664f6ac130fc11efad5e4e80 Sanitationadobestock 98576186

Sources and Harborages of Pathogens in the Plant

June 3, 2024
Effective pathogen control requires identifying and managing the sources and harborages in the processing environment.

By James Davis of OSI Group


Adverse food safety incidents resulting in product loss and market withdrawals present a significant business risk to food manufacturers today. Increasing expectations from consumers and regulatory agencies has heightened the focus on pathogens as their presence in food products comprise a large portion of recalls in the U.S.

While the root cause of each incident varies, and may often be unknown, factors such as pathogen entrance into a controlled zone, prevalence and subsequent movement within the processing environment may permit direct or indirect contamination. These factors are often termed as sources, harborages and vectors, respectively.

Sources can be generally defined as any action, event or design that may permit entry of pathogens into a controlled zone. Likewise, harborages can be defined as any action, event or design that may permit continued residence of pathogens within a controlled zone. Finally, vectors are described as movements, such as by people or tools, that transfer pathogens from one surface or location within the controlled zone to another surface or location.

This article will focus on identifying and managing the sources of pathogens and harborages.


Identify & manage the sources

Preventing pathogens from entering the controlled zone(s) in the manufacturing facility is the critical first step of an effective control program. When pathogens enter the controlled zone, they have the potential for product contamination from persistent harborage in product zones or via a vector from harborage in non-product zones. Facilities should begin by clearly defining (e.g., mapping) the boundaries of the pathogen-controlled zone.

People: Improper employee behaviors, such as failing to follow good manufacturing practices (GMPs) upon entering the pathogen-controlled zone, can inadvertently introduce microorganisms. Common issues observed include improper handwashing technique and donning soiled or previously used personal protective equipment (PPE), such as frocks from processing or storage areas external to the pathogen-controlled zone.

Active control systems, such as gates or turnstiles, to ensure handwashing is executed properly can reduce incidence of pathogen entrance -- along with storage of PPE in the same risk zone. Additionally, routine monitoring of practices across all shifts is an important action to ensure continued compliance to facility requirements.

Environmental Ingress: The ingress of potentially contaminated air, liquids or other debris into the pathogen-controlled zone from external areas has been a key root cause for several recent microbiological issues in the industry. Key examples of liquids ingress include ceiling leaks and drain back-ups or backward drainage flow in shared systems to controlled zones.

Ingress via air has been associated with improper flow into pathogen-controlled zones, along with inadequate filtration of outside air through incorrect filter sizing or improper installation, resulting in unsealed junctions. Also observed are failure to adequately filter process air used in air knives or as compressed air on equipment surfaces.

Measures to ensure prevention of issues associated with environmental ingress routine inspection for integrity (i.e., effective sealing from outside) of ceiling panels, interstitial spaces (e.g., roof voids), roofs, ventilation systems and any penetrations through these structures.

It is recommended to monitor room air pressure differentials and microorganism load regularly for hygienic maintenance. Additionally, routine jetting (i.e., high-pressure cleanout) of main and branch piping of drainage system is highly recommended to ensure adequate flow of wastes.


Process controls (HACCP)

Foundational to pathogen control is ensuring effective critical control points (CCPs) are established and validated in the facility’s HACCP plans. Ineffective CCPs or CCP failures pose significant risk in introducing pathogens into the controlled zone. Failures presenting highest risk are those of undercooked product that may be the result of equipment damage or issues or improper adjustment in the cooking process.

Where undercooked product is observed and has entered the pathogen-controlled zones, robust corrective and preventative actions (CAPAs) are necessary to restore hygienic conditions prior to the resumption of production operations. CAPAs typically include, but are not limited to, execution of the Seven Steps of Sanitation (see graphic) for affected areas, along with additional environmental monitoring to verify effectiveness of the actions. Facilities should have a written procedure in place with detailed instructions on the steps required in the event of a CCP failure.

Transferred Materials: As part of the manufacturing process, ingredients, materials, supplies, tools, and utensils may be required to enter the pathogen-controlled zone. These items, if not properly controlled or monitored, may present a source of pathogens where contamination is not realized. Common examples include primary and secondary packaging materials (e.g., film, including outer bag or cover, cartons and boxes), maintenance or contractor tools and infrequently used equipment.

Facilities should take inventory of all materials that enter the pathogen-controlled zone across all operating shifts. With this information, the facility can analyze each input for risk of contamination, level of environmental monitoring of materials required and any control measures that may be necessary. Typical control measures to reduce risks when transferring materials often include using captive (i.e., remains in controlled zone) transport equipment such as carts or hand trucks in combination with a transition zone (e.g., vestibule) for “hand-off.” Captive maintenance tools cleaned with the routine sanitation process in the zone is also considered best-practice.

Process (Design) Separation: Incomplete physical separation of equipment and infrastructure components between zones of different risk are a potential source of pathogens and are often overlooked when not easily visible. Common examples where contamination events have occurred due to inadequate separation between risk zones on equipment include converging entrance and exit exhaust ductwork on ovens, lack of barriers to control overspray during sanitation from one area to another and shared clean-in-place (CIP) systems.

Examples for infrastructure include shared ventilation systems between processes and shared drainage systems between risk zones with improper flow of liquid wastes.

To determine appropriate corrective and preventative measures, the facility should first perform a design assessment of equipment and infrastructure to identify areas of inadequate separation. Maps of drains and ventilation ducting that may not be visible should also be reviewed. Monitoring accessible points can assist in determining risk, however, system modification may be necessary.

Traffic Patterns: Uncontrolled employee or transport device (e.g., pallet jacks) movement into pathogen-controlled zones from areas external present a potential source. This may be the result of using non-designated pathways such as side doors or emergency exits or failing to implement a footwear cleaning or disinfection program into pathogen-controlled zones. This is also a concern in facilities that rely on passive traffic controls (e.g., signs, training, painted lines) rather than active controls (e.g., permanent corridors, restricted access doors).

For effective traffic control, facilities should map people and transport equipment movement into and within the pathogen-controlled zone. At entrances to the zone, it is recommended to utilize a chemical treatment as an intervention for footwear and wheels of transport devices. This may include the use of floor treatments such as disinfectant granules and entryway foamers, and the use of mechanical footwear disinfecting devices.

Facilities may also consider the installation of active, physical barriers (e.g., rails, restricted access doors) to restrict traffic through only designated paths. Validation and routine verification of traffic intervention methods is critical to ensure effectiveness.


Identify & manage harborage

In addition to resolving the sources of pathogen entrance into a processing area, removal of existing pathogens from identified harborage points in equipment and facilities is also critical to prevent recurring issues in the future.

Equipment Hygienic Design: As equipment in the processing area often comes into direct or indirect contact with product and product zones, poor design of components plays a significant role in the potential for harborage. Accessibility of surfaces for cleaning is a key factor in identifying areas of harborage within equipment.

Surfaces with either limited access (i.e., difficult to reach) or are currently inaccessible, pose the highest risks for potentially harboring pathogens. Many examples of poor designs exist, which can result in harborage on surfaces:

  • Within bolted connections (e.g., lap joints)
  • Within hollow tube framework and rollers
  • Within unwelded seams (e.g., where skip welding is observed)
  • With rough textures (e.g., scratches, unsmooth)
  • Between installed equipment mounted very close to other equipment or infrastructure areas

To assist in the identification of harborage points on equipment, facilities are encouraged to evaluate their equipment by using a sanitary design guidance document, such as the North American Meat Institute’s (NAMI) Sanitary Equipment Design Principles checklist. This document will assist in identifying poor design practices with higher risk of pathogen harborage.

Once identified, facilities can implement CAPAs to lower the risks associated with non-compliances. This may include implementing a routine equipment disassembly process, use of heat-treatment interventions (i.e., steaming), modifying the routine sanitation process or component redesign or replacement. Validating and routinely verifying CAPAs are critical in the ongoing maintenance of hygienic operations.

Facility Hygienic Design: As with equipment, infrastructure surfaces with challenges in accessibility also present a risk of harboring pathogens. Common points of harborage may include unsealed penetrations or joints in walls or ceilings, inability to clean interior surfaces of cooling units and exposed porous construction materials (e.g., unsealed concrete curbs).

Additionally, infrastructure components that are not fully contained within the room envelope are often overlooked or inaccessible, and therefore missed in the sanitation process. Examples include ventilation ducting for air supply and exhaust systems and drains.

Similarly to equipment assessments for poor design, facilities should take inventory of infrastructure surfaces that pose a risk of harborage. NAMI’s 11 Principles of Sanitary Facility Design can be used as a guide during evaluations. As with equipment, CAPAs should be undertaken to address the potential for harborage through sanitation program modifications, repair, or replacement, or with disassembly of selected components.


Sanitation execution

Effective execution of the sanitation process is a critical part of pathogen control programs, ensuring continued removal of pathogens that may enter and reside within the processing area. Failure to implement the fundamentals of routine and non-routine cleaning allows for an increasing level of microorganism load within the controlled zone.

Facilities are recommended to follow the Seven Steps of Sanitation, which are the industry defined best practices for effective and efficient cleaning. These steps should form the basis of written cleaning procedures for routine and non-routine sanitation activities.

Routine monitoring to include pre-operational visual and surface sampling (e.g., ATP, TPC) will ensure compliance. Non-routine cleaning activities should be defined in a Master Sanitation Schedule (MSS), based on hygienic design analyses, which may include disassembly of components with surfaces that are normally inaccessible during routine sanitation. Tasks should be clearly defined with frequencies validated to ensure that interior surfaces remain free of pathogens.

Floor Conditions: As floors are exposed to a variety of environmental conditions, soils and traffic patterns, they are collection points for microorganisms. Damages to floor surfaces, as well as at junction points with other infrastructure components, are often points of harborage.

Cracks and delamination of coating material is typically observed in the following areas: heavy traffic pathways, difficult-to-inspect areas underneath equipment, at junction points with feet or frame supports for heavy equipment and at junctions with drains. Excessive surface roughness of floor coatings may also present difficulty in removing soils.

To reduce the occurrence of pathogen harborage, facilities should implement a routine inspection process to identify damages or issues associated with integrity, particularly at junction points. Repairs should be undertaken in a timely manner before harborage extends further into the floor structure.

As a best practice, measures should be undertaken to minimize the amount of liquids or food residues from equipment onto floors via the use of drip pans or directing waste piping to drains instead of across floor surfaces. Additionally, as with equipment, an effective program to minimize harborage of pathogens must include appropriate execution of the sanitation process on a routine basis.

Cleaning of floors should follow the best practice guidance of the Seven Steps of Sanitation, along with pre-operational inspection and operational environmental monitoring to confirm continued acceptable hygienic outcomes.

Utilizing key principles to identify potential sources and harborage points of pathogens allows facilities to initiate corrective and preventative control measures to their programs to ensure a high-level of food safety for the manufacturing process.

James Davis is the Global Sanitation Senior Director at OSI Group (, an $8 billion sales global supplier of custom, value-added food products to the world’s leading foodservice and retail food brands. James leads the company efforts in sanitation and hygienic design of equipment and facilities, with emphasis on food safety risk management. In this role, he develops and implements standards, training and policies to drive consistency in sanitation and hygienic design ensuring a high level of food safety for the organization. James collaborates and participates in industry associations to develop and implement best-practices and new standards.

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