23 October 2015
Foodborne pathogens, such as Listeria, E. Coli and Salmonella are a significant threat to population health. Outbreaks of infections with these pathogens are often hard to bring under control, and even harder to track, as the food we eat often takes a complex, multinational journey from farm to fork. Surveillance to detect and resolve outbreaks of foodborne infections is, therefore, an important part of the work of public health microbiology laboratories across the world. As with other areas of infectious disease surveillance and outbreak control, there has been much discussion of how whole genome sequencing (WGS) could be used to improve both the sensitivity with which outbreaks are detected (or ruled out) and the delineation of their origin and routes of transmission.
In England the national reference microbiology laboratory at Colindale now routinely uses WGS for the surveillance of Salmonella infections. Their recent study demonstrates how the technology was used to inform management of a UK hospital-based outbreak that was ultimately linked to eggs from factories in southern Germany.
Recognising the need to encourage the wider use of WGS for managing foodborne disease across the region, the European Centre for Disease Control and Prevention (ECDC) has convened a group of experts from member nations of the EU to provide guidance on this topic. The guidance focuses on the technical challenges to achieving accurate and meaningful results from WGS, and considers the additional resources needed to ensure that analysis of outbreaks involving multiple countries can be efficiently and effectively investigated using a combination of genomic data and more traditional (but still essential) ‘shoe leather’ epidemiology.
Having recently completed the PHG Foundation’s work on moving pathogen genomics into practice, I am heartened to see ECDC signalling the importance of a transition to WGS by public health laboratories across Europe. In particular I welcome their emphasis on the need for collaboration between nation states and their clear understanding that this must be underpinned by effective mechanisms (such as common databases and standards for nomenclature) to enable sharing of genomic and epidemiological data between states. It is also fantastic to see a clear commitment to working on a joint strategy between ECDC and the European Food Standards Agency (EFSA), to ensure their work on supporting the genomic analysis of both human and non-human (i.e. animal) infections is undertaken in a joined-up way. This is consistent with the importance we place on taking a ‘One Health’ approach to implementing genomics for surveillance of infections.
It is clear that effective communication of information (be that data, samples or technical knowledge) will be crucial to the effective deployment of WGS for monitoring foodborne disease outbreaks across Europe. Achieving this can be a significant challenge even at the national level. At the transnational level - where different regulatory, cultural and health systems abound – these challenges are likely to be even greater. For example, varying national requirements to provide samples and information on foodborne disease to public health authorities and varying regulatory frameworks with respect to the sharing of personal data, already negatively impact on the effectiveness of transnational outbreak investigations. Genomics cannot itself solve these problems, and indeed its effectiveness will be hampered in just the same way as the effectiveness of existing surveillance methods by failures to gather and share information in a time frame that allows public health action to be taken.
Despite the challenges ahead, I am optimistic. It is clear that there is now a global drive to harness the benefits of genomics for the management of infectious disease. Initiatives such as the Global Microbial Identifier are working tirelessly to breakdown some of the barriers that stand in the way of realising the benefits of this potentially transformative technology at an international level. At the PHG Foundation we are confident that our report and its recommendations will prove to be a valuable resource to countries worldwide who are grappling with the challenges of implementing genomics for the management of infectious disease.