National TB strain typing service: what we do

Guidance on the national tuberculosis (TB) strain typing service, including its work, achievements, objectives, and future direction.


The national strain typing service was established in England in 2010 in response to ‘Stopping tuberculosis in England: an action plan from the Chief Medical Officer’ (2004), which identified molecular strain typing of all Mycobacterium tuberculosis complex isolates as a major component of TB control.


The main objectives of the national strain typing service are to:

  • provide access to typing results in local or national incidents of suspected transmission, enabling the prospective, proactive, local-led application of strain typing for TB control and public health protection
  • understand the national and local epidemiology of TB, including identifying risk groups for TB attributable to recent transmission
  • understand the molecular epidemiology of TB, including circulating strains, lineages and virulence
  • monitor TB programmes by analysing the trends in estimates of recent transmission
  • meet international obligations for molecular surveillance, Europe-wide and globally
  • create a national repository of strain types

The results of TB strain typing, combined with epidemiological data, can:

  • help identify TB patients potentially involved in the same chain of recent TB transmission
  • assist in initiating timely and appropriate control measures following cluster and outbreak investigations
  • provide an opportunity to better understand the epidemiology of TB in a given setting

Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeats (MIRU-VNTR) strain typing

The M. tuberculosis complex genome possesses repetitive sequences of DNA located at specific loci. These repeats:

  • are referred to as MIRU (mycobacterial interspersed repeat units) and VNTR (variable number tandem repeats)
  • vary in number between different loci and different strains

‘Mycobacterium tuberculosis strain typing: a guide to data production and distribution’ covers how and why Public Health England (PHE) is using 24 loci MIRU-VNTR data, including how the data is:

  • generated
  • analysed in the laboratory
  • reported

The ‘national TB strain typing service factsheet’ provides an overview of MIRU-VNTR strain typing in the UK, including:

  • the methods used
  • where typing is performed
  • how the results are used
  • the advantages and disadvantages in relation to other genotyping methods

Cluster investigation handbook

Following the evaluation of the first 3 years of the national tuberculosis strain typing service and resulting recommendations, PHE produced the TB strain typing and cluster investigation handbook’. This handbook features:

  • guidance and support to public health staff involved in the investigation of clusters
  • agreed standards and criteria for the investigation of clusters
  • guidance on the recording of the processes and outcomes of such investigations

The second edition of the 'TB strain typing and cluster investigation handbook' (PDF, 1.55 MB, 54 pages) is also available.

Strain typing module

PHE developed bespoke software called the Strain Typing Module (STM), which is part of the Enhanced TB Surveillance System (ETS), to identify molecular clusters and manage cluster investigation at a national and local level.

The software generates routine reports of molecular clusters for local and national teams, so staff can review the demographic, clinical and social risk factor information for cases in these clusters, and better direct cluster investigation and public health action.

To find out more, see the ‘enhanced tuberculosis surveillance strain typing module: user guide’, which includes detailed screen shots of the software.


PHE uses a shorthand ‘cluster name’ to identify a molecular cluster rather than the full 24 character code. The nomenclature should remain consistent over time and throughout the country to:

  • allow information to be shared easily sub-nationally
  • ensure that all cases are included in the cluster at a national level

Service evaluation

An independent evaluation was conducted alongside the implementation of the service between January 2010 and March 2013. Descriptive, qualitative and quantitative methods were used to explore the structures, processes, outputs and outcomes of the service. The major recommendations were to:

  • continue the timely universal typing of all culture-confirmed TB cases
  • make epidemiological analysis of the data the high priority
  • reconsider cluster investigations, specifically, investigate local clusters in response to local demand, and limit investigating national clusters to those of public health importance

To find out more, see the ‘Tuberculosis (TB) strain typing service evaluation’.

Data analysis

Analysis of the first 4 years of data has been carried out for the UK, and is published in the ‘Tuberculosis (TB) in the UK’ annual reports .

Published 1 April 2014