Fera uses WGS to find OriGen of bacterial contamination

By Joseph James Whitworth

- Last updated on GMT

Whole Genome Sequencing- based service launched by Fera

Related tags Bacteria

Fera Science has launched a service using Whole Genome Sequencing (WGS) to identify the source and trace the route of bacterial contamination.

OriGen takes samples from the product supply and processing chain to establish the source of a contamination and the firm claims it can be accurate enough to pinpoint a single machine as the root cause.

It can find the source of Salmonella, Listeria and Campylobacter. A test for pathogenic E. coli is being made available due to recent outbreaks and demand from the industry.

Contingency response or long term monitoring

Edward Haynes, joint fellow in molecular epidemiology at Fera, said it could be used if a firm has an immediate large issue or an ongoing problem with an organism.

“If customers have a problem organism, so Listeria monocytogenes or a serovar of Salmonella, we get the samples, sequence and analyse and then report back to them,” ​he told FoodQualityNews.

“One example could be long-term persistence of single types, the company does environment monitoring and bins samples after they get a positive or negative result. They could be sent to OriGen to build the database. Conversely, strains could be eradicated after a cleaning event and novel strains brought in and imported into the factory.”

Haynes said the level of information is contingent on the kind of samples.

“With large scale contamination a customer will have lots of isolates, potentially multiple from different pieces of equipment so you can look and see if there is a pattern and if they are disseminated to other locations in the facility, so it might need deep cleaning or even replacing,” ​he said.

“One application is a company that is small-scale or has an immediate large problem, we can send them all they need, and they rapidly send samples back to us and we try and culture the problem organism and feed results back.

Large customers have established environmental monitoring so they are more interested when they get a positive to put to one side, freeze it and build a collection over time.”

Haynes said cost would depend on what customer needs are, as would the turnaround, which could be up to 10 days.

“We started talking about OriGen at the end of the last calendar year, it is a continuation of what we do at Fera as we have a strong capability in plant health,” he said.

“We have developed the capability over the last few years and there was enough interest to turn it into a full tool and in the last six to seven months we have validated the system.

“Some are using PFGE at the moment and WGS is the natural next step, PFGE has got limitations, the technique is labourius, specific training is required and there is some ambiguity and subjectivity in interpretation of the bands. WGS is more discriminatory and the cost has decreased over the last 10 years.”

Finding root cause of issue

When asked about WGS not always finding the source of bacterial contamination, Haynes said looking for a pathogen in fresh produce is like looking for a needle in a haystack.

The difference is we are not tracking through large amounts of produce to find illness cases, food processing plants know the problem. They do intensive swabbing and swabs are processed narrowing down the target area,” he said.

To start with a gross contamination event and a recall is reactive but it becomes more preventative and horizon scanning when it links into environment monitoring.”

Haynes added it was working towards UKAS accreditation for WGS to show repeatability.

Fera said a recall means huge expense, reputational damage and the cost of cleaning and sanitising machines and production lines in an attempt to remove the contaminant that caused the initial problem.

Even after all that work there is no assurance that the problem won’t occur again, it added.

Andrew Hudson, head of microbiology for Fera Science, said manufacturers know how expensive a recall can be and how much damage a contaminated product batch can do to their reputation.

“With OriGen they’ll have the assurance that they are doing everything they can to find the root cause of the issue – and the confidence that they won’t have to see another costly recall due to the same product," ​he said.

“WGS allows for a new level of precision in dealing with bacteria entering the food supply chain, dramatically increasing the chances of minimising future contamination from the same source.”

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