Food Safety Magazine

Process Control | December 2016/January 2017

Environmental Monitoring in the Era of
Whole-Genome Sequencing

By Jennifer McEntire, Ph.D.

Environmental Monitoring in the Era of Whole-Genome Sequencing

The U.S. Department of Agriculture-Food Safety and Inspection Service (FSIS)-regulated community is accustomed to pathogen environmental monitoring programs, but the topic may challenge some U.S. Food and Drug Administration (FDA)-regulated facilities as they update their food safety practices to comply with various aspects of the Food Safety Modernization Act. Ever since the ready-to-eat (RTE) meat category began tackling this topic, resources have poured out, providing guidance and recommendations on how to develop and implement effective environmental monitoring programs for several product types. So what’s the holdup? Unfortunately, it’s not our lack of scientific understanding that is preventing progress. It’s a combination of three things:

1.    Lack of understanding
    •    Around whether or not the facilities need a program
    •    Around corrective actions

2.    Equipment and facility design constraints

3.    Regulatory policies that discourage aggressive testing

Additionally, the scientific advances and rapid adoption of whole-genome sequencing (WGS) to identify, with a greater degree of specificity than ever before, the isolates found when regulators swab a facility take the concern around environmental monitoring to a whole new level.

Lack of Understanding
Food safety and quality managers should make the time to read some of the great environmental monitoring articles and guidance documents available. Several resources are cited in the “Environmental Monitoring Resources” sidebar on page 70, and several industries offer workshops on this topic. One thing that these resources have in common, and one thing that historical issues support, is that no RTE operation should feel confident that the “low-risk” nature of their product makes them immune to issues with postprocess contamination. When products ranging from ice cream to peanut butter to caramel apples have food safety issues traced to the postprocess environment, it’s clear that such issues are less related to the product and more related to the conditions: leaking roofs, condensate, cracks in floors, construction, poorly designed equipment, etc.

This is why FDA is requiring facilities producing any RTE food with postprocess exposure (without an in-package kill step) to show that they have considered the potential for contamination with environmental pathogens, generally defined as Listeria monocytogenes (Lm) and Salmonella. There may be instances where the facility evaluates the risk and determines that a preventive control is not warranted; however, the food safety plan must show that it was at least considered.

One point of confusion centers on the definition of an RTE food. FDA, in the final Preventive Controls for Human Foods rule, defines RTE as “any food that is normally eaten in its raw state or any other food, including a processed food, for which it is reasonably foreseeable that the food will be eaten without further processing that would significantly minimize biological hazards.” This definition is much broader and more expansive than what most of the food industry would have considered RTE. Within the fresh produce industry, for example, intact fruits and vegetables were historically considered not RTE because they are raw agricultural products (RACs) that need to be washed before consumption. However, it’s increasingly recognized that being an RAC and being RTE are not mutually exclusive. The knowledge that someone may eat an apple or pop a cherry tomato in their mouth without first washing it places intact produce squarely within the RTE definition. Claiming that your product is not RTE so that you don’t have to worry about environmental monitoring is not going to fly.

So what should you do when you realize that FDA may consider your food RTE? Consider the potential for postprocess contamination. It’s up to each facility to evaluate the risk and determine the extent to which Good Manufacturing Practices (GMPs) help keep food safety in order. Most notable outbreaks and recalls related to environmental contamination occurred in situations where GMPs were not perfectly implemented, so going back to basics should be the first step.

If you determine that there is a concern about environmental pathogens contaminating product that adherence to GMPs might not fully address, then couple a strong sanitation program with aggressive monitoring for environmental pathogens for the best outcome. Of course, facilities may choose to verify the adequacy of sanitation using ATP (adenosine triphosphate) checks, aerobic plate counts and yeast and mold counts, but these are insufficient when it comes to postprocess pathogen monitoring. On the other hand, there is little point to conducting environmental monitoring when you know that cleaning and sanitation are not adequate.

Once you are confident in the cleaning and sanitation program, refer to existing industry (or FDA) guidance to develop a plan. There are a few common practices you should reevaluate:

•    Swabbing during pre-op, not production

•    Compositing

•    Trending and corrective actions

Swabbing during pre-op, not production
A practice I’ve observed is that facilities tend to swab and sponge after sanitation, before product is running. The advantage of this approach is that if the tested area is a product contact surface, it can be resanitized before production begins, so that product is not implicated if a positive result is obtained. However, this approach may not provide an accurate picture of the environment. Assuming a harborage is hidden and difficult to access, it may be better to run the line for a while so that the bacteria have time to work their way into areas more likely to be swabbed.

Facilities should also think carefully about the value of compositing (in this case, combining separate samples into a single sample). Some companies composite samples taken within the same zone; others may composite swabs taken within close proximity of one another. If a positive is found, think about how you will pinpoint the true positive. The obvious approach is to swab the sites individually. But if all follow-up retesting results are negative, where did that original positive come from? You don’t know, and you’ve lost the opportunity to vector out and hunt down the original source. Considerable thought should be given to balancing resources against the number of sites that should be tested and determining the best overall approach.

Trending and corrective actions
The “seek and destroy” mantra, which was greatly effective at virtually eliminating postprocess contamination with Lm in the RTE meat industry, seems to be permeating the entire food industry. Word seems to have spread that finding an occasional positive is a good thing because it shows diligence and an aggressive approach. Naturally, you need to trend positive results to show that you do maintain control over the production environment and that positives are not a symptom of a persistent problem. If they are, FDA may pull your facility registration.[1]

However, now that the industry is really looking for positives, the stumbling block seems to be what to do when a positive is found. Do you simply reclean, sanitize, retest and move on? I’ve seen this approach in some environmental monitoring plans. The flaw is that you can’t be certain if the positive is due to a transient organism that just happened to be passing through the facility, or if you swabbed a point of harborage where the organism had taken residence or if you found an organism that had traveled from a harborage site.

If the positive was truly a transient organism, then cleaning and sanitizing should eliminate it, and retesting should be negative. If you found the harborage and truly eliminate it through cleaning and sanitizing, then retesting should be negative. However, what if the positive was due to an organism that had been part of a larger community and broke free? Retesting after cleaning and sanitizing should yield a negative, but you might have a false sense of security because you didn’t actually eliminate the root of the problem. This is why vectoring out and sampling locations that are close to the initial positive should be done. It’s also why plotting positives on a physical map may also reveal that seemingly one-off positive results are actually related to one another.

In reviewing environmental monitoring programs for food manufacturing facilities, a common weakness is the investigation into the root cause of the positive test result. Expect that FDA inspectors as well as auditors will be examining your treatment of positive environmental findings.

Equipment and Facility Design Constraints
This issue of Food Safety Magazine contains an excellent article by Joe Stout about hygienic design (“Hygienic Design: How Our Thinking Has Evolved”). Hygienic design, of both equipment and facilities, goes hand in hand with risks associated with environmental pathogens. Well-designed, properly maintained equipment that is operating in a well-designed facility can be effectively cleaned so as to limit the opportunities for environmental pathogens to establish themselves and potentially contaminate product.

Environmental Monitoring Resources

•    Innovation Center for U.S. Dairy. 2015. Control of Listeria monocytogenes. Guidance Document for the Dairy Industry.

•    GMA. 2009. Control of Salmonella in Low-Moisture Foods.

•    National Pasta Association. 2015. Mitigation and Control of Salmonella in Dry Pasta.

•    United Fresh Produce Association. 2013. Guidance on Environmental Monitoring and Control of Listeria monocytogenes for the Fresh Produce Industry.

Additionally, the Produce Marketing Association maintains a list of resources related to Listeria:

Over the past decade or two, the food safety community has learned a lot about the ability of both Salmonella and Listeria to take residence in food processing facilities. Unfortunately, many food processing plants and/or the equipment in them are more than a couple of decades old. They may not have been designed with these issues in mind. If you’re operating under such conditions, you may dream of tearing down the old facility and building a new one. That’s seldom realistic, and Joe Stout points out in his article that it may take years or generations to switch out equipment. However, one should not stick their head in the sand and give up. There is a continuum of effort that can help limit the possibility of an issue with the establishment of environmental pathogens in your facility, even if you’re stuck with less-than-ideal conditions:

•    Understand cleaning and sanitation

    °    Do individuals with responsibility for cleaning and sanitation understand their role in food safety? How are they included in conversations related to positive environmental test results?

    °    How often do certain pieces of equipment need to be broken down? What was the rationale behind the master sanitation schedule?

•    Consider traffic flow—humans, forklifts, products

•    Provide an opinion on new equipment purchases

•    Provide input on other capital improvements such as floors, construction, etc.

Regulatory Implications
There is, understandably, tremendous concern about embarking on an environmental monitoring program that could put a company at risk. At issue is the testing of zone 1, product contact surfaces. FDA considers that if a product contact surface tests positive for Listeria spp. (the vast majority of which are not pathogenic), then, in the absence of determining the species, FDA assumes that it is the pathogenic species monocytogenes. Why not just speciate? For many products, such as fresh produce and other highly perishable items, the time required to keep the product on “hold” eats into its shelf life, such that it may require disposal of the product. Why not just skip testing for all species and just test for monocytogenes? The point of an environmental monitoring program is to nip issues in the bud, before they become full-scale problems. Testing for Listeria spp. provides a much greater chance of finding a positive, which reveals an issue that needs to be addressed, even if the pathogen is not present.

In the absence of a policy shift from FDA, how can one evaluate their product contact surfaces? The process outlined below describes an intense evaluation of a line; it is not the routine environmental monitoring program. It can be used to establish a thorough understanding of the zone 1 environment while minimizing the amount of product at risk. This type of approach should be part of a comprehensive, in-depth analysis and assumes that current GMPs are in place and the routine environmental monitoring program, including corrective actions, is well established.

1. First, create a clean break on the packing line, from the beginning to the end of where the edible product is exposed to the environment. If you’re confident that all food contact surfaces are sanitized, your normal cleaning/sanitation should be adequate.

2. Run all moving parts for an hour. This is important to squeeze and shake out hidden microorganisms that are not exposed to normal sanitation procedures. Only run product if needed for the equipment to run.

3. Stop the line and swab as many food contact surfaces as possible. Because this is done only periodically and not weekly or monthly, this is the time to be aggressive. Many companies report that when regulators do a “swabathon,” they take hundreds of samples. You should too! Send all swabs for Listeria spp. testing.

4. If product was run, reclean and resanitize per normal procedures. If no product was run, just resanitizing may be enough. This creates a clean break at the other end of your environmental testing. If product was run, hold until results are known or discard.

5. If you can afford to hold the line down until results are known, do so. Otherwise, resume production.

6. If results are all negative, you have evidence that the line did not have an entrenchment, with confidence proportional to the degree of swabbing performed. You will want to keep a record of what was done and when, and the results.

7. If any results are positive, you have evidence of a possible entrenchment. Even though the approach cannot determine whether the Listeria was pathogenic, it’s critical to react as if it were Lm: Shut down the line and investigate until the entrenchment is found and destroyed. This will probably require more than just resanitizing. A good investigation will identify possible factors leading to the harborage and determine steps to prevent a recurrence.

8. Because 1) the contamination originated with you, 2) you discovered it and 3) no product was distributed into the marketplace, there is no requirement to file a report in the Reportable Food Registry.

There is a new twist in the world of liability, and that relates to WGS. FDA, FSIS and the U.S. Centers for Disease Control and Prevention have made it clear that WGS is the technology of the future when it comes to outbreak investigations. Rather than simply evaluating the number of positive Lm swabs an investigator finds, these agencies will be determining whether there is a resident strain or two that appear in numerous locations and/or during multiple inspections over time.

Several companies have asked whether they should begin using WGS to better understand their production environment. I feel that WGS could provide insight into an investigation—but only after all other approaches have been exhausted. As noted above, a positive for Listeria spp. needs immediate attention. The decision to speciate would come later in an investigation. Using WGS takes it a step even further. Industry should ask regulators whether a proactive company-led investigation using WGS will be used by the agency to support a judgment of “insanitary conditions,” or whether it will be viewed in a positive light, demonstrating an aggressive and protective approach to food safety. About 20 trade associations representing the food and beverage industries, and spanning FDA- and FSIS-regulated products, have recently begun discussing these and other issues so that we can provide our members with the best advice on how to view environmental monitoring for pathogens in light of WGS.

Final Thoughts
No one wants their product to cause foodborne illness. Historically, the food associated with a case of foodborne illness was rarely discovered. WGS will change that, and I predict that we’ll see many more instances where regulators are able to link illness with an environmental test result. Now more than ever, it’s critical that facilities undergo a thorough evaluation of their environment. Ignorance is not bliss, because in this day and age, if your facility is host to resident pathogens, they will be discovered. For the sake of your consumers and your reputation, it’s better that you take control of the situation yourself.   

Jennifer McEntire, Ph.D., is vice president of food safety & technology at the United Fresh Produce Association.



Categories: Facilities: Design, Hygienic Equipment Design; Food Types: Ready-to-Eat; Process Control: Intervention Controls; Sanitation: Environmental Monitoring