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.
- Genomic Epidemiology of Respiratory Pathogens
- Human Microbiomes
- Streptococcus pnuemoniae
- Non-typeable Haemophilus influenzae (NTHi)
Dr Cleary's research attempts to understand the role of the upper respiratory tract microbiome in health and 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.
Speicific reasearch includes examining 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.
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.
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)
- 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 Students
MSc Public Health: MEDI6068: Communicable Disease Control – Module Co-lead
MSc Genomic Medicine: MEDI6245: Communicable Disease Control with Genomics – Module Co-lead
MSc Genomic Medicine: MEDI6234: Genomics Guided Treatments - Lecturer
MSc Allergy: Allergic Airways Diseases. Lecture: Airway Microbiome and Asthma
BM5 Year 1 Microbiology: Lecturer - Bacterial Colonisation and Infection, Bacterial Toxins
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.
External roles and responsibilities
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.
Lecturer in Microbial Genomics and Microbiomes, Southampton NIHR Biomedical Research Centre and University of Southampton (2022 – Present)
Career Track Post-Doctoral Fellow, Microbial Sciences, Southampton NIHR Biomedical Research Centre and University of Southampton (2017 – 2022)
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)
- WUN - Research Mobility Award (2017)
- Hayes-Burnet Award (2014)
- Faculty of Medicine, Deans Postdoctoral Awards – Education (2021)