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Know your enemy – how genomic sequencing can help ensure safe food

10 August 2023

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Scientists at the Quadram Institute have shown how genome sequencing can be used to better understand the causes, sources and risks posed by food poisoning bacteria. This suggests genomic surveillance could be a valuable tool to ensure food safety.

Microbes on foods that cause illness, long term complications, loss of earnings and costs to businesses place an estimated £9 billion burden on the UK each year. Salmonella bacteria make a significant contribution to this, with around 30,000 cases. This figure may be an underestimate as not all cases are reported. There are a number of different types of Salmonella, and they can cause gastrointestinal disease through infections associated with a range of different foods. This presents challenges when trying to detect or trace causes of the disease, or pinpoint vulnerabilities in the food supply system, and how these may change with shifts in dietary patterns or food production.

To help address this, researchers from the Quadram Institute and University of East Anglia on the Norwich Research Park have been deploying next generation sequencing techniques to better understand Salmonella populations on our food.

The study was funded by the Biotechnology and Biological Sciences Research Council (BBSRC), part of UKRI, and the Food Standards Agency and published in the journal Microbial Genomics.

Over 18 months, they collected a range of foods from different retail outlets in Norfolk and identified any Salmonella bacteria present. They then sequenced the entirety of each sample’s genome. Whole genome sequencing like this not only identifies the type of Salmonella but gives an indication of how related two samples are. If two samples have highly similar genomes, they are more likely to have come from the same source. It also lets researchers identify genes that give the bacteria specific properties, such as an enhanced ability to cause infections or resist antimicrobials.

The study also incorporated the genomes of Salmonella isolates from infected people, which are routinely collected, sequenced and made publicly available by the UK Health Security Agency (UKHSA). This opens the door to linking Salmonella outbreaks to foods.

The survey found that overall Salmonella prevalence on foods on sale was low: 9.6% of raw chicken, 3.7% of raw prawn and 1.3% of raw pork samples were contaminated. None of the prawn samples were closely related to human-derived isolates, suggesting that prawns are unlikely to contribute to Salmonella infections in the UK.

The picture in chicken was different. 17% of imported chicken samples contained Salmonella that were closely related to human-derived isolates, but in domestic chicken the figure was only 2.3%. However, most of the imported chicken samples were frozen whilst the domestic chickens were mostly chilled, so the differences may be due to unsafe cooking practices associated with frozen chicken.

A quarter of the infected foods were found to harbour diverse Salmonella strains that wouldn’t have been detected if only a single isolate was sampled. This might hamper outbreak tracing efforts and shows the power of whole genome sequencing to differentiate closely-related but different strains.

Another advantage of whole genome sequencing is that it allows a higher resolution of genetic analysis. In this study the researchers looked at each sequence for genes known to confer resistance to antibiotic drugs. 5.1% of chicken and 0.64% of pork samples, but no prawns, had genes that would make them resistant to multiple antibiotics. This information could be useful for directing treatment; although most cases are self-limiting, vulnerable or immunocompromised patients may need antibiotics, so screening could ensure the most effective choice of treatment is given.

Whole genome sequencing identified foods associated with clinically important Salmonella and foods with genetically diverse Salmonella, which may hinder outbreak investigations and source attribution” said Dr Samuel Bloomfield from the Quadram Institute and lead author of the study.

”Food sources, farming and production practices, and consumer behaviour are constantly changing, altering the types of foods associated with foodborne disease. The prevention of future salmonellosis outbreaks relies on continued surveillance of Salmonella on retail food with the high resolution of whole genome sequencing to relate food and human isolates.”

This article was originally posted by our partner, the Quadram Institute, on their website here.

Image: Salmonella bacteria growing on BSA/XLD agar. Credit: Quadram Institute.

Reference: Genomic diversity and epidemiological significance of non-typhoidal Salmonella found in retail food collected in Norfolk. Samuel J. Bloomfield, Nicol Janecko​, Raphaёlle Palau, Nabil-Fareed Alikhan​, Alison E. Mather. Microbial Genomics DOI: 10.1099/mgen.0.001075

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