The program at last month’s FPSA Annual Conference included a Food Safety and Sanitary Design Panel Discussion sponsored by Food Safety Summit and National Provisioner. One of the topics before the panel was FDA inspections and genomic sequencing. This article provides a brief review of the discussion.

“Swab-a-thons”: What happens when FDA inspectors visit

If you’ve had an FDA inspection recently, you know that they have changed. It used to be that one inspector would come and visually inspect your operations, delving deeper when necessary. Now, as many as six inspectors may show up and take hundreds of samples in different zones of your facility. The purpose of these “swab-a-thons” is to not just to look for environmental pathogens in the facility, but also to collect samples to be sequenced and entered into GenomeTrakr, an open-access database that can be used to trace the contamination sources of current and future outbreaks.

The FDA likens GenomeTrakr to the FBI’s fingerprint file:

“A person commits a crime, and the detective uses DNA evidence collected from the crime scene to track the criminal down.

An outbreak of foodborne illness makes people sick, and the U.S. Food and Drug Administration (FDA) uses DNA evidence to track down the bacteria that caused it.”

This approach represents a significant departure from how the agency worked in the past. Let’s look at the technologies the FDA uses to identify the source of contamination.

The old way: Pulsed-field gel electrophoresis

The traditional approach to analyzing samples was pulsed-field gel electrophoresis, or PFGE. This technology is still in use today, but it’s quickly being replaced.

At a very basic level, PFGE works like this:

  • A bacterial sample is collected and the DNA is chopped into fragments.
  • The fragments are put into a gel and exposed to an electric field that separates them according to their size, creating a specific pattern.
  • That pattern can then be compared to the patterns of known pathogens.

The CDC notes that PFGE is like comparing two books based on the number of chapters they each have. If you have the same number of chapters, you may have the same two books. But, then again, you may not.

For a more scientific explanation, view this resource from the CDC.

Pulsed-field gel electrophoresis

Source: CDC

The new way: Whole genome sequencing (WGS)

Whole genome sequencing kicks it up a notch. As the name suggests, it works by sequencing the pathogen’s entire genome.

Following the book analogy, WGS is like comparing two books word for word to see if they’re the same. In other words, the testing is getting a lot more sensitive. The CDC notes: “Using whole genome sequencing, we have found that some bacteria that appeared to be different using PFGE are actually from the same source. This has helped solve some outbreaks sooner.”

Whole genome sequencing

Source: CDC

The FDA started using WGS in 2013, and by 2019, this is how all inspections will be done.


The power of the new system lies in the ability of the FDA to precisely track the source of outbreaks by associating genomes of pathogens found in contaminated food with genomes in the GenomeTrakr database. Now, outbreak investigators can link hundreds of illness cases to food, as opposed to just the handful they could in the past, by finding small outbreaks, linking them together, and associating them with a specific food or food ingredient as well as a specific food facility.

There are currently more than 160,000 sequences in GenomeTrakr, and more than 5,000 are being added every month.


What this means for food processors

As one panelist noted, this situation is increasing the “pucker factor” among food processors and their suppliers. But, as they say, an ounce of prevention is worth a pound of cure. Here are some steps to take, if you haven’t already:

  • Stay informed. The FDA provides extensive resources about WGS and how it’s being used.
  • Conduct your own swab-a-thons. You’re better off understanding what may be lurking in your facility before inspectors knock on the door. A panelist relayed the story of one company that conducted its own swab-a-thon and offered $100 to any employee who found a pathogen (he also offered a pro tip: check the drain).
  • Follow best practices for sanitary design, proper sanitation, etc. This is more important now than ever. The FDA expects to find pathogens in your facility, but that won’t necessarily translate into you getting cited or fined. Implementing — and following — best practices on a daily basis will help protect you against citations and recalls.

For more food safety content, check out the PROCESS EXPO Expert-in-Residence series. You’ll find articles about designing for food safety, preventive controls, safety for low-moisture foods, and more.