM, Bentley, SD, Faust, S & Clarke, S 2022, 'Changes in serotype prevalence of Streptococcus pneumoniae in Southampton, UK between 2006 and 2018', Scientific Reports, vol. 12, no. 1, 13332. https://doi.org/10.1038/s41598-022-17600-6

Rani, FM, Lean, SS, Rahman, NIA, Ismail, S, Alattraqchi, AG, Amonov, M, Cleary, DW, Clarke, S & Yeo, CC 2022, 'Comparative genomic analysis of clinical Acinetobacter nosocomialis isolates from Terengganu, Malaysia led to the discovery of a novel tetracycline-resistant plasmid', Journal of Global Antimicrobial Resistance, vol. 31, pp. 104-109. https://doi.org/10.1016/j.jgar.2022.08.019

Theodosiou, AA, Laver, JR, Dale, AP, Cleary, DW, Jones, CE & Read, RC 2022, 'Controlled human infection with Neisseria lactamica in late pregnancy to measure horizontal transmission and microbiome changes in mother-neonate pairs: a single-arm interventional pilot study protocol', BMJ open, vol. 12, no. 5, e056081. https://doi.org/10.1136/bmjopen-2021-056081

Mohd Rani, F, Rahman, NIA, Ismail, S, Cleary, D, Clarke, S & Yeo, CC 2022, 'Draft genome sequences of two Acinetobacter soli clinical isolates from a tertiary hospital in Terengganu, Malaysia', Microbiology resource announcements, vol. 11, no. 4, e0008222. https://doi.org/10.1128/mra.00082-22


Rani, FM, A Rahman, NI, Ismail, S, Othman, N, Abdullah, FH, Cleary, D, Clarke, S & Yeo, CC 2023, 'Whole genome sequence analysis of two Acinetobacter oleivorans clinical isolates from Terengganu, Malaysia, revealed the carriage of several virulence factors', International Journal of Infectious Diseases, vol. 130, no. Supplement 2, pp. S143-S143. https://doi.org/10.1016/j.ijid.2023.04.351

Din, NS, Rani, FM, Ismail, S, A Rahman, NI, Othman, N, Abdullah, FH, Cleary, D, Clarke, S & Yeo, CC 2023, 'Whole genome sequencing of Acinetobacter baumannii clinical isolates from Terengganu, Malaysia (2017 – 2018) revealed the predominance of the multidrugresistance ST2, GC2 lineage', International Journal of Infectious Diseases, vol. 134, no. Supplement 1, pp. S11-S11. https://doi.org/10.1016/j.ijid.2023.05.044


Cleary, D, Jones, J, Campling, J, Lahuerta, M, Hayford, K, Southern, J, Gessner, BD, Bentley, SD, Faust, SN & Clarke, SC 2023, 'Changes in paediatric pneumococcal carriage in Southampton UK during the SARS-CoV2 pandemic', 16th European Meeting on the Molecular Biology of the Pneumococcus, Rithymna, Greece, 23/05/23 - 26/05/23.

Golm, D, Law, A & Cleary, D 2023, 'The interplay between prenatal health behaviours, neurodevelopmental diagnoses and alterations in the gut microbiome: an umbrella review', 56th Annual Meeting of the International Society for Developmental Psychobiology, Utrecht, Netherlands, 26/07/23 - 28/07/23. <https://www.xcdsystem.com/isdp/program/fl8EZVu/index.cfm?pgid=2892&sid=27201&abid=101482>

Houghton, R, Cleary, D & Clark, T 2023, 'Undiagnosed acute undifferentiated fever is associated with longer hospital admissions in immunocompetent adults', European Congress of Clinical Microbiology and Infectious Diseases, Copenhagen, Denmark, 15/04/23 - 18/04/23.

Review article

Lister, AJJ, Dombay, E, Cleary, DW, Sulaiman, LH & Clarke, SC 2023, 'A brief history of and future prospects for pneumococcal vaccination in Malaysia', Pneumonia, vol. 15, no. 1, 12. https://doi.org/10.1186/s41479-023-00114-8

View all publications in research portal