Managing cross-contamination and cross-contact across the food supply chain

    1. Food Safety Certification
    2. Food Safety Topics


Cross-contamination and allergen cross-contact incidents are frequently indicated as causes of food recalls. According to U.S. Food and Drug Administration (FDA) Enforcement Reports, food products recalled from January 1 through August 30, 2017 due to contamination from pathogens was approximately 40%; those from undeclared allergens also accounted for approximately 40%.(1) While the specific cause of contamination events from pathogens or the presence of allergens in non-labelled product is not always known at the time of reporting, cross-contamination and cross-contact incidents are often later identified as likely contributing factors. For example, of product recalled in 2017 for pathogen contamination, approximately 50% of products reported were potentially contaminated or confirmed as contaminated with Listeria monocytogenes and 35% with Salmonella, both environmental pathogens well known for their prevalence in food production environments.(1) Undeclared allergens frequently occur as the result of labeling errors but may also result from ineffective cross-contact controls such as was identified in a recent non-dairy cracker meal and bread coating product recall affecting meat companies.(2)

As the food industry has experienced in past years, supplier recalls from pathogen contamination can have significant impacts on the supply chain. A recent example includes the 2016 CRF Frozen Foods recall involving over 450 products across more than 40 brands; the incident resulted in 8 illnesses and 1 death from listeriosis across 4 U.S. states.(3,4) Upon inspection of the Washington facility, FDA investigators noted unsanitary and difficult-to-clean processing equipment, utensils, and building infrastructure in the Establishment Inspection Report—many of which were noted as potential sources of contamination/ cross-contamination.(5)

To prevent foodborne illness and recalls, management of cross-contamination and cross-contact risks are critical at every level of the supply chain beginning with the producer through use by food service establishments and consumers. In the following white paper, TUV USA highlights some common cross-contamination and cross-contact risks throughout the supply chain along with a discussion on effective controls.

What is the difference between cross-contamination and cross-contact?

Generally, cross-contamination refers to the transfer of microorganisms to food products from other sources such as raw materials, equipment surfaces, utensils, etc. as a result of improper handling, which renders the food unsafe.(6,7) Historically, the term cross-contamination has also been used to describe allergen contamination in product not formulated with the allergen or contamination of identity preserved (IP) foods from materials, which comprise the integrity of the food’s unique characteristics (e.g., GMO, organic).

However, in recent years—particularly in the U.S. for FDA regulated food—the term cross-contact is increasingly used in lieu of cross-contamination to describe unintentional contamination from allergen residues, which may result from production, handling, manufacturing, storage, or transportation activities especially where equipment is shared. The U.S. FDA acknowledged that this shift in descriptors is to more accurately represent the nature of allergens, which are not “contaminants”, but rather proteins constituting a normal component of food.(8) References to allergen cross-contact are described by the FDA in regulation and guidance documents related to the Food Allergen Labeling and Consumer Protection Act (FALCPA) and several Food Safety Modernization Act (FSMA) rules, including Preventive Controls and Sanitary Transportation rules.(9,10,11,12)

FSMA and beyond

Cross-contamination and cross-contact controls are an important part of FSMA regulation and most prominently discussed in the Preventive Controls rules. Specifically, Preventive Controls regulation requires both sanitation and allergen controls to protect food from allergen cross-contact as well as sanitation controls to prevent food from becoming contaminated with pathogenic microorganisms from unclean sources such as raw materials, equipment surfaces, and personnel clothing. (10,11) In similar fashion, the Sanitary Transportation rule requires preventive measures to protect exposed food from contamination and cross-contact during transportation, which includes container sanitation in between loads. (12) Control measures such as preventing ill workers from contact with produce, personnel and visitor hygiene, effective sanitation of equipment/ tools/ containers, water quality, and appropriate soil amendment use are all requirements of Produce Safety regulation aimed at preventing contamination/ cross-contamination of fresh produce from human pathogens.(13)

Going beyond country legislation, cross-contamination controls have been a long-standing pillar of Global Food Safety Initiative (GFSI) benchmarked schemes. Now in its 7th edition, the GFSI Benchmarking Requirements was updated to improve the identification of allergen cross-contact risks amongst susceptible operations and implementation of effective controls for allergen management while previous requirements for segregation and cross-contamination controls remain.(14) Prior to publication, many benchmarked schemes had already established standard requirements for cross-contact evaluation as a part of the allergen risk assessment, while others recently updated or are in the process of updating their standards for re-benchmarking. What is notable is increasing congruency between food safety management requirements of country-specific regulation and GFSI schemes in the areas of cross-contamination and cross-contact.

And moving outside of food safety, are those cross-contact controls required of IP systems such as those developed to meet non-GMO verification standards or organic, non-GMO, and gluten labeling regulations. In the context of IP, cross-contact may result from exposure to foods or residues that compromise the integrity of the IP claim and, in the case of gluten, can trigger an allergic response in sensitive or intolerant individuals. Cross-contact controls such as identification, segregation, and sanitation are important components of IP systems.

Cross-contamination and cross-contact risks

FSMA regulation and Global Food Safety Initiative (GFSI) benchmarked schemes require cross-contamination and cross-contact controls such as zoning, sanitation and allergen management to prevent hazards in food; however, such controls must be specific to the risk if they are to be effective. For example, a sanitation control of flushing to remove allergen residues may be appropriate to reduce the risk of cross-contact in products not containing the allergen but would not be effective in preventing cross-contamination from pathogens. Similarly, effective cleaning and sanitization methods would be very different in dry versus wet environments to prevent cross-contamination from environmental pathogens. Thus, a thorough hazard analysis (or risk assessment) that fully considers sources and routes of cross-contamination and cross-contact to ensure controls are appropriately matched to the risk is of primary importance before determining effective controls. Described below are some examples of cross-contamination and cross-contact scenarios that can support in the development of a hazard analysis that effectively evaluates cross-contamination and cross-contact risks.

Primary Producers

Numerous cross-contamination risks exist in primary production systems especially at the point of lairage and slaughter for meat and harvest/ post-harvest handling of produce. Whether you are conducting a hazard analysis for your operation or a supplier risk assessment of a raw material supplier, consider the following primary production cross-contamination risks (this is not an exhaustive list):

Animal production(15)

• Contaminated feed, water, and environmental sources—especially those susceptible to fecal contamination such as milking systems—in animal production

• Defecation during transportation resulting from stressful conditions and causing fecal contamination of the vehicle and other animals

• Cross-contamination from the environment and infected animals during lairage (i.e., holding pen for the purpose of resting animals before slaughter)

• Cross-contamination from water, equipment surfaces, and carcasses during scalding, defeathering, evisceration, and chilling

... A lack of segregation between “clean” and “dirty” processes in the slaughter facility

... Contaminated fingers of the picker machine during defeathering

... Contaminated scald water (i.e., poultry and pigs)

... Unclean equipment during evisceration

... Contaminated water for immersion chilling (i.e., poultry)

• In pig slaughter, two studies observed that approximately 30% of carcasses contaminated with Salmonella were the result of cross-contamination

• Contamination of seafood is commonly a result of

... Fecal contamination from polluted water

... Improper hygiene during handling and transportation

... Infected food handlers

Agricultural production(15,16,17)

• Contaminated irrigation water from improperly constructed or unprotected wells

• Runoff from adjacent land used for animal grazing or improperly sited field facilities (i.e., toilets)

• Unclean knives or harvest equipment

• A lack of segregation between “clean” and “dirty” processes in the packinghouse

• Recirculated water in dump tanks and flume systems

• Improperly disinfected water used for postharvest cooling (e.g., vacuum cooling, hydrocooling)

• Unclean or difficult-to-clean containers or harvest bins (e.g., wood, reusable plastic containers [RPCs])

• Difficult-to-clean packinghouse equipment (e.g., conveyor belts, rollers, brushes) leading to product build-up, biofilm formation, and pathogen growth niches

• Substandard packinghouse facilities leading to pooling water, rain intrusion, roosting areas, pest ingress, and difficult-to-clean ceilings, walls and floors

• Ill workers


Many cross-contamination risks described in primary production systems such as substandard facilities, dirty equipment, and unhygienic workers carry through to manufacturing operations, yet their impact can be more profound where food is ready-to-eat (RTE) and not treated with a process step lethal to the pathogen or where recontamination post-treatment occurs. Cross-contact risks are escalated in the manufacturing environment as well, largely due to a multitude of raw materials, ingredients, and processing aids handled on site. In a food manufacturing environment, consider the following cross-contamination and cross-contact risks (this is not an exhaustive list):

Cross-contamination risks(15,18)

• A lack of segregation between low-risk and high-risk processes

... Contamination of cooked product from uncooked (raw) materials

... Traffic routes (e.g., personnel, raw materials, work-in-progress, forklifts)

• Substandard facilities leading to improper drainage, leaky pipes or roof, excessive condensation, pest ingress, and difficult-to-clean ceilings, walls and floors

• Uncontrolled dust from materials with a known pathogen prevalence rate (e.g., milling of high-risk grains, nuts, spices)

• Contaminated air or water used to clean product or equipment

• Unclean equipment, utensils, containers, and conveyances or those that are in direct contact or close proximity to the floor and traffic areas

• Food handlers, maintenance workers, and visitors not practicing good hygiene

• Personal clothing—especially footwear—or contaminated personal protective equipment such as dirty aprons and gloves

• Unprotected primary packaging

Cross-contact risks(19)

• Unverified raw materials, ingredients and processing aids

• Food handlers, maintenance workers, and visitors not following the site’s allergen management or IP practices

• Lack of identification—especially distinctive identification such as color coding—of all materials, work-in-progress, finished product, and rework

• Inadequate separation of materials and product in storage and across all process steps of the operation

• Spillage of allergenic or unverified IP materials

• Unverified changeover between production runs

• Shared equipment, utensils, containers, and cleaning tools

• Uncontrolled dust from allergenic or unverified IP materials

• Contaminated work wear

Storage and Distribution operations

In storage and distribution operations, opportunities for cross-contamination and cross-contact may be reduced due to packaging barriers, but risks remain and must be controlled especially for bulk transport and exposed or damaged materials and product. Consider the following cross-contamination and cross-contact risks (this is not an exhaustive list):(20)

• Unclean or substandard storage facilities

• Spilled materials or product during unloading or storage resulting from poor forklift handling

• Unclean containers or tanker trucks

... Unclean containers can transfer contaminants to exposed food or packaging and encourage pest harborage

... Food contact surfaces of tankers pose risks to food safety due to the potential to transfer harmful microorganisms and allergenic residues when not adequately cleaned in between loads

• Transporting mixed loads

• Spilled materials or product during loading or transportation resulting from ineffective packing (e.g., poor packing material or pallet configuration)

• Poor worker hygiene

Cross-contamination and cross-contact controls

Once potential cross-contamination and cross-contacts risks are identified for the operation, select and apply controls that mitigate each risk. This can be challenging as cross-contamination often requires two-fold control measures, which are focused on (1) reducing or eliminating the presence of the pathogen from entering the production environment and (2) preventing the transfer of the pathogen to food. Controlling for cross-contact requires full knowledge of all materials especially where allergens or IP contaminants may be hidden in derivative ingredients or processing aids. Summarized below are some key controls in preventing cross-contamination and cross-contact across supply chain operations.

Typical controls applied to prevent cross-contamination and cross-contact include supplier approval and monitoring programs to ensure the safety and/or integrity of materials purchased. To prevent cross-contamination, they also include zoning to demarcate and segregate low-risk and high-risk production areas. Zones should be controlled to prevent personnel or equipment from low-risk areas from entering high-risk areas along with stricter hygiene controls in areas where high-risk product is handled (e.g., cooked product). To prevent cross-contact, controls are largely focused on distinctive identification and segregation. Designated traffic routes for personnel, forklifts, materials, product, and waste should also be implemented to reduce the potential for cross-contamination and cross-contact, as appropriate.

Sanitation controls are critical in preventing both cross-contamination and cross-contact. Validated sanitation procedures, which demonstrate effectiveness in removing pathogens and food residues, including allergenic proteins, are the first step in developing sanitation controls. Frequent sanitation must be applied to prevent material or product build-up; this prevents the transfer of food residues to finished product and eliminates food sources enabling pathogens and pests to proliferate. Sanitation practices must be routinely monitored, verified and recorded to ensure effective implementation.

Additional cross-contamination controls may include water disinfection in tank, flume, and chilling processes to ensure the microbiological quality of water. The goal of water disinfection in these processes is to prevent the water from becoming an inoculation source; thus, it is important to maintain a residual level of the sanitizer. Water disinfection should consider temperature, water pH, sanitizer concentration, organic load, and monitoring parameters/ limits.

Lastly, training employees, contractors, and visitors to be aware of and understand their role in preventing cross-contamination and cross-contact is a fundamental component for ensuring the effectiveness of all other controls. Training programs should emphasize how to follow site procedures for hygiene and allergen management as well as how to implement site controls for preventing cross-contamination and cross-contact for which employees have responsibility.


1 U.S. Food and Drug Administration (FDA). 2017. Enforcement Reports.

2 Rousseau, O. 2017. Cross-contamination a cause of huge US meat recall. Global Meat News.

3 U.S. Food and Drug Administration (FDA). 2016. FDA Investigated Listeria Outbreak Linked to Frozen Vegetables.

4 Centers for Disease Control and Prevention (CDC). 2016. Multistate Outbreak of Listeriosis Linked to Frozen Vegetables (Final Update).

5 U.S. Food and Drug Administration (FDA). 2016. Establishment Inspection Report: CRF Frozen Foods, LLC.

6 World Health Organization (WHO). 2006. Five Keys to Safer Food Manual.

7 U.S. Department of Agriculture. 2013. Be Smart. Keep Foods Apart. Don't Cross-Contaminate. Fact Sheet.

8 U.S. Food and Drug Administration (FDA). 2013. Frequently Asked Questions and Answers--Proposed Rule: Current Good Manufacturing Practice and Hazard Analysis and Risk-Based Preventive Controls for Human Food.

9 U.S. Food and Drug Administration (FDA), Center for Food Safety and Applied Nutrition (CFSAN). 2006. Guidance for Industry: Questions and Answers Regarding Food Allergens, including the Food Allergen Labeling and Consumer Protection Act of 2004 (Edition 4); Final Guidance.

10 U.S. Food and Drug Administration (FDA). 2015. 21 C.F.R § 117: Current Good Manufacturing Practice, Hazard Analysis, and Risk-Based Preventive Controls for Human Food.



11 U.S. Food and Drug Administration (FDA). 2015. 21 C.F.R § 507: Current Good Manufacturing Practice, Hazard Analysis, and Risk-Based Preventive Controls for Food for Animals.

12 U.S. Food and Drug Administration (FDA). 2016. 21 C.F.R § 1 subpart O: Sanitary Transportation of Human and Animal Food.

13 U.S. Food and Drug Administration (FDA). 2015. 21 C.F.R § 112: Standards for the Growing, Harvesting, Packing, and Holding of Produce for Human Consumption.

14 The Consumer Goods Forum. 2017. The GFSI Benchmarking Requirements version 7.0.

15 Carrasco, E., A. Morales-Rueda, R.M. García-Gimeno. 2012. Cross-contamination and recontamination by Salmonella in foods: A review. Food Research International. 45: 545–556.

16 U.S. Food and Drug Administration (FDA). 2013. Environmental Assessment: Factors Potentially Contributing to the Contamination of Fresh Whole Cantaloupe Implicated in a Multi-State Outbreak of Salmonellosis.

17 Tomas-Callejas, A., G. Lopez-Velasco, A.M. Valdez, A. Sbodio, F. Artes-Hernandez, M.D. Danyluk, T.V. Suslow. 2012. Evaluation of Current Operating Standards for Chlorine Dioxide in Disinfection of Dump Tank and Flume for Fresh Tomatoes. Journal of Food Protection. 75(2):304–313.

18 Almond Board of California. 2010. Preventing Salmonella Recontamination: Pathogen Environmental Monitoring Program Guidance Document.

19 FoodDrinkEurope. 2013. Guidance on Food Allergen Management for Food Manufacturers.

20 U.S. Food and Drug Administration (FDA). 2010. Guidance for Industry: Sanitary Transportation of Food.

About the Authors

Lori Carlson provides independent technical writing, training and consultation services to the food and beverage industry. She has over a decade of experience in verification and validation, risk assessment, food safety and quality management systems, GFSI benchmarked schemes, regulatory compliance, and third party certification. Lori has authored numerous white papers, magazine articles and guidance documents and has contributed to the development of various food safety standards and food professional training courses for GFSI scheme owners and certification bodies. Contact the author through LinkedIn.

Ralf Thomsen joined TUV USA, Inc. as Managing Director in 2015. He previously served as Managing Director of TUV UK Ltd and was responsible for overseeing the merger and acquisition activities of TUV NORD Systems GmbH & CO.KG.

Ralf has an MBA with a focus on international management and market development. He is a Chartered Engineer (CEng) registered in the UK and has a wealth of experience in various leadership roles, which oversee services in technical surveillance, health and safety, training, and product certification. Ralf's LinkedIn Profile.

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