Genome sequencing making inroads and could play role in FSMA

By Joseph James Whitworth contact

- Last updated on GMT

WGS is being used by the FDA and CDC in outbreak investigations
WGS is being used by the FDA and CDC in outbreak investigations

Related tags: Food safety, Dna sequencing, Nutrition

Genome sequencing is helping to be more precise in foodborne outbreak investigation but has not recognised its full potential yet, according to a microbiologist.

Advances in genetic mapping and DNA sequencing could make it easier to determine quickly whether people in different locations have been sickened by food from a single source.

Robert Brackett director of the Illinois Institute of Technology’s (IIT)’s Institute for Food Safety and Health (IFSH), said whole genome sequencing (WGS) is becoming the go-to technology.

“PFGE (pulsed field gel electrophoresis) is still the standard, epidemiologists have put so much effort in PFGE in health labs but they are quickly turning to WGS. Prices of equipment have come down and the speed of analysis is better,” ​he told FoodQualityNews.

“Five or 10 years ago to sequence cost $100,000 now it is under $50 and you can do many in a day.

“WGS has more granularity and it is more attributable so a case from an outbreak can be traced to a company or facility and it also excludes companies from scrutiny.

“In the 2006 spinach E.coli outbreak all bagged spinach was suspected and all producers were harmed, today we can focus more clearly who is responsible and the rest are in the clear.”

Industry inroads

Brackett referenced the Mars and IBM partnership​, the 100k genome project and Nestlé’s interest as moves by companies in the space but said obstacles remain.

“There has been a leap forward in peoples’ knowledge but applications are in the infancy and it has not recognised its full potential," ​he said.

“The key limits are in the IT or bioinformatics side of the technology, there are not enough familiar with the use of the technology in this way in the industry.

“We are doing work with FDA partners in our role as an intermediate between the regulatory authorities and food companies.

“We are in initial stages of a WGS consortium and we have spoken to Mars about their partnership with IBM. We could conduct research or provide a framework they could work with.”

He is also working closely with the Institute of Food Technologists (IFT) FutureFood 2050 program. It highlights people leading efforts to find solutions to a healthier and better-nourished planet to feed 9 billion-plus people by 2050 as predicted by the United Nations in 2013.

Role as part of FSMA

Brackett said the technology may have a big role to play within the Food Safety Modernization Act (FSMA) rules being finalised such as the preventive control section in August this year.

It could verify if the intervention does eliminate the hazard, he added.

A European Food Safety Authority (EFSA) event last year recommended WGS be initiated as soon as possible to exploit its potential.

It said a definition of standards for data quality and analysis and interpretation are needed as without these, comparison between multiple laboratories and analysis will be very complex, error-prone and unreliable.

Legal obstacles are expected and a balance must be struck between desirable complete openness from a food safety point of view and privacy and related concerns as part of confidentiality.

Approach perspective

Brackett said his time as directing the US Food and Drug Administration’s Center for Food Safety and Applied Nutrition (CFSAN) from 2004 through 2007 before becoming SVP and chief science and regulatory officer for the Grocery Manufacturers Association has given him a perspective of different sectors.

“Businesses are just getting started with it but the food industry recognises it is an here-to-stay technology," ​he said.

“For example if you had Listeria, or any other bacteria, in your plant where is it coming from? Companies can use WGS to find out where the Listeria is and trace it back to where it came from.

“It can be used in supply chain management, if you have an ingredient with a persistent associated contamination it helps the buyer get a reason to change supplier. The scrutiny is on the ingredient and the suppliers’ quality control, in the past they could say we tested ours and we did not have a problem.

“It has not reached the small firms, maybe there will be service providers or consulting labs do it for them as they won’t have their own on site facilities.”

IFSH is a food science research institute that works in the areas of food safety and defense, and nutrition for stakeholders in government, industry, and academia.

It can assess and validate novel food safety and preservation technologies, processing and packaging systems, microbiological and chemical methods, health promoting food components, and risk management strategies.  

Related topics: Food Safety & Quality

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