October 4, 2016

Whole Genome Sequencing and Food Safety

In recent food safety conferences, prominent researchers and key regulatory officials have indicated that the use of Whole Genome Sequencing (WGS) in surveillance and investigative programs is increasing.  WGS technology is not new, but it is a hot topic that has raised many questions and the interest of several stakeholders in the last several months.

Just this year, several events on this topic have taken place, including a “genomics day” event hosted in June by the Institute of Food Technologists (IFT), several sessions hosted at the International Association for Food Protection (IAFP) Annual Meeting in July, two industry webinars in August hosted by industry stakeholders, including Western Growers, and a three-day meeting hosted by the Illinois Institute of Technology (IFSH) at the end of September.  With the potential and growing use of WGS in the food safety arena, this technology requires continuing attention.  But, what is the current state of WGS at the regulatory and private industry levels?

Whole Genome Sequencing may still be unfamiliar to many people, but the term simply refers to a laboratory process that determines the entire set of genes or genome of an organism (complete DNA make-up of an organism).  According to U.S. Food and Drug Administration (FDA) representatives, WGS enables the agency to better understand variations within and between species and organisms with a precision that other technologies, such as Pulsed-field Gel Electrophoresis (PFGE) do not allow.  The FDA is transitioning to WGS and has been using this technology to perform basic foodborne pathogen identification during foodborne illness outbreaks because of its ability to differentiate between even closely related organisms.  This allows outbreaks to be detected and stopped sooner, which results in fewer clinical cases and illnesses.

Furthermore, this technology has contributed to efforts such as the GenomeTrakr network, the first distributed sequencing-based network of laboratories to utilize WGS for pathogen identification.  It consists of public health and university laboratories that collect and share genomic and geographic data from foodborne pathogens.  Data collected includes isolates (strains of microorganisms) from routine FDA and state laboratory inspections, historical collections, past outbreaks, environmental monitoring/surveillance and food sampling for imports.  The data does not include names to prevent privacy issues.  This database is publically available and can be accessed online at any time.  When a match between a clinical and environmental sample is found in this database, an investigation is triggered to determine a contamination source.

To put this in perspective, the 2009 peanut butter outbreak resulted in more than 700 illnesses in 46 states that resulted in hospitalizations and deaths.  With the use of GenomeTrakr, two years ago an outbreak was detected faster than the one in 2009; this outbreak resulted in only six illnesses and no deaths.  The company implicated was able to recall this product, which was clearly in the best interest of this company and consumers.

While tracking and tracing of food pathogens is the most basic food safety application at the regulatory level, WGS has the potential to be used by the produce industry as a tool to monitor emerging pathogens, spoilage organisms and the effectiveness of sanitary controls.  WGS provides not only higher resolution, but also cost savings.  While DNA-based pathogen surveillance is not new, it was expensive when first introduced.  The cost of WGS has decreased dramatically in the last 10 years, from $3,500 to sequence an entire bacteria genome to $40 per genome in 2016, according to Dr. Ruth Timme, who is a research microbiologist with the FDA.

Dr. Timme was a featured speaker at a recent industry webinar and concluded that WGS is a powerful high-resolution tool for current standard investigations behind the scenes.  She confirmed that FDA’s procedure for outbreak investigations is still the same, but what is new is the use of WGS, a tool with higher resolution.  She also shared that there is already routine surveillance of pathogens along the supply chain.  Karen Jarvis, another research microbiologist with the FDA who also was a featured speaker, shared that while there are several opportunities and potential applications ahead, there are some challenges, including capacity building, a transition period from PFGE to WGS, the need for training and use of bioinformatics (collecting and analyzing biological data) as well as the participation of the private industry.

Immediate benefits of WGS to growers, shippers, processors and distributers may not be perceived right away by many, but they could be of great value when realized, especially during earlier intervention if focused on prevention.  For example, potential applications could allow a better understanding of the pathogens along the supply chain, at facilities and during transportation, sanitation and other activities.  In addition, identifying spoilage organisms is another area to explore and finally, early foodborne pathogen detention can translate to less product recalled, fewer impacted customers and less damage to brand recognition.

It does not appear WGS is not going away anytime soon, instead, it is likely to become a more frequent topic of discussion in the near future.  Western Growers is engaging on this topic, if you are interested in learning more about this subject, access an informative industry webinar on WGS at http://goo.gl/Z4bgbU or contact me at [email protected].