Respiratory Infection

Principal Investigators

Tuberculosis

Professor Marc Lipman leads clinical research into the optimum treatment and management of tuberculosis, the commonest cause of death globally due to an infectious disease. He directs the UCL-TB network, with UCL being the first WHO Collaborating Centre for TB Research and Innovation in the UK. He also chairs NTM Network UK, the largest non-tuberculous mycobacterial clinical research network in the UK. 

Dr Rishi Gupta uses a range of data science methods to improve the diagnosis, prognosis and treatment stratification of tuberculosis with the overall aim of developing and evaluating tools to better predict disease and enable personalised treatment approaches. 

COVID-19 and other respiratory viruses 

Dr Rishi Gupta uses data science methods to improve the diagnosis and management of infections caused by respiratory viruses, work that had an instant impact when applied to COVID during the 2020-21 pandemic. The Stimulate-ICP study of treatments of 'long' COVID is led by Melissa Heightman and Toby Hillman, and Jeremy Brown is local PI of the Phosp COVID study of long-term consequences of severe COVID infection.

Dr Marko Nikolić has used novel techniques analysing gene expression by cells from the upper respiratory tract to perform groundbreaking work on why children are less susceptible to severe COVID than adults. He is now applying these techniques to human infection models of COVID, and to investigating influenza interactions with the respiratory epithelium. His work also extends to understanding how the human immune system develops prenatally.

Dr Anob (Nobby) Chakrabarti has a background in computational RNA biology, and uses -omics and machine learning / AI methods to study the molecular mechanisms by which influenza viruses and coronaviruses interact with host intracellular machinery.

Bacterial Pneumonia

Professor Jeremy Brown leads a laboratory investigating the pathogenesis and developing new vaccine approaches for acute bacterial pneumonia, mainly S. pneumoniae (causes an estimated 1 million deaths per year) and leading to phase 1 trials of novel vaccines. More recently, his laboratory has started to develop novel treatment approaches for the highly antibiotic-resistant bacteria Acinetobacter baumannii.

Selected publications

1. Ramos-Sevillano E ... Brown JS (2024). Essential role of proline synthesis and the one-carbon metabolism pathways for systemic virulence of Streptococcus pneumoniae. mBio 2024;15(11):e0175824
2. Obolski U, Swarthout TD, Kalizang'oma A ... Brown JS, et al (2023). The metabolic, virulence and antimicrobial resistance profiles of colonising Streptococcus pneumoniae shift after PCV13 introduction in urban Malawi. Nat Commun. 2023 Nov 17;14(1): 7477.
3. Hill H, Mitsi E, Nikolaou E ... Brown JS, et al (2023). A Randomized Controlled Clinical Trial of Nasal Immunization with Live Virulence Attenuated Streptococcus pneumoniae Strains Using Human Infection Challenge. Am J Respir Crit Care Med. 2023 Oct 15;208(8): 868-878.
4. Feehan K, et al. Jeremy Brown, et al (2024). Post-resolution macrophage-derived lipids shapes long-term tissue immunity and integrity. Nat Comms;15(1): 4326.
5. Shaw ES, Stoker NG, Potter JL … Lipman M (2024) Bedaquiline: what might the future hold? The Lancet Microbe 2024;5: 100909.
6. Gupta RK, Calderwood CJ, Yavlinsky A ... Lipman M, et al (2020). Discovery and validation of a personalized risk predictor for incident tuberculosis in low transmission settings. Nat Med. 2020 Dec;26(12): 1941-1949.
7. Yoshida M, Worlock KB ... Nikolić MZ, Meyer KB (2022). Local and systemic responses to SARS-CoV-2 infection in children and adults. Nature. 2022 Feb;602(7896): 321-327.
8. Lindeboom RGH, Worlock KB … Nikolić MZ, Teichmann SA (2024). Human SARS-CoV-2 challenge uncovers local and systemic response dynamics. Nature. 2024 Jul;631(8019): 189-198.
9. Barnes JL, Yoshida M, He P … Teichmann SA, Meyer KB, Nikolic MZ (2023). Early human lung immune cell development and its role in epithelial cell fate. Science Immunology.
10. Gupta RK, Harrison EM, Ho A, … ISARIC4C Investigators (2021). Development and validation of the ISARIC 4C Deterioration model for adults hospitalised with COVID-19: a prospective cohort study. The Lancet Respiratory Med.
11. Samuels THA, Molloy SF, Lawrence DS...Gupta RK (2025). Personalised risk prediction tools for cryptococcal meningitis mortality to guide treatment stratification; a pooled analysis of two randomised-controlled trials. The Lancet Global Health.
12. Halleggar M, Chakrabarti AM, Lee FCY et al (2021). TDP-43 condensation properties specify its RNA-binding and regulatory repertoire. Cell; 184(18): 4680-4696.
13. C-MORE/PHOSP-COVID Collaborative Group (2023). Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study. Lancet Respir Med. 2023 Nov;11(11): 1003-1019.
14. Ferran E, Chan C, Sheikh N ... Lipman M (2025) Population-level frequency of fluoroquinolone resistance by whole-genome sequencing drug predictions in Mycobacterium tuberculosis complex isolates in England from 2017-2023. Clin Infect Dis.

Funding and Partners

Professor JS Brown (PI), D. Ferreira (coPI), M. Nikolic (coPI).
Medical Research Council Experimental Medicine (2024-2027). MRC Reference: APP11997.
Award: £1,800,128.

Professor JS Brown (PI), G. Lertmemongkolchai, R. Stabler, B. Wren.
Medical Research Council DPFS award (2024-2027). MRC Reference: MR/Y008693/1.
Award: £1,547,785.

Professor JS Brown, B. Wren
Wellcome Investigator Award joint award (2021-2026).
Award: £1,800,000.

Dr M.Nikolić (PI)
Chan Zuckerberg (2021-2025). Organ Maturation in Preparation for Birth
Award: $1,500,000.

Dr M Nikolić (PI)
MRC Clinician Scientist Fellowship (2022-26)
Award: £1,605,629.

Dr M Nikolić (PI), Professor D Gilroy
BBSRC Programme Grant (2023-26).  How inflammatory resolution shapes tissue immunity. 
Award: £1,500,760.

Dr R Gupta (PI)
NIHR Advanced Fellowship (2024-2029). Precision biomarker-guided management of Tuberculosis contacts (PRAGMATIC).
Award: £1,300,000.

Esmail (PI), Dr R Gupta (Co-I)
Wellcome Trust (2025-2029). Optimal treatment to prevent progression of radiologically apparent, bacteriologically unconfirmed TB (RadioTB).
Award: £5,000,000.

Dr R Gupta (PI)
Royal Society International Science Partnerships Fund International Collaboration Award (2024-2027). Next Generation Assays To Unpick The Spectrum Of Tuberculosis in Madagascar and South Africa.
Award: £316,000.

Dr R Gupta (PI)
BMA Foundation for Medical Research (2023-2026). Precision RNA-guided evaluation for viral respiratory infections.
Award: £63,000.

Dr A Chakrabarti (PI)
Wellcome Early Career Award (2023-2028). Disentangling viral RNA structural dynamics and RNP condensation in a patient-derived model of airway epithelial infection.
Award: £1,079,237.

Professor M Lipman (Co-I)
NIHR Programme Grant (2021-2026). A person-centred Needs Informed model of Care for people with HIV (NICHE), to improve wellbeing, mental health and reduce socio-economic disadvantages and stigma.
Award: £2,500,000.

Professor M Lipman (Co-I)
Horizon 2020 Grant (2022-2025). ENDing COVID-19 Variants of Concern through cohort studies: END-VOC.
Award: €2,000,000.

Professor M Lipman (Co-I)
NIHR HTA Programme (2023-2028). Reintroduction of anti-tuberculosis therapy following drug-induced liver injury: a randomised clinical trial.
Award: £1,900,000.

Dr TE Hillman (PI), Dr M Heightman (co-CI)
NIHR Long COVID stream COV-LT2-0043 (2021-2025). STIMULATE-ICO: Understanding Long-COVID to Address and Transform Existing Integrated Care Pathways.
Award: £6,966,349.

Facilities / Techniques

• UCL-TB cross-disciplinary TB research network spanning UCL and our global partners 
• UCL WHO Collaborating Centre for TB Research and Innovation 
• Prediction research: molecular biomarker discovery and evaluation, multivariable modelling using statistical and machine learning 
• Infectious disease epidemiology: Individual participant data meta-analysis, stratified treatment trial design 
• Bioresource for Adult Infectious Diseases (BioAID) multi-centre cohort study of adults presenting to emergency departments with suspected acute infections 
• Phosph COVID a multicentre UK consortium investigating long term consequences of severe COVID infection 
• The STIMULATE-ICP consortium trial conducted across 6 sites in England, investigating the mechanisms, care pathways, and responses to treatment in Long COVID patients 
• scRNA sequencing of samples from human and animal models of infection  
• Bioinformatic analysis of functional genomic and transcriptomic data, development of bespoke methodology e.g. analysing RNA structures and RNA-protein interactions 
• Machine learning/AI as applied to sequencing data. 
• Molecular microbiology, infection models, and immunological techniques for investigating bacterial pathogenesis and immunity for pneumonia pathogens.