FSA report brings wider failure to implement pathogen genomics into focus

By Leila Luheshi

14 April 2016


It was great to see the launch yesterday of the Food Standards Agency’s Chief Scientific Advisor’s report on whole-genome sequencing of Foodborne Pathogens, and not only because this report references the landmark PHG Foundation publication on this topic from 2015, Pathogen Genomics into Practice, and supports many of its recommendations.

I was delighted to see the FSA acknowledging the vital role that pathogen whole genome sequencing, provided to them by the Gastrointestinal Bacteria Reference Unit at Public Health England (PHE) Colindale, is already playing in enabling them to investigate foodborne infectious disease outbreaks more effectively and in facilitating more targeted and rapid regulatory action to bring them under control and reduce harm to the public.

We need more!

As I am sure the FSA and PHE would both agree, however, there is still much to be done to maximise the benefits that pathogen whole genome sequencing (WGS) has to offer to protect human health. Not least in the area of foodborne disease investigation, where it is critical that the animal and human health communities should co-develop a shared strategy to obtain and analyse genomic information obtained from their respective surveillance and investigative activities. Thankfully, the team at PHE Colindale (lead by Dr Kathie Grant) have already established, and are continuing to develop, sequencing and analysis services for the most common foodborne pathogens. Extending this approach to the same pathogens isolated from animals by the Animal and Plant Health Agency should be a natural next step, as part of the One Health approach advocated by Prof. Guy Poppy (the Chief Scientific Adviser to the FSA) in his report.

Save money… work with a friend

A key recommendation of our Pathogen Genomics into Practice report is that there should be a health system wide approach to the implementation of this technology. There are two main reasons for this: one is simply that it is more efficient. Laboratories across the many parts of our health service must build on existing expertise and make use of existing resources developed by the early pioneers rather than ‘reinventing the wheel’ and set up their own infrastructure and services from scratch, wasting precious tax payer cash. The other is that the data generated, and analytical methods developed must not become ‘siloed’ within individual laboratories and organisations, as they will have broad utility across locations and organisations, and much of the return on the investment in genomic infrastructure (such as sequencing and analysis capacity) will be lost unless this utility is achieved.

Pathogens without borders?

In this respect, the FSA is leading the way by participating in an international initiative, the Global Microbial Identifier project that aims to enable the international sharing of pathogen genomic data. However, it would be unfortunate, to say the least, if we were to find ourselves co-developing our approach to the implementation of this important tool for the management of infectious disease with international partners, whilst neglecting to do the same with the organisations within our own borders. In this regard, we believe it is vital that all health related organisations with a role to play in managing infectious disease in the UK (the NHS, PHE, FSA, APHA and their respective departments of state, primarily the Department of Health and DEFRA) work together to develop an approach to the implementation and utilisation of pathogen genomics. 

After all, infectious diseases have no regard for the painstakingly constructed and heavily defended boundaries between (and even within) these organisations. And the people affected by these pathogens care equally little for whether their particular disease is the prime responsibility of one organisation or another. 

The need for a larger vision

A coherent cross-organisational approach to using genomics in the management of infectious disease is not going to emerge from the primordial swamp of public sector organisations involved all by itself. Despite the obvious advantages for both cost-efficiency and scientific and clinical effectiveness, there are currently no incentives in place to make this happen. If this painstakingly slow and piecemeal approach to implementation continues, what will emerge will be a series of disconnected initiatives, each limited in scale by reliance on small, organisation specific funding mechanisms (often research based), that fail to realise the benefits of genomics that only manifest when it is implemented at scale and in a way that emphasises linkage of data and sharing of knowledge as widely as possible.

Who will step up and take charge?

Who can change this? If the experience of the 100,000 Genomes Project is anything to go by (and it may not be) building the type of cross-organisational enterprise necessary to realise the full health benefits of genomics requires political commitment at the highest level. It also requires some up-front funding. It therefore remains a source of immense disappointment to me that pathogen genomics is not able to shelter under the political and financial umbrella of Genomics England. Rather, it has been effectively cast aside in favour of a sole focus on human genomic medicine – despite the very real impact of infectious diseases on human health. Given the huge impact that organisations such as PHE and FSA have already shown pathogen genomics can have on protecting the health of the public, and given the stated aims and ambitions of our current government to lead the way in using genomics to improve the health of our population, this decision seems inexplicable. 

It is hard to comprehend why we as a nation are investing more than £250 million over the next five years in developing human whole genome sequencing for medical benefits that are for the most part yet to be established (although I am sure in time they will be) when, for a fraction of that amount, we could be accelerating the introduction of pathogen whole genome sequencing. This is an application of genomics that we are already reasonably certain would prevent serious illnesses such as TB, helping us manage the growing threat of antimicrobial resistance to human health, and offering us immediate protection against the threat of future pandemics.

Genomics and policy newsletter

Sign up