Dr David William Cleary

Supervisor Details

Contact Details

Dr David Cleary

Institute of Microbiology and Infection, University of Birmingham

Scientific Background

Research Interests

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.

Research Groups

Institute of Microbiology and Infection

Supervision Style

In three words or phrases: Supportive, student-focussed, objective driven.

Provision of Training

Initially I will take responsibility for your training and will make sure you have all the basic tools to begin your PhD. I will always be actively supportive of your desire to acquire new skills/experience through attendance at external courses/visits to other laboratories

Progression Monitoring and Management

As you progress through your PhD I expect you to become more independent in terms of progression monitoring - where you actively keep me up-to-date of what you are doing and how you are getting on. That said, I understand that every PhD journey is unique and whilst I will set out expectations in terms of when I’d like updates, I will always be available for advice and guidance. I encourage members of my group to engage with mentoring schemes so that they have a varied support network, and I will ensure that they are aware of and have access to peer support groups

Communication

I am known to email at all hours of the day and night. This is my issue, not yours, and therefore there is no expectation that you do the same. I am very happy to have informal methods of communication e.g., WhastApp or Slack group, as keeping communication free flowing is something I value very highly. Whilst I expect you to keep up with my/ team communications I will expect you to manage your work/life balance, but my door is always open, and I am happy to discuss any issues that are impacting your ability to fulfil your potential.

PhD Students can expect scheduled meetings with me:

In a group meeting

At least once a fortnight

In year 1 of PhD study

At least once a week

In year 2 of PhD study

At least once a fortnight

In year 3 of PhD study

At least once a fortnight

These meetings will be a mixture face to face or via video chat or telephone. I am usually contactable for an instant response on every working day.

Working Patterns

The timing of work in my lab is flexible, and other than attending pre-arranged meetings, I expect students to manage their own time.

Notice Period for Feedback

I need at least 2 weeks' notice to provide feedback on written work of up to 5000 words.

MIBTP Project Details

Current Projects (2025-26)

Primary supervisor for:

Pneumococcal colonisation and microbiota interactions in the ageing airway

See the PhD Opportunities section to see if this project is currently open for applications via MIBTP.

Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).

Pneumococcal colonisation and microbiota interactions in the ageing airway

Secondary Supervisor(s): Dr Michael Cox

University of Registration: University of Birmingham

BBSRC Research Themes: Integrated Understanding of Health (Ageing)

Project Outline

Bacterial colonisation of the upper respiratory tract (URT) is pre-requisite of multiple respiratory tract diseases including pneumonia, otitis media, sinusitis, exacerbations of chronic obstructive pulmonary disease (COPD), and, less commonly, diseases resulting from bacteraemia such as meningitis. Preventing bacterial colonisation would significantly reduce global morbidity and mortality due to these infections. An estimated 4 million deaths are attributed to these infections annually (1) and escalating levels of antimicrobial resistance (AMR) will increase this burden. Even in the UK, recent analysis has shown that the burden of non-SARS-CoV2 infections in adults remains a significant problem (2).

There are significant gaps in knowledge regarding pathogen colonisation and intra-microbiota interactions which impact disease outcomes in the ageing airway. Not only is there growing consensus that a reliance on pathogen isolation has led to an underestimation of adult carriage of the important respiratory pathogen Streptococcus pneumoniae (the pnuemococcus) (3), but there is also no data regarding the prevalence and/or function in older adult populations of commensal species such as Corynebacterium (4) and Dolosigranulum (5) that are considered beneficial to human health and in some cases have been shown to impact colonisation (6).

Understanding these interactions between pneumococci and commensals in the ageing airway not only underpins our understanding of disease risk, but will reveal novel interventions, such as microbiome modification using said commensals, that reduce the requirement for antimicrobial use in already susceptible populations.

In this innovative project we propose the following aims:

1. Determine the carriage prevalence of pneumococci in adult populations using molecular approaches, with a focus on differences between healthy and those with co-morbidities and underlying respiratory health conditions e.g., COPD and asthma.

2. Using a combination of culture, genomic and culture-enriched metagenomics approaches, the student will generate an inventory of important pneumococcal-commensal interactions. This will focus initially on commensals with known co-exclusion interactions such as Corynebacterium sp. or Dolosigranulum sp.

3. Examine interactions using in vitro models. Using strains identified in Aims 1 and 2, interactions will be examined using solid and liquid media growth inhibition assays and mixed species biofilm models. Host interactions will be examined using air-liquid-interface (ALI) epithelial models.

The student will be exposed a broad range of areas including infectious disease epidemiology, analysis of bacterial genomes, metagenomics and microbiome analysis, cell-culture, and host-bacterial responses.

References

1. T. Ferkol, D. Schraufnagel, The Global Burden of Respiratory Disease. Annals of the American Thoracic Society 11, 404-406 (2014).

2. Hyams C et al. Incidence of community acquired lower respiratory tract disease in Bristol, UK during the COVID-19 pandemic: a prospective cohort study. The Lancet Regional Health Europe 21:100473 (2022) DOI: https://doi.org/10.1016/j.lanepe.2022.100473.

3. Miellet WR et al. Streptococcus pneumoniae carriage studies in adults: Importance, challenges, and key issues to consider when using quantitative PCR-based approaches. Front. Microbiol. 14:1122276. doi:10.3389/fmicb.2023.1122276 (2023).

4. Tran et al. Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses bioRxiv doi: https://doi.org/10.1101/2023.06.05.543719.

5. Ramos SF et al. Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum, a Candidate Beneficial Bacterium from the Human Microbiome mSystems Vol. 6, No. 5 DOI:https://doi.org/10.1128/msystems.00425-21.

6. Brugger SD et al. (2016) Commensal–Pathogen Interactions along the Human Nasal Passages. PLoS Pathog 12(7): e1005633. https://doi.org/10.1371/journal.ppa.

Co-supervisor on projects with Dr Michael Cox and Professor Joan Geoghegan.

Previous Projects (2024-25)

Primary supervisor for:

Pathogen colonisation and microbiota interactions in the ageing airway