Will FDA Suspend Your Food Facility Registration Based on Environmental Results?

By Kathy Knutson, Ph.D.

In October 2018 FDA suspended the registration of Working Cow Homemade, Inc., of Florida. Working Cow is an ice cream manufacturer, ceased operations, and has cooperated with FDA. As part of its decision to suspend their registration FDA determined: 

  • Insanitary conditions were observed during inspections in both 2017 and 2018.
  • Following a 2017 inspection, an environmental sample tested positive for Listeria monocytogenes. Per FDA protocol, the whole genome sequencing data for the pathogen was uploaded to the Genome Trakr database.
  • In 2017, Working Cow conducted a recall. According to FDA, Working Cow did not implement corrective actions after the 2017 findings and recall.
  • In September 2018, the CDC informed the Florida Department of Health of a genetic match between the 2017 environmental Listeriaand a 2018 patient plus two patients in 2013.
  • Working Cow has a Florida customer base that includes potentially immunocompromised adult consumers at nursing homes and assisted living facilities.
  • A 2018 Listeria monocytogenes environmental isolate matched the 2017 environmental isolate, making the pathogen a potential resident strain.

The pathogen was not isolated from the finished product.

If Listeria monocytogenes is found in the environment from an area after a kill step and before the packaging is sealed, there is the potential for the pathogen to be transferred from the environmental site to a food contact surface and then to the product. This concept is recognized in the scientific community and is the justification for environmental monitoring programs which verify the effectiveness of equipment and facility sanitation programs, employee hygiene, and employee training programs. A pathogen in zone 4 can go to zone 3, in zone 3 can go to zone 2, and in zone 2 can go to zone 1. While every facility is different and there is no single citation of what constitutes each zone, here is one description:

  • Zone 1 – Direct product contact & indirect product contact (surfaces from which contaminants can drip, drain or be drawn onto product contact surfaces), includes pressurized air
  • Zone 2 – Equipment non-product contact areas immediately adjacent to processing equipment
  • Zone 3 – Facility non-product contact areas within processing, packaging & ingredient/finished product cooler areas, i.e. floors; walls; ceilings; overhead piping, conduit & structural supports; drains; forklifts & pallet jacks that enter processing & packaging areas
  • Zone 4 – Facility and equipment non-product contact areas located outside of the processing, packaging & ingredient/finished product cooler areas, i.e. warehouses, dock areas, break rooms, hallways

I understand the thinking that the pathogen from the environment could get into the ice cream and as a consultant I have seen the certainty of a problem break down when the details and specifics are thoroughly evaluated. Questions to ask as sites evaluate their pathogen control programs are: What is the proximity of the finding to the finished product? Is there a history of environmental sample results related to detection of pathogens? What is the laboratory’s positive control culture to ensure the reported results are correct?

PulseNet was formed in 1996 enabling laboratories to use the genetic matching method of pulsed-field gel electrophoresis (PFGE). FDA started to transition from PFGE to whole genome sequencing (WGS) after investigating a 2012 Salmonella outbreak. Isolates have been added to the Genome Trakr database at an exponential rate, and laboratories have converted or are in the process of converting from PFGE to WGS.

WGS use and values are evolving in risk assessment and investigations. There are several different WGS equipment manufacturers. The laboratory method for WGS at FDA is not the same method used by CDC. One uses SNPs, and the other uses alleles. A “match” is not always a perfect match, and there is debate among FDA, CDC, academic, and commercial laboratories as to how close the specific genetic data must be for a “match.”

The analogy I use is calling twin babies “identical” where there may still be a few physical differences; identical twins are genetically identical and a “match.” Fraternal twins are not genetically identical and clearly not a match. When WGS is conducted on an environmental isolate and a patient isolate of a pathogen to see if they match, the data may show genetic differences. The scientific community has not agreed on how much of a difference can be measured and the isolates be labeled as genetically identical.

WGS data lives forever in Genome Trakr, so it is conceivable and perhaps likely that environmental samples taken in your facility this week could be matched to a pathogen from six years ago, but without an isolate from your finished product! Even though the concept is mind-boggling, this is where enforcement currently lies in and CDC today.

So to answer my question, Will FDA Suspend Your Food Facility Registration Based on Environmental Results?, based on recent history with FDA using the tool of WGS as the “Holy Grail” for proving microbiological contamination, the answer could be is “Yes.” When there is a match between an environmental pathogen with a finished product isolate or a patient isolate, FDA will be on your doorstep. Your work is to train employees, re-emphasize and enhance current Good Manufacturing Practices, build a strong and positive food safety culture, re-evaluate your current FDA-compliant food safety plan to ensure effectiveness, and keep records that prove your food safety and corrective action efforts are occurring daily.

In conclusion, the food manufacturing and retail food industry need to prepare themselves for the increased use of all types of genetic screening of environmental and finished product isolates by not only FDA or CDC, but by state food safety regulators, third-party auditors and their customers. One way to prepare is to learn as much as possible about whole genome sequencing (WGS), identify private laboratories that conduct WGS and learn about their methodology and equipment. This will allow you to get out ahead of this new regulatory tool that has the potential of improving the safety of the US food supply but with potential damaging consequences in cases where matches are found.

Posted in 2019, 2019 March, EASeNews, Issue of the Month.