From The Editor | September 11, 2017

FDA Swab-A-Thons: What To Expect In The Search For Pathogens

By Sam Lewis, editor, Food Online

FDA Swab-A-Thons: What To Expect In The Search For Pathogens

The FDA and food manufacturers are both on the same mission: make food safer. But, increased scrutiny during FDA inspections has left many food industry professionals with increased anxiety. Here, food industry attorney Shawn Stevens answers my questions about the FDA’s process of microbiological sampling, how the agency is incorporating Whole Genome Sequencing into its sampling processes, and what food companies can do to alleviate regulatory worries. Stevens will be speaking at the 2017 Annual AAFP Conference held September 19 to 21 in Springdale, AR.

Food Online: “Swab-a-thon” is a huge buzz word in the food industry right now. Regarding, microbiological sampling, can you describe the process the FDA goes through in each zone of a food facility and what the agency is looking for in each?

Stevens: “Swab-a-thon” is a huge buzz word, and the FDA doesn’t like it when I use it. But, I’m not going to stop because that’s exactly what’s happening. About three years ago, the FDA started digging deeper for contaminants. The days of the FDA leaving after a visual inspection are long gone. Under its new policy, the FDA arrives at a facility and takes about 150 samples; mostly in zones 1, 2, 3, and some in zone 4. It’s a swabbing lollapalooza. And, it’s not only the facility itself that companies need to worry about keeping free of contaminants; finished products and ingredients are part of the sampling process as well.

Even the most sophisticated companies can have contamination they are unaware of and, in some cases, a facility may have a big problem it doesn’t know even exists until the FDA comes in. Nobody is exempt from pathogens hiding in hard-to-reach places. Let me tell you, it’s never fun when the FDA shows up unannounced; it’s even less fun when the FDA is the one telling you that you have a problem. Swabbing frenzies are the latest thing and, as far as I can tell, the FDA is only going to become more invasive in facilities as time goes by.

Food Online: Let’s assume the FDA finds microbiological pathogens after swabbing a facility. Are certain zones, pathogens, or percentages of positive swabs more likely to trigger a recall? If, so what are they?

Stevens: Absolutely. In a facility producing ready-to-eat (RTE) products that have already shipped, any Zone 1 positive will almost always lead to a recall. For this reason, if the FDA is sampling in your facility, and you produce RTE products, it’s best to hold all the products manufactured on any lines and equipment sampled until the swab-a-thon is over. If any other Zone is highly contaminated, a recall could be required as well. As little as 5 percent, 10 percent, or even 15 percent positives could lead to a recall.

It would be stressful enough if all the FDA was looking to do was eliminate contaminants from food facilities, but that’s not the case anymore. The FDA is now taking the positive samples they are finding and comparing them to the 1,000,000 human isolates in the PulseNet database. There are nearly 1,000,000 unsolved foodborne illnesses the FDA is dying to solve. It seems obvious that a positive found in Zone 1 might lead to a recall but, to the FDA, a positive in a drain matching an unsolved human illness will send the agency into a frenzy; your company will be blamed and may be held accountable — even if the illness occurred five years ago. A recall will result and, depending on the severity of what happened, under new FDA/DOJ policy, a criminal investigation could result.

Food Online: Whole Genome Sequencing (WGS) is another hot topic in the industry. How is the FDA utilizing it in its microbiological sampling?

Stevens: The CDC and the FDA have unquestionably moved to WGS. It is the new standard and it is not going away. And, WGS is one of the most-noteworthy tools the CDC is using today, if not the most-significant tool they have ever used. The resolution of this technology is so advanced, it’s allowing pathogens and correlations to be detected that in the past were impossible to find. Those pathogens and correlations that, in the past, remained undetected are now coming to the surface.

For the FDA, this is very exciting. When the FDA now shows up at a facility for an inspection, they are searching for pathogens. The samples they are taking in the drains, on equipment, on the floors, and in the ingredients or finished products are part of a hunt. They are looking for positives and are hoping to find them. More so, the FDA is hoping one of those positive samples found in a facility matches one of the 1,000,000 human isolates stored in the CDC’s PulseNet database. Each positive match the agency finds closes one of the nearly 1,000,000 open cases; that’s the FDA’s goal, to close all of those open cases and eliminate pathogens from food facilities. WGS is an incredibly powerful tool and, in the end, it should provide an enormous incentive to food companies to have plans in place to prevent and/or remove any contaminations existing in their facilities before the FDA arrives.

Food Online: Many food makers fear that genetic sampling tools, such as WGS, in the hands of the FDA will put them at risk for regulatory actions and negative consequences. What would you recommend these companies do to alleviate their fears?

Stevens: Their fears are very real. Over the next 10 years, every food company in the U.S. will be inspected repeatedly by the FDA. It’s not a matter of if; it’s a matter of when.

Lying awake at night thinking about pathogens isn’t going to prevent the FDA from finding a positive sample in your facility. What is going to reduce the risk of them finding a contaminant is to prepare. Know your facility. Know your products, your suppliers. What does your Food Safety Plan look like? Is it effective? Is it being followed? Are you documenting that? Wouldn’t it be better to find out today that things might not be as perfect as you thought, so the opportunity is there for you to rectify any imperfections existing in your facility prior to the FDA showing up at your doorstep?

Denial and ignorance have never helped anyone, especially not when dealing with the FDA. Companies need a very-proactive and very-smart strategy. The truth and facts are ultimately what will help you sleep at night. Test your facility yourself; play FDA for a day. Where would you look if you were an FDA agent on the hunt for pathogens, where could they possibly be hiding? Find the pathogens and then destroy them, then test again and again. If this is done correctly, some of this work can be protected. Set yourself up to be the best position possible when the FDA arrives.

About Shawn Stevens
Shawn Stevens devotes his entire practice to representing the food industry. For more than a decade, Stevens has worked nationally with food industry clients (including the world’s largest food processors, national restaurant chains, and food distributors, and grocers) helping them protect their brand by proactively reducing their food safety exposure, complying with complex food safety regulations, coordinating recall efforts, and defending high-profile foodborne illness claims. 

In addition to his legal consulting practice, Food Industry Counsel LLC, Stevens serves as the only food safety and food quality mediator in the nation, helping parties who have food safety or quality disagreements (whether in advance of or during litigation) resolve their disputes. Stevens also speaks regularly to national audiences on a wide variety of emerging scientific, regulatory, and legal food safety trends. Additional information about his food safety and quality consulting and legal practice can be found at