Whole genome sequencing could help control disease

A study into one of the UK’s leading causes of gastroenteritis has shown how whole genome sequencing can improve its surveillance and control of the disease.

Clostridium perfringens bacteria are responsible for an estimated 80,000 cases of diarrhoea in the UK each year, either from food poisoning or from non-foodborne nosocomial origin. In very rare cases, C. perfringens infection can develop into more severe forms. For vulnerable groups such as the elderly living in care homes, a longer-lasting debilitating chronic infection may occur that can be fatal.

To help combat this problem, researchers have said we need more information about how these bacteria spread and infect people.

A team from the Quadram Institute have collaborated with Public Health England to analyse C. perfringens foodborne and non-foodborne outbreaks over a seven year period in England and Wales. Working with the University of Cambridge, they have used whole genome sequencing to carry out an analysis of the bacterial strains associated with causing human gastroenteritis.

109 samples of C. perfringens isolated from disease cases or foods suspected of causing infections in England and Wales between 2011 and 2017 had their whole genome sequenced. This allowed an analysis of the genes present that are responsible for toxin production, as well as related characteristics that aid infection, such as antimicrobial resistance. Comparative analysis of the different genomes allows the researchers to see how the different strains are related – a key way of tracing where they may have originated from.

The team found that nine distinct outbreaks associated with care homes in North East England, over a period of five years, were caused by very closely related strains of C. perfringens. This indicated a potential common source linking them, although the exact source cannot be pinpointed after the event.

Using whole genome sequencing for routine surveillance, particularly in places such as care homes where vulnerable people need protection, could be crucial in preventing future outbreak spread and in rapidly pinpointing the sources of contamination.

As well as monitoring for outbreaks, wider surveillance could provide data from diverse sources that will help researchers understand more about the bacteria, how they survive and why they cause disease.

The data obtained in the study showed that the genes that encode the key toxin responsible for causing gastroenteritis are not limited to the bacterial chromosome, but may also be carried on virulence plasmids that can be transferred around bacteria.

More data is required to further understand how the virulence factors are spread and will help identify reservoirs of persistent bacteria. The hope is this will help to improve intervention strategies and ways of preventing outbreaks and infections, and ultimately, protect vulnerable communities.