2830: Eliminating in-country TB transmission in the UK: defining the added value of whole genome sequencing
This project aims to learn from past cases of tuberculosis in the UK and how they can predict which persons are likely to be infected in the future.
About the project
What the project aims to do
Tuberculosis (TB) is a bacterial infection which can be lethal if left untreated. The main aim of this project consists of learning from past cases of tuberculosis in the UK to predict which persons will likely be infected in the future. These results will allow more precise public health interventions that should lead to the elimination of person-to-person transmission of this pathogen in the UK. To achieve this goal, we will:
- analyse tuberculosis genomes (that is, genetic information contained in the bacteria) collected by the UK Health Security (UKHSA) since 2018, in order to infer past transmission events
- connect these transmission events to patients’ data in order to identify the features most likely associated with tuberculosis transmission
Why this project is important
The number of tuberculosis infections in the UK has been declining in recent years thanks to public health interventions. These measures notably include an automatic tuberculosis detection programme for all migrants arriving in the UK (which account for about 75% of tuberculosis cases - ‘Tuberculosis in England, UKHSA 2021 report’).
However, the elimination of tuberculosis community transmissions (which are responsible for 25% of tuberculosis infections in the UK) is a costly process involving the tracing and testing of all contacts of the persons infected, and has so far failed in several parts of the country. A better understanding of tuberculosis community transmission in the UK is therefore required in order to improve public health interventions and to eliminate these tuberculosis community transmissions.
Who the data is about
The data includes:
- all patient notifications with Mycobacterium tuberculosis (MTB) whether microbiologically or clinically diagnosed, notified between 1 January 2018 and 31 December 2029
- residency in England at the time of sample collection or notification
- mycobacterial sequencing data
- gender (male or female)
- ethnicity
How the data will be used
The tuberculosis whole genome sequencing data and depersonalised patient’s medical and social data, all already collected by the UKHSA, will be transferred to Imperial College London. TB sequencing data will be analysed to identify transmission events between TB genomes. Using the patient medical (for example, type of TB infection and TB symptoms) and social data (for example, approximate geographical location), we will then identify which TB patients should ultimately be targeted for contact tracing. We will also estimate the cost effectiveness of the proposed contact tracing measures using modelling analyses and also analyse transmission trends over time.
How often data is needed
Data will be released annually.
How this project will benefit public health and the public
We hope this research project will help UKHSA to eliminate TB community transmission by providing a set of rules to prioritise contact tracing in a cost-effective way. For each future TB infection occurring in the UK, our project will predict which person should be prioritised for contact tracing, given the epidemiological and social characteristics of the person infected.
Planned project outputs and communication
The project will be featured in:
- peer-reviewed scientific journals
- an internal report (publication not intended)
- a conference presentation
- press release
Lawful processing of personal and special category personal data
The data needed for this project is not personal data.
Legal basis for using personal data (Article 6)
Not applicable.
Legal basis for using special category personal data (Article 9)
Not applicable.
Common law duty of confidentiality
The data needed for this project is not confidential patient information.
How is the duty of confidentiality set aside
Not applicable.
National Data Opt-Out
Will opt-out preferences be applied?
No
Where ‘No’, why?
The National Data Opt-Out does not apply to anonymised data.
Digital Object Identifier
Not assigned to this release.
Organisation’s Research Organisation Registry (ROR) ID
Amendments
Since initial approval, UKHSA has agreed the following amendments:
| Reference | Scope of amendments |
|---|---|
| A1 | Extension to contract term |
| A2 | 1) Change of address and storage location, 2) Change to security assurances, 3) New planned project output and communication added, 4) Additional years of data to be received and change of format of the data, 5) Change to the project scope, 6) Extension to contract term |
Updates to this page
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Changes to the approval to update 1) the scope, 2) project outputs and communications, 3) the cohort years and 4) added the amendment table documenting amendments to the original proposal.
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First published.