Real time genomic epidemiology comes to England

Leila Luheshi

18 August 2014

Public Health England has recently reported that they are investigating an outbreak of Salmonella infection across England. To date this outbreak has affected over 150 people and in addition to cases being identified across several English regions, there also appears to be a link to cases of the disease in France and Austria.

Vital to investigating such outbreaks is the ability to distinguish between people with sporadic Salmonella infections, which occur all year round, from those whose infection is part of this particular outbreak.  The health protection team are also, of course, trying to identify the food source most likely responsible for spreading the infection so widely. Their ability to achieve these aims depends heavily on the resolution of microbiology methods available to distinguish between individual cases of infection; higher resolution methods, such as whole genome sequencing (WGS) , offering higher discriminatory power than methods such as phage typing or serotyping.

In this week’s health protection report from PHE  it was exciting to note, therefore, that whole genome sequencing had been used as part of the investigation of this Salmonella outbreak, contributing to the view that cases of this infection spread across different regions of England really do appear to share a common source, although the source has yet to be identified.

Why does this matter?

PHE has recently launched its Pathogen Genomics service, which aims, amongst other things, to provide whole genome sequencing of pathogens to enable more effective investigation of outbreaks such as these.  Using whole genome sequencing allows the similarities and differences between bacteria isolated from people or food/environmental sources to be measured much more precisely, allowing improved detection, definition and, ultimately, outbreak resolution. Previously, however, this type of analysis was only available on a research basis and was typically applied retrospectively to understand what had happened in past outbreaks.  This meant it did not affect the management of the outbreak itself, although lessons could still be learned for the future.

By contrast, the use of WGS by PHE in the ongoing Salmonella outbreak appears to be a great early example of how making pathogen genome data available in near-to ‘real time’ can be used to good effect in managing an outbreak while it is still underway. While it remains to be seen whether this information will ultimately contribute to the resolution of this outbreak remains to be seen, it is nevertheless a very positive sign to see this important service being made available in England.

Learning the lessons

At PHG Foundation we’re currently engaged in a major project to develop policy recommendations to support the effective implementation and use of pathogen genomics in England.  With this in mind, we hope that experience of using WGS in outbreaks such as this will be built upon and shared so that the lessons learned can be shared with microbiology services wishing to implement pathogen genomics in England and beyond.