A sanitation program is a key component of any food processor's or food handler's food safety plan. A well-written and well-executed sanitation program can mitigate, or reduce to an acceptable level, all three classifications of hazards (microbiological, chemical, and physical) in a hazard analysis. Sanitation is one of the four preventive controls (process controls, allergen, sanitation, and other) in the Preventive Controls for Human Food rule of the Food Safety Modernization Act (FSMA). Sanitation has long been a major prerequisite program for Hazard Analysis and Critical Control Points (HACCP). Consequently, it is imperative that the sanitation program be functioning and performing according to expectations.

Verification is one method of ensuring that the sanitation program is being consistently implemented and is performing to the expectations of the food safety plan's hazard analysis. Verification is one of the seven principles of HACCP. It is required by the U.S. Food and Drug Administration (FDA) and U.S. Department of Agriculture (USDA) in various regulatory statutes. A facility is required to perform verification.

Many methods are available for verifying the viability of a sanitation program, and most facilities use a combination of different methods to ensure that the sanitation program is performing as expected.

Some tools for sanitation verification include:

  • In-process or finished product testing
  • Testing a sanitation cycle for temperature, chemical concentration, flowrate, etc., according to the validated sanitation recipe/procedure
  • Visual inspection: In food facilities, a pre-operational inspection is completed between changeovers and before starting production; however, the human eye cannot see a microorganism or an allergenic protein, and so caution must be taken if this is the only sanitation verification method chosen
  • Records review: Reviewing all log sheets and documentation associated with the sanitation program to ensure it was completed according to procedure, and that the personnel completed the necessary tasks according to schedule
  • Rapid testing methods including ATP or lateral flow allergen testing
  • Microbial environmental monitoring.

All of these methods and others are industry standards for verifying sanitation effectiveness.

Environmental Monitoring Programs

The food processing environment and equipment must be tested for microbiological contaminants. As previously stated, an environmental monitoring program (EMP) can serve as a verification tool for a sanitation program. In addition, an organized and well-managed EMP can save a facility from a potential costly (or business-ending) recall and/or downgraded product. Aside from recalls and operational efficiencies, there are many more benefits to a robust EMP including:

  • Serving as an early warning system, enabling the pathogen to be found in the facility before it makes its way into the product
  • Identifying potential maintenance issue or harborage locations in the facility
  • Reducing the number of hazards requiring a preventive control or critical control point (CCP) in the food safety plan, and controlling the hazard before it increases to a preventive control or CCP level
  • Providing a methodology for data collection and trending
  • Meeting customer, third-party, and regulatory requirements.

Environmental monitoring is a requirement in both USDA and FDA facilities. FSMA 21 CFR 117.165(3) states:

"Verification activities. You must verify that the preventive controls are consistently implemented and are effectively and significantly minimizing or preventing the hazards. To do so you must conduct activities that include the following, as appropriate to the facility, the food, and the nature of the preventive control and its role in the facility's food safety system: […]

(3) Environmental monitoring, for an environmental pathogen or for an appropriate indicator organism, if contamination of a ready-to-eat food with an environmental pathogen is a hazard requiring a preventive control, by collecting and testing environmental samples."

USDA requires swabbing as part of a verification of sanitation in a facility's food safety plan in Pathogen Reduction; Hazard Analysis and Critical Control Point (HACCP) Systems final rule (9 CFR Part 417).

In addition to regulatory requirements, third-party audits including the Global Food Safety Initiative (GFSI) approved auditing schemes, also require EMPs. For example, Safe Quality Foods' (SQF's) Food Safety Code: Food Manufacturing, Edition 9, states in

"A risk-based environmental monitoring program shall be in place for all food and pet food manufacturing processes and immediate surrounding areas, which impact manufacturing processes. The responsibility and methods for the environmental monitoring program shall be documented and implemented."

The code explains the requirements in further elements.

Environmental monitoring programs have several common names and acronyms in the industry. A quick search through Food Safety Magazine's archives reveal several including:

  • EM (Environmental Monitoring)
  • EMP (Environmental Monitoring Program)
  • EMPC (Environmental Monitoring Pathogen Control)
  • PEM (Pathogen Environmental Monitoring).

All have the same purpose—"seek and destroy"—i.e., proactively looking for microorganisms on the equipment and in the environment before the product is comprised. There is no "one-size-fits-all" PEM program in the industry, because each PEM program is based on the risks unique to each processing facility, equipment, product, people, history, etc. A facility making a dairy product will have a much different program than a facility packaging fresh-packed potatoes. PEM programs can be expensive and, therefore, must be configured properly to be functional and provide the right information to make data-based decisions.


PEM can serve two purposes for sanitation:

  1. For sanitation verification. Did you start out clean? Did the sanitation practices, policies, and procedures achieve the desired cleanliness standard? Test during post-rinse or pre-operational inspections.
  2. When the facility is at its "dirtiest." Right before sanitation (or at least 3–4 hours into production), test the equipment and facility to determine if any microbiological contaminants came in via cross-contamination during the processing period, verify facility sanitary design, or validate production and sanitation procedures.

An effective program has a mix of both PEM purposes. A best practice when determining the timing of sample collection is to also vary the days and times of sampling locations. If staff know that Tuesday is swab day, there may be some bias in how the area is cleaned ahead of time. However, if any day could be swab day, then the bias can be eliminated.

Swabbing Locations

When deciding where to swab, many facilities use a zonal approach (Table 1). Zone 1 starts with product contact surfaces, and Zones 2–4 move increasingly further away from product contact. Envision a dart board. Product contact is in the center (the bullseye); in darts, the most points are achieved by hitting this area. Moving further away from the center moves further away from product contact, resulting in fewer "points."

TABLE 1. Zonal Approach for Swab Sampling

A valuable PEM program samples all four zones at some frequency.

Standard or Random Locations

An effective PEM program has a mix of standard sampling sites and randomly selected sites. For sanitation verification or routine situations, some sampling locations will be sampled every time after sanitation. However, some sampling locations should be random. Train and encourage staff who are collecting samples to look around the facility. Instruct them to look for areas they think may have a problem and sample those sites. Remind them not to look solely at eye level. Twenty to 30 percent of swabs should be taken from above eye level, and 20–30 percent should be taken below eye level. Do not swab only what is easy to see right in front; crouch down under equipment and use ladders to see above. Design sampling devices so that a person can easily collect samples from different heights and locations. (Case in point: The author once retrofitted a telescoping paint device to swab overhead air vents.) If an area is difficult to clean (under equipment and higher than a person can reach), then it is less likely to be cleaned. Swab the area that is the most difficult to clean to determine if microorganisms are present. If the difficult-to-clean area is free of microbiological contaminants, then the easy-to-clean places probably are, as well.

Results from random sampling can be very powerful data; however, random sampling requires extra documentation. This documentation must describe some method of recording what was sampled, and where. Never underestimate the power of pictures—they are an excellent tool to help record the actual sample location. A picture of the sampled area with a finger pointing to the location removes any doubt as to what/where was sampled. If a third-party lab is testing the samples, it could take up to a week before a facility knows the results. Having good documentation of what was sampled will help an investigation if the site comes back positive or out of specification. In addition, understanding what locations have been sampled across the site will help in identifying trends and making decisions on what needs to be increased or decreased as part of continuous improvement. The data needs to drive decisions. Use trends to determine appropriate testing sites and frequencies.

Examples of some good sampling locations include:

  • Cracks, crevices, niches—all difficult-to-clean locations
  • Tight corners, bends, and sharp edges that may harbor biofilms
  • Locations that provide a transfer location between zones
  • Areas that show issues with sanitary design
  • Areas that are exposed due to traffic patterns (of people, trash, forklifts, etc.)
  • Areas that routinely have pooling water or collect debris
  • Sampling sites that are closest or could affect open product, packaging, or ingredients
  • Locations after the kill step (heat or pasteurization) and before final packaging (high priority)
  • Problem areas, or areas that historically have had positive or out-of-specification results.

Do not think only of equipment and infrastructure; think about water quality and air quality, too. When wet sanitation cleaning recipes are validated, it is essential that the cleaning chemicals clean the equipment, not the water. If the water is contaminated, then all the active compounds in the chemical will be used to clean the water, and nothing will be left over to actually clean the equipment. Regulators and third-party audits require minimal water testing from the main water sources. Also think about all the point-of-use areas of water, such as hoses, sinks, mop stations, etc. Ensure that the water coming from those sources (both the water itself and the equipment/piping) are not contaminating the product and environment.

What about air? The air touches the product and equipment; consequently, the air must not contaminate the environment. Third-party audits require microbiological testing for product-contact compressed air. In addition, the air in the processing and packaging areas should be tested. Pour plates can be placed in the room, or a forced-air testing unit can be utilized. Also take a sample of the filters on the HVAC system, and make sure to test only the final filter, as the pre-filter likely will have microbiological growth since its job is to filter the air.

It is important not to forget about people. We are walking hazards to the product. Test the hands, tools, equipment, personal protective gear, uniforms, etc., of employees to ensure that they will not contaminate the product with microorganisms as they go about their daily tasks.

Quantity of Samples

The number of samples can be tricky and must be based on a risk assessment. One of the key factors is facility size. Industry recommendations include 30–60 sampling sites per 50,000 square feet. Another consideration is the product risk. If a facility manufactures a ready-to-eat product, then more sampling sites are required than if a facility makes a product that will be sent to another manufacturer to be further processed.

In addition, age and previous test results can influence the number of samples. If a facility or equipment is older, then there is a higher chance of cracks and crevices and repairs that have been damaged with use and time. Wear and tear on equipment and infrastructure will require additional swabs. A new piece of equipment or a new facility may not require as many swabs.

Sample Collection Instruments

It is important to use a wide variety of tools or sampling instruments to manage the many different situations and materials in a food processing facility. The old adage, "if you only have a hammer, then every problem is a nail," can be used. If only one tool is available for sampling, then every location cannot be sampled.

Check with third-party testing labs and production/lab equipment suppliers to procure several types of sampling instruments. Also remember the purpose of the swab and what types of chemical components the product comprises. Use those factors to determine what type of swab is needed—e.g., a dry swab, a swab enriched with a broth, a swab with a chemical neutralizer, etc.

Testing for Microorganisms

A PEM program should test for a mix of indicator organisms and a mix of pathogens based on product susceptibility and risk. An indicator organism is a mark of overall hygiene conditions. An indicator organism indicates that an area or a piece of equipment is not cleaned to an acceptable microbiological condition. It implies that suitable growth conditions exist for a host of microbiological contaminants, including pathogens. Frequently used indicator organism tests are coliforms, standard plate count, or Enterobacteriaceae.

As for pathogens, a facility must analyze its product to determine the pathogens of concern based on the product's chemical and physical properties. What are the product's pH, moisture, and water activity level? At what temperature is the product stored? Common pathogens that are routinely tested for in a PEM program are Listeria, Salmonella, Cronobacter, Staphylococcus species, etc. A strong PEM program will test for a multitude of pathogens at some frequency, rather than only one pathogen. For example, if the product is wet, Listeria is a common pathogen of concern. Ten months of the year, the facility will test swabs for Listeria. To verify that Salmonella is also not present, twice a year the facility will send swabs for Salmonella testing, as well. If a facility processes flour products, then the pathogens of concern are Salmonella and possibly Escherichia coli. An infant formula plant will test for Cronobacter and Salmonella. The pathogens being tested for in the PEM program must match the pathogens of concern for the product(s) manufactured and processed at the facility.

Different areas of the plant may require different pathogen testing. For example, a dry facility may test for Salmonella routinely in the processing area. If the facility has a wet area, then Listeria tests will be performed in that area. As stated previously, an effective PEM program looks at the risk level of the facility and the product(s) to determine the appropriate indicator organism and the appropriate pathogen testing.


Any presence of a pathogen is cause for concern and is considered out of specification. For an indicator organism, the value that is considered out of specification depends on the sampled zone. For example, for the indicator organism Enterobacteriaceae, common specification limits in cfu (colony forming units) are shown in Table 2.

TABLE 2. Common Specification Limits (cfu) for Enterobacteriaceae

If the results show a positive or out-of-specification indicator organism, then a root-cause analysis must be performed according to the corrective and preventive action program. To find the root cause of the issue, a facility must conduct a series of vector swabs. Vectoring starts with the positive sample location and fans out looking for the root cause of the issue. For example, if the positive test result is the floor surface at the bottom of a set of stairs, then the floor is probably not the root cause. However, the equipment near that area of the floor could be harboring the microbiological contaminant. A trained analyst must start at the positive location and determine likely locations that could be causing the contamination. The analyst will need to swab a series of locations to find the actual location that is allowing the microorganism to proliferate. Think of the floor as the center and start fanning out to find the actual source.

Even if the facility does not have any positive results, do not ignore the negatives—trend the data. Many commercially available software packages are designed to help trend environmental results. An Excel spreadsheet also can be used to trend data. The important thing is to look at sampling sites and make decisions. PEM programs are expensive and should be part of a continuous improvement program. If a sampling location is routinely negative, then the testing frequency may be able to be reduced on that site, and areas that require more scrutiny can be given greater attention and expense. For example, if a site is on the weekly list but has not been out of specification for the past six months, then the sampling frequency for that site could be moved to monthly, and another location that needs more attention can be given more time and testing.


PEM programs are a key prerequisite program to a sanitation program and to any facility's overall food safety program. Regulators, customers, and third-party auditors all require some sort of PEM program. There is no one-size-fits-all PEM program for facilities; rather, a PEM program is based on a facility's risk factors and what product(s) the facility manufactures. Good documentation and records are important to prove to customers and regulators that the PEM program is functioning and actively looking for microbiological contaminants in the environment.

Results from a PEM program should be used to make data-based decisions. The key to any good program is to catch the microbiological contaminant in the environment before product is impacted. Do not be afraid to routinely sample random sites, and ensure that analysts are trained to look for any potential problem areas. Getting a positive is not necessarily bad, and is usually expected. If a facility never has a positive test, then the PEM program is likely not effective and needs additional scrutiny. Good luck, and find those microbiological contaminants!

Janna Hamlett, Ph.D., is an Assistant Professor at the University of Idaho Extension and a Food Processing Specialist with TechHelp, Idaho's Manufacturing Extension Partnership Center. She has over 15 years of experience in the food manufacturing industry, with a background in quality and operations management including numerous certifications in lean processing management, personnel safety, and food safety and quality programs.