What Does It Take to Satisfy Food Regulatory Preventive Controls Requirements?


Both the FDA and USDA expect food manufacturers to have effective control of environmental pathogens in the exposed product processing environment for Ready-to-Eat Foods. The agencies require that effective Sanitation Preventive Controls have specific emphasis on pathogen persistence (21 CFR Part 117). The FDA acknowledges that L. monocytogenes is widespread and can persist on equipment and in harborage sites within the processing environment. Consequently, a manufacturer should expect to find L. monocytogenes or Listeria spp. on an “occasional” basis. (Draft Guidance For Industry: Control of L. monocytogenes in Ready-to-Eat Foods (January 2017). In the Draft Guidance, the FDA notes that corrective actions be risk-based relative to a number of factors including:

  • Whether the detection involved a Food Contact Surface (“FCS”) or a non-FCS,
  • Whether findings were on a single sample or multiple samples, and
  • The proximity of a non-FCS detection relative to FCS.

However, the FDA did not include specific performance criteria or guidance on acceptable total numbers or rates of pathogen findings over extended time periods, leaving manufacturers to apply their best judgment as to what sanitation controls would be considered adequate. Unfortunately, a manufacturer’s judgement may differ from the agencies’, which is problematic when there is concern by the agency and can ultimately lead to enforcement action.

Manufacturers must consider the complex and numerous factors in determining the type and magnitude of control, but at the end of the day, they are essentially left to guess at what will be sufficient to satisfy regulatory expectations.

The case study below illustrates an instance where a manufacturer’s prevention efforts were not considered sufficient by the FDA. We discuss some potential solutions and tools, such as environmental pathogen mapping software, that could help a food manufacturer better recognize contamination patterns or recurrences, and potentially avoid such regulatory consequences.

Case Study:

The FDA recently issued a warning letter to an ice cream manufacturer citing concerns over the safety of food processed in the facility. In the letter, the agency cited that repeated findings of L. monocytogenes in the food processing and handling environment had led them to conclude that sanitation controls were not adequate to ensure that the potential hazard posed by exposure to the contamination was minimized or prevented. The agency looked at both the rate of pathogen occurrence and the likelihood that the food processing and handling environment harbored a resident strain of the pathogen.

In its 2021 investigation, the FDA swabbed the manufacturer’s processing and handling environment. It found a 9.4% incidence of L. monocytogenes (8 of 85 swabs positive), and in the period from 2017 through 2021, a total of 17 L. monocytogenes isolates were reported. In addition to the number of positive findings, the FDA considered a number of other factors in issuing their warning letter. In particular, the FDA conducted whole genome sequencing and recovered three different strains from the facility. Fourteen of the 17 isolates were genetically identical to three isolates that the FDA had previously recovered from the manufacturer’s facility in 2016, indicating the possibility of a “resident pathogen or harborage site” in the facility.

What triggered the FDA’s concern, were several factors including:

  1. The location of the positive findings included bacteria exposed processing/handling areas on surfaces adjacent (Zone 2) to food or FCS;
  2. The relatively high rate of occurrence 9.4% (2021); and,
  3. The persistence of resident strains over a several year period.

What Manufacturers Can do to Help Ensure Environmental Controls are Adequate:

A successful environmental pathogen swabbing program is not necessarily solely tied to the number of swabs collected, but also to how effectively sampling is targeted and how the results are utilized. The reality is that successful control of environmental pathogens not only demands action to correct each positive finding, but additional actions to address problems reflected by the aggregate of results. Specifically, regulators expect processors to recognize and address patterns and trends that indicate a problem with persistence of the contaminant. Of course, with the heavy amount of work and attention necessary to address each pathogen finding at every sampling site, it can be overwhelming for the team at the plant to additionally identify trends in data relative to one another.

Pathogen persistence may be quite obvious when the same swab site repeatedly shows positive findings; however, it can be infinitely more difficult for the plant team to identify a swab site that experiences infrequent recurrences, or those related to clusters or patterns on surfaces related to other surfaces. Trends that go unnoticed will remain unaddressed, creating a critical failure in the feedback loop necessary to verify successful control of hygiene.

How Mapping Software Can Help:

Mapping, tracking, and trending of environmental testing data can help provide important feedback that may not otherwise be evident from paper-based, excel-based, or other record keeping systems.

First, data mapping provides a visual representation of the equipment and environment:

  • Mapping enables evaluation of monitoring data on surfaces relationally to each other, whether they are adjacent, upstream, downstream, above, below, or in another room, creating the opportunity to identify problems that may be related to equipment, facilities, traffic patterns, or adjacency to other areas.
  • Mapping facilitates immediate recognition of findings relative to the sanitary zone of the sample location. Reliable mapping software should allow response teams to easily identify issues related to Zone 1 (food-contact) or beyond it (Zones 2, 3, or 4), thus helping prioritize corrective actions relative to risk.
  • The visual representation helps ensure effective collaboration across the departments that comprise a response team (e.g., QA, sanitation, maintenance, production, operations, etc.) so they can quickly and easily recognize and respond to hotspots, trends, patterns, and other problems. Highlighting locations with positive findings permits response teams to immediately focus directly on sites where positive findings have occurred.
  • Mapping provides a visual representation of progressive time and place for contamination detection, allowing a response to consider other sites that are potentially influential and may also require investigation or corrective action.

Second, mapping helps response teams to see where historical sampling has been performed and contamination has not been problematic. The locations of swab sites that show historical absence of contamination is meaningful because it can allow the response team to focus investigation elsewhere.

Third, mapping can allow response teams to see where equipment and environment sampling has not been performed or has not been performed with sufficient frequency, and thus may need to be evaluated. The response team can expand their investigation accordingly.

  • Potentially influential surfaces that have no representation at all indicates a potential ‘blind spot’ in the program. Identifying such blind spots for sampling may be warranted to evaluate nearby or related surfaces which could be influential in the detection finding under investigation, which are currently not recognized.
  • Mapping can also reveal other blind spots such as instances where influential surfaces nearby an affected area have been historically shown not to be problematic, but where the sampling frequency was low.

Beyond mapping, quantitative trend data is extraordinarily important for understanding the frequency of occurrence. An automated software data tool should provide trending reports that can help crystalize an understanding of the extent of positive occurrences by highlighting the percent of positive results relative to all zones, each individual zone, and to each specific swab site.

  • It is especially important to track recurrences at each specific site to recognize findings, even if infrequent. Infrequent but repeated Salmonella or Listeria findings may signal existence of contamination condition(s) that might not be initially recognized as significant, but that ultimately lead to problems in finished product and potentially a recall crisis. For example, infrequent Salmonella findings in a floor drain nearby a dryer typically get addressed with aggressive corrective action that includes intensified cleaning and re-sampling. The corrective action can appear to resolve the contaminant at that sampling site, with sampling returning to normal surveillance frequency. However, when the prevalence results are trended over longer periods of time (e.g., over a month, quarter, or year), a very different pictures can emerge, often indicating a significant problem. A tool that notifies the team of high recurrence rates can trigger corrective action relative to the trend, thus impacting potential for persistence of pathogens.

Analyzing the data for trends can highlight problems and trigger investigation and corrective action to address them. Addressing trends separate and apart from individual pathogen findings in the environment is the key to effectively identifying potential issues with persistence of pathogens and controlling them.

Automating the tracking and trending for prevalence of environmental pathogens or pathogen indicators relative to the overall facility, each Zone, and each site is necessary on a routine, ongoing basis to ensure effective and timely feedback information exists and the team can respond. Automated mapping software provides other benefits for an environmental management program.

  • Mapping software reduces the burden of managing the sheer amount of environmental pathogen testing results. Automating results upload to the tracking and trending system and issuing autogenerated notifications for individual non-conformance findings and trends for each zone, sampling site, and the overall facility eliminates the need to manually track or enter data into spreadsheets.
  • Sub-typing information such as Whole Genome Sequence (WGS), serotyping, ribotyping, biotyping, etc., can be tracked within the system to identify relationships between locations.
  • Mapping software also provides for a common platform to allow effective collaboration with sanitation and corporate personnel, associates from other facilities and within the same company, and even with chemical suppliers, testing laboratories, or other partners as needed.
  • Finally, when faced with audits by regulatory agencies, customers, or third parties, mapping software can help provide those stakeholders with information of current hygiene status, providing confidence in a facility’s environmental pathogen management program.

So, how does a manufacturer reduce their exposure risk due to environmental pathogen persistence and potential regulatory action? One answer is information. Automated mapping software can provide trends, insights, historical perspectives, and audit ready records necessary for a well-functioning food safety team to have confidence in their environmental management program and bring peace-of-mind regarding their product, brand, and bottom line.


Many food manufacturers use automated environmental management tools, such as eBacMap.com software to map, track, and trend the results of their environmental pathogen monitoring programs. The cloud based eBacMap.com software helps them successfully recognize and respond to individual findings, as well as trends and patterns. Frequently, LIMS and lab data can be configured so that clients can mass upload directly into the eBacMap.com software, providing convenient access and immediate insights into their environmental pathogen status. Our client services team welcomes your questions about eBacMap.com and we invite you to click on the link below to request a demonstration of the software.


Melissa Calicchia, M.S., C.F.S.
Chief Science Officer