With the recent launch of its infectious diseases strategy, Public Health England (PHE) has outlined is ambitions for the next five years in terms of its core mission “to prevent, detect, respond to and reduce the impact of infectious diseases in our population”.
The strategy outlines ten priorities that will form the focus of PHE’s efforts, supported by development of their workforce, new ways of collaborative working and taking advantage of new technologies. These priorities include efforts to optimise vaccine use, halt the rise in sexually transmitted infections, strengthen England’s Health Protection System and address infectious diseases linked to health inequalities.
WGS as a core technology
A number of the priorities stand out – in particular, priority seven which is to “embed whole genome sequencing (WGS) in PHE labs and optimise the use of WGS-based information”. In our 2015 report Pathogen Genomics into Practice we outlined the advantages and challenges of implementing pathogen genomics services and the areas where WGS could have an impact, including in supporting infection control efforts (see also). It is heartening to see the recommendations from this report in action, and that the culmination of efforts by PHE and other stakeholders has led to the establishment of WGS as a key technology in the detection and control of infectious disease. This will only build on and strengthen current WGS activities within PHE, which was the first to offer the routine use of WGS in the management of tuberculosis, and has established a central WGS service which provides routine sequencing for a number of pathogens of national importance such as Salmonella and E. coli.
Emerging technologies
Another priority (three) considers how PHE could make the most of advances in technology to improve the collection, processing and management of data, with the specific goal of improving disease surveillance, detection and control. Although genomic data is only one of a myriad of data types that PHE interact with, there are common issues around data management that are universal to all data. One issue the PHG Foundation has worked on is around data sharing – in the context of infectious diseases, appropriate sharing of genomic and associated metadata can have an impact on tracking pathogen spread and movement and detecting outbreaks. A recent example is of WGS being used to investigate an outbreak of Salmonella food poisoning in several European countries – efforts which were supported by data sharing between the affected countries.
Impact of WGS as part of the toolkit
Many of the priorities in the strategy require multidisciplinary and collaborative efforts to manage, including using WGS as part of the toolkit to deal with these challenges. Tackling antimicrobial resistance (AMR; priority two) is one issue that has been on the international agenda for some years and is also in the UK government’s national risk register for civil emergencies as a factor that will have an impact on disease risk in the mid- to long-term. We have written before about how WGS could contribute to the management of AMR, for example through supporting disease surveillance efforts and appropriate prescribing. While WGS is not the panacea when it comes to tackling AMR, as a technology it has an important supportive role in helping health authorities in the UK, and globally, achieve their goals.
This supportive role will also have an impact on the delivery of strategy five, which is focussed on strengthening PHE’s response to major disease incidents and emergencies. While conventional next generation sequencing is not quick enough to generate information in a fast developing disease outbreak, evidence is being gathered on the use of long-read sequencing technologies for this purpose. One recent example was the use of long-read sequencing during the 2018 Lassa fever outbreak in Nigeria: a pilot study was conducted within 10 days a provided sufficient information to reassure the authorities that extensive human-to-human transmission was not taking place. As a result, resources could be more appropriately spend managing the rodent disease vector.
Strengthening the future of infectious disease genomics
The next five years will prove crucial in terms of supporting and embedding the use of WGS within infectious disease services. PHE’s latest strategy is an important step in building on the hard work that has already taken place and in consolidating genomics expertise within the service. We look forward to seeing the vision for infectious disease genomics become a reality.