Recently, significant changes have been made to how the US Food and Drug Administration (FDA) conducts investigations of food manufacturing facilities. For starters, note that I did not say FDA inspections; they are now investigations. This change in semantics indicates a shift from a superficial “look around” a facility to diving into records and sometimes taking hundreds of environmental pathogen samples. The Food Safety Modernization Act (FSMA) has prompted many of these changes, and has given the FDA increased power and access to records. The FDA is also now much more likely than in the past to involve the Department of Justice if there is any possibility of criminal intent. Along with this significant new regulatory authority, the industry has seen major leaps forward in microbial strain tracking technology, the most important being Next Generation Sequencing and its use for Whole Genome Sequencing (WGS). 

It is now common for the FDA to conduct intense environmental swabbing exercises for facilities that produce ready-to-eat (RTE) products, which are exposed to the environment and have no kill step for pathogens after packaging. These investigational activities have been nicknamed “swabathons” by the industry. Typically, these swabathons involve a team of 3 to 6 FDA investigators, and will involve a deep dive into the guts of the food processing facility. The team will take samples of hard-to-reach areas that are also difficult to clean and sanitize. One goal of these swabathons is to find environmental pathogens to be sequenced and then compared to public health databases to see if there are close matches to strains that have caused illnesses.

The results of WGS can also be used by the FDA to determine if there are any persistent or resident strains. Persistent strains are strains that are re-isolated at a later date, for example at a second swabathon a year later. Finding the same strain after time has elapsed could indicate that the strain has persisted in the environment. This could be an indication that corrective actions were not adequate, or even that the facility is operating under insanitary conditions. It could also be the basis for a potential recall of a product manufactured in that facility. However, it could also mean that the same strain is being re-introduced to the facility via raw ingredients or other fomites such as pallets. Resident strains, also called “house bugs,” are similar to persistent strains, but may appear in multiple places throughout the facility. A good strain tracking method combined with a good data management system is necessary to begin to differentiate these types of occurrences.

Insight into how the FDA conducts swabathons can be found in Chapter 4 of the FDA Investigations Operations Manual, 2016. Some interesting information from this manual includes: instructions to take a minimum of 100 to 300 samples, focus Salmonella swabbing to Zones 2, 3 and 4, but mostly 2; focus Listeria swabbing to zones 1 and 2; and not to give the facility much, if any, forewarning about a swabathon because any special sanitation could limit the finding of environmental pathogens. We have heard that in some recent swabathons, many samples have been taken in Zones 3 and 4, and positive findings in these areas have led to some recalls. This is causing many manufacturers to do special or expanded samplings of their facilities, since they may have limited data, especially of Zone 4 sites, which are outside of the exposed RTE area. At a recent public meeting, it was mentioned that at least one swabathon included swabbing the buttons on the soda machine in the break room, which would be considered Zone 4.

These FDA swabathons are causing a great deal of concern and anxiety for food manufacturers. However, manufacturers could view this as a good opportunity to proactively conduct intensive internal swabbing studies to better understand the microbial ecology of the facility and to correct issues before the FDA comes knocking on the door. This type of intensive study can also serve as a verification of the routine monitoring program and can direct decisions to strengthen the process. Some legal experts are recommending these special studies be conducted under attorney-client privilege. Someone very knowledgeable in the art of environmental pathogen hunting (Seek and Destroy) should be employed to help with this type of study. Additionally, strain tracking should also be considered for this type of study. To determine whether or not persistent strains are present, the study may have to be repeated. Any positive findings will require further investigation and corrective actions.

Do you need help with your environmental monitoring program to prepare for a potential FDA swabathon? Mérieux Nutrisciences offers an array of Environmental Monitoring Solutions that combine services from our technical, digital, research and training groups into customizable packages to meet your needs. From EMP development to data interpretation, we provide companies with the tools and technologies to ensure their EMPs encompass effective preventative controls that align with regulatory requirements, including FSMA.


Meet the Author

Tim Freier, Ph.D
Division Vice President, Scientific Affairs and Microbiology, America, Mérieux NutriSciences

Tim Freier is the Division Vice President, Scientific Affairs and Microbiology, America at Mérieux NutriSciences. He has over 25 years of experience working in various food safety and quality related positions in food facilities and in the microbiology lab. Tim has worked extensively in the area of pathogen environmental monitoring and exploring and implementing new food safety technologies.

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