TB in England: moving closer to deployment of whole genome sequencing
2 October 2015
PHE's annual Tuberculosis (TB) in England report, released on 1 October, contained encouraging news on two fronts: another fall in the number of cases, and an update on the whole genome sequencing pilot.
The number of TB cases in England has fallen for the third year in a row to 6,520 (12 per 100,000 population) down from a high of 8,276 in 2011 (15.6 per 100,000 population). Despite this decline, the incidence of TB in England is still high compared to other countries in Western Europe, for example 9 per 100,000 in France and 6 per 100,000 in Germany.
The decrease is mostly due to a reduction in the number of cases diagnosed in those not born in the UK. Many of these cases are due to reactivated latent TB infection, which often occurs many years after the original infection. One of the pillars of PHE's TB strategy, launched in January 2015, is screening for latent TB in high-incidence areas in the UK, and the continued screening of individuals from high-incidence countries for active TB before they enter the UK on visas of longer than six months' duration. While many other factors have contributed to the decrease in cases, it is hoped that the collaborative TB strategy will contribute to a continued reduction.
The report also outlines developments in the progress of the TB whole genome sequencing (WGS) pilot, started in July 2014 at the Public Health England Regional Centre for Mycobacteriology in Birmingham. Sequencing has been carried out in parallel with standard tests for species identification, resistance profiling and relatedness on all mycobacteria that grew in culture, which were obtained from patients newly diagnosed with TB. This approach has allowed a direct comparison between WGS and existing laboratory methods. While the full results from the pilot are still being analysed and have not been released, the report states that "… the project will provide evidence to validate the processes to the standard required by the UK Accreditation Service (UKAS) for accreditation of a clinical service" and that "PHE is close to deploying the use of whole genome sequencing for TB for the NHS throughout England".
The implementation of a TB WGS service, and the validation and accreditation of this service will provide a valuable learning opportunity for how whole genome sequencing can be applied to other pathogens and to infectious disease services in general. In our Pathogen Genomics into Practice report, we outline several key features of the system that need to be in place in order to facilitate implementation and support development of services that are of consistent quality and available nationwide. In particular, the sharing of knowledge and expertise with other parts of the health system will ensure that duplication of effort is avoided as future services are developed and brought online.
The implementation of an accredited clinical service using whole genome sequencing for the management of tuberculosis will be a milestone in the development of infectious disease services. However the opportunities to learn from and improve on processes, procedures and the implementation of genomics services for the management of other pathogens, and for use in infection control efforts, should not be missed.