Whole genome sequencing can improve surveillance and control of Clostridium perfringens, say researchers.

Clostridium perfringens bacteria are responsible for an estimated 80,000 cases of diarrhea in the United Kingdom each year either from food poisoning or a non-foodborne origin. It is the second most common foodborne pathogen after Campylobacter with cases often under reported because of mild illness.

For many people, symptoms are unpleasant but normally only last up to 24 hours. For vulnerable groups such as the elderly living in care homes, a longer-lasting debilitating chronic infection may occur that can be fatal. Enterotoxigenic Clostridium perfringens is estimated to cause 55 deaths per year in England and Wales.

Analysis of historical outbreaks

Researchers at the Quadram Institute worked with Public Health England (PHE) to analyze Clostridium perfringens foodborne and non-foodborne outbreaks over seven years in England and Wales. With the University of Cambridge, the team used whole genome sequencing (WGS) to analyze bacterial strains associated with causing gastroenteritis.

WGS has more discriminatory power in profiling outbreak strains, when compared to the PHE laboratory technique of fluorescent amplified fragment length polymorphism analysis.

A total of 109 samples of Clostridium perfringens isolated from disease cases or foods suspected of causing infections in England and Wales between 2011 and 2017 had their whole genome sequenced, according to the research published in the journal Microbial Genomics.

This allowed analysis of the genes responsible for toxin production, as well as characteristics that aid infection, such as antimicrobial resistance. Comparative analysis of the different genomes allowed researchers to see how related different strains are, which helps trace where they may have come from.

The team found nine outbreaks associated with care homes in North East England over a period of five years were caused by closely related strains of Clostridium perfringens. This indicates a potential common source, although what this was could not be pinpointed.

WGS for routine surveillance

Dr. Lindsay Hall, from the Quadram Institute, said the study shows how cutting-edge approaches can be used profile and track important bacteria associated with food poisoning.

“We hope to use the information generated to identify potential strains of Clostridium perfringens that may be associated with outbreaks so that we can in the future develop intervention strategies to try and prevent spread.”

Using WGS for routine surveillance could be crucial in preventing future outbreaks and to rapidly pinpoint sources of contamination. Wider surveillance could provide data from diverse sources to help researchers understand more about the bacteria, how they survive and why they cause disease.

The study showed the genes that encode the key toxin responsible for causing gastroenteritis aren’t limited to the bacterial chromosome but may also be carried on virulence plasmids that can be transferred around bacteria.

Human cases of Clostridium perfringens diarrhea are primarily caused by type F strains (formerly classed as enterotoxigenic type A), which produce enterotoxin (CPE), encoded by the cpe gene.

More data will help understand how the virulence factors are spread and identify reservoirs of persistent bacteria. This will improve intervention strategies and ways of preventing outbreaks and infections to protect vulnerable communities.

Researchers received funding from the Biotechnology and Biological Sciences Research Council, the Wellcome Trust and Food Standards Agency.

Typical symptoms which occur within eight to 14 hours after ingestion of contaminated food include intestinal cramps and watery diarrhea without fever or vomiting, and normally last 12 to 24 hours.

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