Centre for Infectious Disease Epidemiology 

The Centre for Infectious Disease and Epidemiology (CIDE) undertakes research on the epidemiology, prevention and treatment of infections including tuberculosis, hepatitides, HIV, and other common problems such as antimicrobial resistance and vaccine preventable diseases particularly among vulnerable populations. Our research has a significant translational element. We collaborate with a range of experts, from basic scientists to mathematical modellers and health economists. CIDE hosts the cross disciplinary UCL-TB Centre (https://www.ucl.ac.uk/tb).

CIDE is based at the Mortimer Market Centre and led by Professor Ibrahim Abubakar, with some studies coordinated from Public Health England, Colindale, London.  Our team includes epidemiologists, nurses, public health physicians, modellers and health economists, study managers and administrators and PhD students.

For CIDE staff profiles, click here

Current Research Studies:

Our work is funded through programme and strategy awards from the MRC and NIHR as well as post doctoral and senior research fellowships from NIHR. We undertake research in the UK as well as collaborate with scientists at the Africa Centre and NICD in South Africa, FioCruz in Salvador, Brazil, India, Netherlands and the USA.


This project is led by Prof Abubakar, together with researchers at Public Health England, Imperial College London, Queen Mary University of London, University of Birmingham and Brunel University. This cohort study has recruited nearly 10,000 participants who are being followed up to assess the predictive value of IGRA tests and the tuberculin skin test.

Further information: http://predictstudy.org.uk/ and https://www.ucl.ac.uk/tb/research/uk-predict

Next Generation Test for Latent TB study

Led by Professor Abubakar, in collaboration with UCL Immunology, Dr. David Lowe, Dr. Marc Lipman, Dr. Jo Southern, Dr Charlotte Jackson and Dr. Karen Kempsell (Public Health England). This study will evaluate a number of promising approaches to improve the predictive value of latent TB tests in a cohort of contacts of TB patients in London.


This project, led by Prof Abubakar, in collaboration with a range of NHS hospitals in London, Public Health England, Dr. Jo Southern, Dr. Mark Jit and Dr. Peter White, aims to:

  • Determine the prevalence of latent and active tuberculosis among migrants attending A&E Departments.
  • Investigate the cost effectiveness of screening for latent and active TB in migrants attending A&E Departments.

HALT: Hepatitis

This project is led by Dr. Helen Stagg and aims to evaluate the cost-effectiveness of measures to improve active case finding and case holding in hard-to-reach groups for hepatitis C virus infection. The HALT hepatitis study has completed enrolment and is in follow up phase.

HALT: Latent TB

This project is led by Professor Abubakar and aims to assess completion rates of two different LTBI treatment regimens (daily rifampicin/isoniazid vs. weekly rifapentine/isoniazid) and evaluate the cost effectiveness of using this regimen to treat latent TB.

TBTVacc – UK Brazil Collaboration

This project is led by Professor Abubakar in collaboration with Dr. Sergio Arudda at FioCruz, Brazil, Professor Laura Rodrigues at LSHTM, Dr. Helen Stagg, Dr. Charlotte Jackson and Dr. Lele Rangaka. This project funded by RCUK includes a literature review, mathematical modelling and a pilot study in Brazil on the efficacy of BCG following treatment of latent TB infection.

Improving the management and reducing the transmission of drug resistant tuberculosis (DR-TB) in the UK

This NIHR funded project led by Dr. Helen Stagg aims to inform clinical knowledge and policy surrounding drug resistant cases, thus improving case management and reducing transmission, by a) determining the effectiveness of different regimens for resistant cases and b) exploring microbiological and clinical markers that could be rapidly adopted as predictors of treatment success. 

Read more here...

Whole-genome sequencing and mathematical modelling of isoniazid resistant tuberculosis in hard-to-reach populations

This project is led by Hollie Ann-Hatherell in collaboration with Public Health England and Imperial College and is supported by UCL CoMPleX. Building on the demographic, clinical, contact tracing and whole genome sequencing data, this project will seek to model the dynamics of the London outbreak and investigate effective mechanisms for control using a mathematical model.

Molecular epidemiology of tuberculosis and HIV Infection in the UK

This project is led by Jo Winter in collaboration with Dr. Helen Stagg and Dr. Valerie Delpech at Public Health England. The project will investigate the risk factors for TB disease in HIV infected individuals and of HIV infection in TB case. The project would also assess the extent of, and risk factors for, transmission of TB in individuals with HIV compared to non-HIV infected persons using MIRU-VNTR typing of TB isolates.

Working conditions and tuberculosis mortality in England and Wales, 1890-1912

In high burden settings, much Mycobacterium tuberculosis (M. tb) transmission is thought to occur outside the home. This project aims to quantify increased mortality from TB associated with occupational exposure to crowded indoor spaces. We are using data from the Registrar General’s decennial supplements, which provide cause specific mortality data by occupation for men in England and Wales at the turn of the 20th century. At this time, TB burden was comparable to that seen in Southern Africa today and antibiotics with activity against M. tb were not yet available. This research is led by Joanna Wolny with supervision from Dr. Helen Stagg, Dr. Charlotte Jackson, Professor Ibrahim Abubakar and Dr. TomYates.

Household vs. community transmission of M. tb., a systematic review

Better understanding where transmission occurs could inform more appropriate TB control interventions. Molecular epidemiology has suggested that, particularly in high burden settings, co-prevalent cases within households are often caused by different strains. We are conducting a systematic review of studies that have collected both residency and strain typing data. We are examining how strain discordancy varies with TB burden and, in a subset of studies, the proportion of M. tb transmission that occurs between rather than within households. This work is being conducted by Dr. Tom Yates and Dr, Rob Aldridge and supervised by Dr. Frank Tanser and Professor Ibrahim Abubakar.

Measuring and modelling ventilation in indoor public spaces in rural KwaZulu-Natal

A growing body of evidence suggests that, in high burden settings, much TB transmission occurs in indoor public spaces. This project seeks to measure ventilation in a set of typical indoor public spaces in a rural community in Northern KwaZulu-Natal. It will also model the likely impact of simple retrofits on ventilation and M. tb transmission. This project is a collaboration between academics at the Centre (Dr. Tom Yates and Professor Ibrahim Abubakar), the Africa Centre for Health and Population Studies (Dr. Tom Yates and Professor Frank Tanser) and the Bartlett School of Architecture (Dr Jon Taylor and Dr Hector Altamirano). The project is funded by the UCL Grand Challenges of Global Health scheme.

M. tb transmission in rural KwaZulu-Natal

A growing body of evidence suggests that, in high burden settings, much transmission of M. tb occurs outside the household. This project, based at the Africa Centre for Health and Population Studies in Northern KwaZulu-Natal, seeks to understand risk factors for M. tb infection in primary school children. We measured infection in 6-8 year old children, obtained data on their social contact patterns and then linked these data to the children’s records in the Africa Centre household surveillance programme. All buildings in the surveillance area are geo-located, which will allow spatial analyses of M. tb infection in this community. This research is led by Dr. Tom Yates with supervision from Professors Frank Tanser, Ibrahim Abubakar and Marie-Louise Newell. The Tuberculin school survey was funded by the KwaZulu-Natal Research Institute for TB and HIV (KRITH) in Durban.

Contributions to other projects

We are also contributing to projects led by:

  1. Internal collaborators including the TB REACH progamme grant led by Professor Andrew Hayward and a UCL BRC funded study on stratification of antimicrobial treatment for TB by whole bacterial genome sequencing directly from sputum tuberculosis led by Professor Judy Breuer. We are also collaborating with Dr Daren Coruana, UCL Chemistry, on a gas phase electrochemistry devise to detect bacteria and with Prof Rachel McKendry, London Nanotechnology Centre, on canti lever sensors to detect antimicrobial resistant bacteria.
  2. External collaborators including a BCG Case Control Study (http://www.nets.nihr.ac.uk/projects/hta/081701) coordinated at the London School of Hygiene and Tropical Medicine, a cluster randomised controlled trial to assess the treatment of latent tuberculosis infection in primary care led Queen Mary University of London, the IDEA study (http://www.nets.nihr.ac.uk/projects/hta/0810602) funded by NIHR, the Health Protection Research Unit in modelling methodology (http://www1.imperial.ac.uk/hprumodelling/respiratory_infections/) at Imperial College and with Public Health England on a study to enhance management and contact tracing among antenatally screened HBV-infected women and chronically infected individuals to improve testing uptake, vaccination and onward referral of household contacts.

The Impact of our work

Our research is multidisciplinary and multi-professional and aims to underpins national and global policy on infectious disease control. Much of our research involves epidemiological studies ranging from clinical trials to observational studies, record linkage, modelling and the analysis of routinely collected data to inform policy. Nationally, our work has informed the development of the collaborative TB strategy which was published by Public Health England in January 2015 (http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(14)61638-X/abstract).

Examples of the national and international impact of our work includes:

Tuberculosis in hard to reach groups

Our evaluation of the Find and Treat Service demonstrated that this intervention is cost effective and led to the commissioning of the service. See http://www.bmj.com/content/343/bmj.d5376.long and accompanying video https://www.youtube.com/watch?v=H01jCZAbKbE. This evaluation is widely cited and has informed NICE guidelines and European recommendations on control of TB in hard to reach groups.

Molecular epidemiology of tuberculosis

The analysis of molecular epidemiological data has provided insights into the spread of tuberculosis and multi drug resistant tuberculosis in the UK (Anderson et al) demonstrating limited transmission in the UK and showing opportunities exist to improve contact investigation. In collaboration with Dr Pam Sonnenberg, we have also recently shown that use of MIRU-VNTR to inform the prospective investigation of clusters is not cost effective (http://thorax.bmj.com/content/early/2015/04/16/thoraxjnl-2014-206480.long). Previous work include contrasting the impact of Beijing strain on TB epidemiology in Peru and the UK (http://erj.ersjournals.com/content/43/2/632.long),

BCG vaccine

Our review of BCG vaccination effectiveness (http://www.journalslibrary.nihr.ac.uk/hta/volume-17/issue-37#abstract) , led to a joint case control study with LSHTM, which should provide useful data to inform future BCG vaccination policy. More recently, we have demonstrated that BCG can protect against tuberculosis infection (http://www.ncbi.nlm.nih.gov/pubmed/25097193), in addition to its proven effect on severe forms of tuberculosis disease.

Latent tuberculosis infection

We reviewed the evidence for latent TB treatment, which informed global guidelines for preventative therapy (http://annals.org/article.aspx?articleid=1895308) and undertaken analysis to inform the targeting of latent TB screening (http://www.ncbi.nlm.nih.gov/pubmed/23828120). In collaboration with Public Health England, we are leading the largest cohort study evaluating the prognostic value of interferon gamma release assays compared to the tuberculin skin test, which has completed enrolment.

Tuberculosis and air travel

Our work on tuberculosis and air travel has informed national and European guidelines (http://www.sciencedirect.com/science/article/pii/S1473309910700281).

HIV and tuberculosis

In a randomised controlled trial using a step wedge design, we were able to show that an educational intervention can impact HIV testing in TB clinics (http://erj.ersjournals.com/content/41/3/627.long). We identified the increased risk of tuberculosis and HIV infection in health care workers http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=8678341&fileId=S0950268811002445)

Tuberculosis in pregnancy

Through a case-case analysis and a cohort study using primary care data, we demonstrated an increased risk of tuberculosis in the post partum period (http://www.atsjournals.org/doi/abs/10.1164/rccm.201106-1083OC?url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&rfr_dat=cr_pub%3Dpubmed&#.VWHCpFlViko)

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