How Whole Genome Sequencing Is Impacting The Food Industry

By Sam Lewis

Regulators are increasingly using Whole Genome Sequencing (WGS) for foodborne illness investigation and regulatory enforcement activities. However, the food industry is at a crossroad on whether or not, and how, to use WGS. Here, Ai Kataoka, scientist in microbiology at the Grocery Manufacturers Association (GMA), answers my questions on WGS’ influence of the food industry.

Food Online: What is WGS? What are its practical applications and commercial advantages?

Kataoka: Whole Genome Sequence is a near complete determination of the full genome of an organism (i.e., bacteria) presented as an ordered list of nucleic acids – As, Ts, Gs, or Cs. WGS describes the technology used to determine the nucleic acid sequence. The WGS outcome is very helpful as it can be used as a microorganism identification (typing) tool with a high level of resolution and precision. The technology often delivers information in less time than conventional molecular typing methods allow. Together with other agencies, the FDA has established a publically accessible database for food related pathogens (GenomeTrakr), which aids it in fast identification of foodborne pathogens associated with illness cases.

There are many other applications for this technology in the food safety field. It can be used as an investigation tool for identifying contaminants in ingredients or the environment and for serotyping or virulence identification. Notably, a single WGS analysis may offer a one-stop analysis for several endpoints, as mentioned above, which can save cost and labor.

Food Online: Conversely, what are the limitations of WGS?

Kataoka: Not only is sequencing technology still evolving, but also data analysis on genome sequence (bioinformatics) is an emerging field. Bioinformaticians, who understand food microbiology, are scarce. Furthermore, typing analysis may be limited by the size of the database of sequences from known pathogens and non-pathogenic organisms. As with other types of molecular analysis, sequence data cannot be used alone to assess an organism of concern; other background information is necessary (source and location isolated, etc.).

Food Online: Are federal agencies — such as the FDA, the CDC, and the USDA — using WGS differently than food makers? How so?

Kataoka: The FDA and the CDC have started utilizing this technology for identifying causative pathogens for foodborne illness outbreak investigations and for research purposes. The USDA has been using it mainly for the research and development in the area of food safety.

For the food industry, in addition to the application for food safety, some companies expand its use for quality control. However, at this point, this technology is still evolving and can be uneconomical. Not many food companies own sequencers or employ bioinfomaticians. Third-party, commercial laboratories can provide sequencing of microorganism; however, it may be difficult to find bioinformatics service focused on food microbiology.

Food Online: What is the implication from government agencies using this technology for foodborne outbreak investigation?

Kataoka: The food industry is still learning how to apply and interpret results gained from the technology and how agencies plan to use it for foodborne illness outbreak investigations. It is challenging to understand agency identification methodologies and how the information is used to make regulatory decisions.

At the same time, FDA has been sequencing isolates, including those obtained from foodborne illness outbreaks and inspections, and uploading the sequence data onto GenomeTrakr. The food industry has concerns about how those data points might be used for regulatory actions. One outbreak investigation report included a statement that the FDA found a close match with the current outbreak isolate and isolates from a past incident in the database (trackback analysis). Therefore, the industry wishes to have more communication with regulatory agencies on their methodologies and decision making process. GMA is working to facilitate productive discussions among all of the stakeholders on how to effectively use the results from WGS to ensure food safety.

Food Online: What resources are available to the food industry to learn more about WGS?

Kataoka: Below are a few resources available to the food industry to learn more about WGS:

• FDA WGS Program
   
• CDC Whole Genome Sequencing
   
• CDC — The Listeria Whole Genome Sequencing Project.
   
• Institute for Food Safety and Health (IFSH) WGS
   
• Next-Generation Sequencing: The Future Of Molecular Genetics In Poultry Production And Food Safety (peer review article)

For a closer look at the current discussion on WGS in the field of food safety, plan on attending the GMA Science Forum in Washington, DC on April 18 – 21 where there will be a panel discussion on this emerging technology.

About Ai Kataoka
Ai Kataoka is a scientist in microbiology with the Grocery Manufacturers Association (GMA).  Ms. Kataoka is responsible for conducting scientific research projects in the area of microbiological food safety.  In addition she provides technical support to member companies including HACCP and Food Safety plan review, and laboratory services such as food microbiology testing.  She also serves as a GMA instructor for a variety of scientific workshops.  She is recognized by the International HACCP Alliance as a HACCP Lead Instructor and FSPCA Human Food Lead Instructor; providing training both domestically and internationally.  She earned her BS in Food Science and Technology from Tokyo University of Marine Science and Technology and MS in Food Science from Kansas State University.