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England world leaders in the use of whole genome sequencing to diagnose TB

Whole genome sequencing (WGS) is now being used to identify different strains of tuberculosis (TB), announced Public Health England yesterday.

This is the first time that WGS has been used as a diagnostic solution for managing a disease on this scale anywhere in the world. This builds on WGS based services for public health investigation of infectious diseases, which offer the opportunities for faster, cheaper and more accurate diagnostics than other testing methods.

The technique, developed in conjunction with the University of Oxford, means patients can be treated with precisely the right medication more quickly. Where previously it could take up to a month to confirm a diagnosis of TB, confirm the treatment choices and to detect spread between cases, this can now be done in just over a week by PHE’s Birmingham laboratory. This slows the spread of the disease and boosts the fight against anti-microbial resistance (AMR).

Some strains of TB are called ‘drug resistant’ which means they need to be treated differently to conventional types of TB. With WGS diagnosis, patients who have a strain of TB which is resistant to specific drugs, will receive the right medication from the start of their treatment. This will shorten the time that patients are infectious and so stop the spread and reduce the prevalence of drug-resistant TB and costs to NHS in hospital care.

PHE is already pioneering the development and early use of WGS to enable the investigation and control of multiple infectious diseases. In future, the application of WGS in other conditions will allow us to test and treat patients at the bedside, rather than needing to wait days and sometimes weeks for results. The implementation of this technology will contribute to achieving the government’s ambition of sequencing 100,000 genomes, a project which will ultimately allow us to better understand major diseases and how to treat them.

Professor Derrick Crook, Director of National Infection Service, PHE, said:

The use of whole genome sequencing to diagnose, detect drug resistance and very accurately type TB is a world first for any disease on this scale. By working closely with our partners, we are now able to use cutting edge science to effectively treat these patients with the right medicines quickly. We are immensely proud of the contribution this makes to the prospects of better treatment of TB globally. This approach will also increasingly be used for many other infectious diseases. Our ambition is to achieve this as quickly as possible so many infections can be better diagnosed and treated.

Health Secretary, Jeremy Hunt, said:

The UK has a proud history of leading the world in science and innovation – this is another global first for our country. These pioneering techniques will change patients’ lives in the NHS as well as being used across the globe to slow the spread of a terrible disease and take the fight to drug resistant infection.

Professor Mark Caulfield, Chief Scientist at Genomics England:

Genomics England are delighted to fulfil the transformative ambition of the 100,000 Genomes Project infectious disease programme for the NHS by finding a faster, better diagnostic approach for tuberculosis which is a major infectious disease causing many deaths world-wide.

Tim Jinks, Head of Drug Resistant Infection at Wellcome said:

Improved ability to diagnose infections and to ensure the correct drugs are given to patients is vital. It’s vital so patients can quickly get the most appropriate and most effective treatment and also to battle against drug resistant pathogens. Drug resistant infections are one of the most critical global health threats of modern times - within a generation likely to take more lives than cancer. Investing in development of new diagnostic tools as well as new drugs is essential.

This world first service has been developed in partnership with Genomics England, National Institute for Health Research (NIHR) and Wellcome Trust. PHE intends, with the support of partners, to continue WGS development to protect the public health.

The work has been supported by the NIHR Oxford Biomedical Research Centre, a partnership between Oxford University Hospitals NHS Foundation Trust and the University of Oxford to enable clinical research for patient benefit and foster innovation to improve healthcare. Professor Derrick Crook is also NHS Consultant Microbiologist at Oxford University Hospitals NHS Foundation Trust.


Better treatment, prevention and ultimately eliminating TB is one of PHE’s main priorities. Diagnosis using WGS will help with better identification and treatment of the disease. The number of cases of TB in England has declined by a third over the last 4 years. There were 5,758 confirmed cases in England in 2015 compared to 8,280 in 2011. However, England has one of the highest rates of TB in Western Europe. PHE aims to continue this decrease by focussing on areas where incidence is highest and the greatest reductions can be achieved. This will ultimately meet the World Health Organisation (WHO) goal of eliminating TB as a public health problem by 2035.

About the National Mycobacterial Reference Whole Genome Sequencing service

By implementing WGS, the new service will revolutionise the diagnosis and treatment of TB and play a significant role in delivering England’s TB strategy. It will support the NHS and the patients it is responsible for by:

  • providing universal access to high-quality diagnostics, with fast and accurate identification of mycobacterial species, and with prediction of drug resistance within days, rather than weeks
  • reducing drug-resistant TB by early detection of drug-resistant mutations, supporting early change to appropriate treatment for drug-resistant cases
  • improving contact tracing and strengthening surveillance and monitoring and with more accurate and rapid determination of relatedness between strains to detect transmission
  • improving the accuracy of information for incident and outbreak investigation, focusing efforts and resources based on links identified by WGS, potentially leading to earlier treatment of infectious patients and their contacts
  • ensuring better integration of TB reference services with clinical and public health management by providing timely, detailed information for action

The new PHE National Mycobacterial Reference Service operates from Birmingham and provides services directly to the NHS. The Birmingham laboratory is pioneering WGS testing.

About WGS service development in PHE

PHE has been working to develop WGS techniques to aid the public health investigation of infectious diseases for some years. WGS is used for the investigation of gastrointestinal disease and other infectious disease outbreaks. PHE wishes to build on its early success and learning by continuing to work with current and new partners to develop WGS techniques, to enhance our ability to investigate and treat infectious disease and in doing so, continue to protect the public health.

NIHR Oxford Biomedical Research Centre

The NIHR Oxford Biomedical Research Centre is funded by the National Institute for Health Research, and is a partnership between the Oxford University Hospitals NHS Foundation Trust and the University of Oxford. The NIHR provides the NHS with the support and infrastructure it needs to conduct first-class research funded by the government and its partners alongside high-quality patient care, education and training. Its aim is to support outstanding individuals (both leaders and collaborators), working in world class facilities (both NHS and university), and conducting leading edge research focused on the needs of patients.

National Institute for Health Research (NIHR)

The NIHR is funded by the Department of Health to improve the health and wealth of the nation through research. The NIHR is the research arm of the NHS. Since its establishment in April 2006, the NIHR has transformed research in the NHS. It has increased the volume of applied health research for the benefit of patients and the public, driven faster translation of basic science discoveries into tangible benefits for patients and the economy, and developed and supported the people who conduct and contribute to applied health research. The NIHR plays a key role in the government’s strategy for economic growth, attracting investment by the life-sciences industries through its world-class infrastructure for health research. Together, the NIHR people, programmes, centres of excellence and systems represent the most integrated health research system in the world. For further information, visit the NIHR website.

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