FDA Draft Guidance Addresses Management of Environmental Pathogen Hazards for Low-Moisture Ready-to-Eat Foods

Background and Overview of Draft Guidance

For purposes of this draft guidance, FDA considers an LMRTE food to be naturally low in moisture or produced from higher-moisture foods through drying or dehydration processes, exhibiting a water activity of 0.85 or below, and “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.”  Examples of LMRTE foods that are covered by this draft guidance are powdered infant formula (PIF), peanut butter, nut butters, powdered drink mixes, chocolate, medical foods in powdered and paste forms, processed tree nuts, milk powders, powdered spices, snack foods such as chips and crackers, granola bars, and dry cereal.   

The background section of the draft guidance explains ways that pathogens can contaminate LMRTE food (e.g., being introduced onto food-contact surfaces (FCSs) from the environment), focusing on Salmonella spp. and Cronobacter spp. as examples of environmental pathogens that have a history of contaminating the production environment of LMRTE foods.  The draft guidance refers to environmental pathogens that are readily removed from a food processing plant through routine cleaning and sanitizing as “transient strains,” whereas an environmental pathogen that becomes established in a food processing plant (either in processing equipment and/or parts of the facility infrastructure) is referred to as a “resident strain.”  With respect to distinguishing between the two, the draft guidance states: “We generally consider the finding of the same environmental pathogen strain through environmental monitoring on occasions separated by at least 60 days to indicate the potential presence of a resident pathogen.”

Additionally, the background section provides examples from several investigations of LMRTE contamination events to distill what the agency considers to be key repeat issues and operational deficiencies that result in pathogen introduction (e.g., contaminated ingredients; environmental exposure during processing; the introduction of water).  The background section also summarizes techniques for cleaning and sanitizing FCSs, emphasizing that no single cleaning technique or sanitizing treatment is appropriate for all circumstances.  

The next section of this memorandum provides four key takeaways from the remainder of the draft guidance, covering the agency’s recommendations for a sanitation program, current Good Manufacturing Practice (CGMP) measures applicable to sanitation programs, sanitation preventive controls and associated management components, and remediation following a pathogen contamination event.  The draft guidance also includes two appendices: a summary of the regulatory framework for the manufacturing and processing of LMRTE foods, and research regarding the adequacy of material flush techniques.

Four Key Takeaways from the Draft Guidance

1. FDA’s recommendations for sanitation programs to prevent contamination of LMRTE foods are generally consistent with industry guidance and leading practices, such as controlling water in dry production environments and implementing clean breaks, however some of the specific recommendations go beyond standard practices. 

The draft guidance emphasizes the importance of establishing and implementing a sanitation program, including CGMPs and sanitation preventive controls (for facilities covered by the PCHF rule).  The agency refers companies to existing resources that address sanitation programs for LMRTE foods, such as the 2009 publication of the Grocery Manufacturers Association’s (GMA; now the Consumer Brands Association) “Control of Salmonella in Low-Moisture Foods” and the Codes of Practice developed by the Codex Alimentarius Commission in 2018 for Low-Moisture Foods and in 2009 for Powdered Formulae for Infants and Young Children.  The agency then goes on to provide more detailed recommendations regarding controlling water in dry production environments. There also is a discussion about evaluating equipment design and engaging in maintenance and inspection programs to help prevent harborage sites.  In particular, FDA recommends redesigning or replacing equipment that cannot be effectively cleaned and sanitized. 

Additionally, FDA recommends establishing routine “sanitation breaks” in which production is stopped and all FCSs in the production system are cleaned and sanitized. For non-continuous production systems, FDA recommends such a break “at the end of your daily production.”  For continuous production systems, the agency recommends implementing a sanitation break “at intervals that are frequent enough to help limit the amount of food that could be affected by a contamination event.”  Further, regardless of whether the production system is non-continuous or continuous, FDA recommends periodic disassembly of equipment to expose, clean, and sanitize surface areas that are not readily accessible during routine sanitary operations.

2. The draft guidance provides detailed recommendations about managing sanitation as a preventive control, including regarding the role of environmental monitoring and product testing as verification activities and the importance of determining root cause along with conducting corrective actions. 

The discussion of sanitation preventive controls in the new draft guidance is particularly notable because it is the first FDA guidance document to address how to develop and implement a sanitation preventive control (as the agency has not yet issued “Chapter 10: Sanitation Controls” within the multi-chapter Draft Guidance for Industry: Hazard Analysis and Risk-Based Preventive Controls for Human Food document).  The LMRTE draft guidance provides a discussion regarding hazard analysis and each of the preventive control management components (monitoring, verification, and corrective actions), as summarized below. 

• Hazard Analysis.  FDA recommends identifying Salmonella spp. as a hazard requiring a preventive control if an LMRTE food is exposed to the environment prior to packaging and the packaged food does not receive a treatment or otherwise include a control measure (such as a formulation lethal to the pathogen) that would significantly minimize Salmonella spp.  Similarly, if the food is PIF, the food is exposed to the environment prior to packaging, and the packaged food does not receive a treatment or otherwise include a control measure (such as a formulation lethal to the pathogen) that would significantly minimize Cronobacter spp., FDA recommends that the hazard analysis identify Cronobacter spp. as a hazard requiring a preventive control.  For ingredients incorporated into PIF through dry blending, the guidance recommends that “you consider in your hazard analysis whether Cronobacter spp. is a hazard requiring a preventive control.”
• Monitoring and Verification.  FDA recommends that sanitation controls include procedures, practices, and processes for the cleanliness of FCSs, including FCSs of utensils and equipment, with monitoring or verification through visual observation.  Examples of sanitation controls include cleaning and sanitizing procedures (including appropriate frequencies for these procedures, concentrations of cleaning and sanitizing compounds, method of application, and contact time).  The agency also recommends considering adapting CGMP measures to function as a sanitation control by combining a CGMP measure with written procedures that includes monitoring or verification. 
• Environmental Monitoring.  FDA cites the PCHF rule for the premise that environmental monitoring is required as a verification activity when contamination with an environmental pathogen is a hazard requiring a preventive control.  In addition to explaining the “seek and destroy” approach that underlies a strong program, the agency provides recommendations for how to evaluate the data generated through environmental monitoring, such as conducting trend analyses and using visual tools (e.g., heat map) to better understand how repeat positive findings could be related.  As discussed further below, FDA also recommends “characterizing” (i.e., engaging in further analysis to identify whether the isolate is the same or closely related to others) any positive isolates identified on a FCS. 
• Product Testing.  The background section of the draft guidance explains FDA’s perspective that finished product testing is most useful when conducted in conjunction with other activities to verify that control measures are functioning as intended, but that finished product testing alone is not adequate as verification that an environmental pathogen hazard has been controlled.² When discussing sanitation preventive controls, FDA recommends periodic sampling and testing because it “can provide a historical reference of performance for the overall food safety system in your plant and verify the adequacy of your control of environmental pathogens over time.”  If testing identifies a pathogen in food, FDA recommends that it be characterized, as discussed further below.
• Root Cause Investigation and Corrective Actions.  The draft guidance provides specific examples of issues to address in corrective action procedures and the importance of working towards identifying the root cause, including potential means of investigation to aid these activities.  In particular, the agency recommends that corrective action procedures include “removal and replacement of contaminated equipment that cannot be adequately cleaned and sanitized.” 

The draft guidance provides specific examples of issues to address in corrective action procedures and the importance of working towards identifying the root cause, including potential means of investigation to aid these activities.  In particular, the agency recommends that corrective action procedures include “removal and replacement of contaminated equipment that cannot be adequately cleaned and sanitized.” 

The agency acknowledges that the root cause of a pathogen contamination event could be challenging to determine and that RCIs can extend over a period of time, depending on the nature of the investigation and the time to receive the results of analytical tests.  Recognizing that some information could take weeks to be received, FDA says “you should not delay taking initial corrective actions (such as collecting and testing environmental samples before cleaning and sanitizing a potentially affected FCS) even if you are not able to identify all appropriate corrective actions until the RCI is complete.”  Further, FDA states that when a contamination event occurs, there must be a sanitation break for all food contact surfaces that came in contact with the contaminated product.  FDA also discusses how to identify affected food and acknowledges that there are some circumstances where the outcome of the root cause analysis could provide a basis to limit the scope of affected food (e.g., conclusive identifying of when contamination occurred).

When restarting production, the draft guidance also recommends implementing “hold and test” procedures and conducting intensified sampling and testing of sites that represent a potential source of the environmental pathogen (including collecting samples several times during production).  The agency also references the International Commission on Microbiological Specifications for Foods’ scientifically-based sampling plans for use during “hold and test” procedures to provide statistical confidence for results of product testing.³

3. FDA recommends characterizing pathogen isolates obtained during routine verification activities or investigative sampling, strongly advocating for the use of Whole Genome Sequencing (WGS). 

For any pathogen isolates obtained during routine verification activities (e.g., environmental monitoring, ingredient testing, or product testing) or during corrective actions (e.g., investigative sampling), FDA recommends further characterizing the isolate so that you can determine whether isolates obtained from different sampling sites or on different sampling occasions are the same or closely related to each other.  The agency explains: “Knowing whether a pathogen isolate is the same or closely related to those previously found on environmental surfaces or in product at your facility can better enable you to identify and implement appropriate and effective corrective actions, including steps to prevent the contamination from recurring.”

After explaining the various methods for characterizing pathogen isolates (i.e., serological methods, molecular methods, and WGS), FDA strongly advocates for the use of WGS during an RCI. The agency’s view is that WGS “has the strongest discriminating power of the methods currently available for characterizing isolates and is particularly useful during an RCI when several isolates are obtained and a goal of the investigation is to determine whether they are the same strain with a common source.”  Notably, the agency also recommends that if you do not use WGS, you should save your pathogen isolates so that you can characterize them by WGS later, if needed. 

4. FDA provides recommendations for remediation following a pathogen contamination event and explains its view that dry-cleaning and material flush techniques are not adequate unless accompanied by a sanitizing treatment. 

The draft guidance says that if you become aware of a pathogen contamination event, you must use microbial testing to identify sanitation failures and possible food contamination, reject (or reprocess) affected food, and take corrective actions.  It also recommends stopping production on the line that produced the food and cleaning and sanitizing all potentially affected FCSs.   

The agency discusses how cleaning and sanitizing are distinct activities that are both necessary, going on to say: “We are not aware of any scientific or technical information that would support a conclusion that dry-cleaning techniques (such as material flush techniques) are adequate to remediate a pathogen contamination event unless accompanied by a sanitizing treatment.”  This is one of several sections in the draft guidance where FDA discusses its perspective on the use of “material flush techniques” (also known as “product push” or “product purge”) for routine cleaning of food processing equipment (e.g., moving hot oil or product through a production system to remove the product that was previously being produced).  The agency states emphatically: “At this time, we are not aware of scientific or technical evidence that demonstrates that cleaning techniques alone, including material flush techniques, are effective in mitigating pathogen contamination on FCSs.”  FDA also provides information on considerations associated with potentially demonstrating the adequacy of material flush techniques without an accompanying sanitizing treatment. 

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Over a decade after the adoption of the FDA Food Safety Modernization Act, FDA has issued long-awaited guidance on critical food safety issues and its corresponding expectations.  The draft guidance is largely consistent with the agency’s longstanding enforcement approach, but nonetheless is particularly significant now that it has been distilled into a single document as draft guidance.  Although manufacturers of LMRTE foods are the primary audience for the draft guidance, manufacturers of all foods at risk of post-lethality environmental contamination should review the draft guidance closely to evaluate current sanitation practices.  As draft guidance, this document is open for revisions before it is finalized.  Affected companies and their trade associations should carefully review the document and provide comments to FDA that highlight any areas of concern. 

Please do not hesitate to contact us if you have any questions, concerns, or if we can provide support drafting comments before the May 7, 2025 comment deadline. 

Authored by Maile Gradison and Anneke Altieri.