Allergens are a crucial part of a comprehensive food safety program and essential to your customer's safety and your regulatory compliance. The same applies to genetically modified organisms (GMOs). Consumers want to know about the presence of GMOs in your products, and labeling laws require you to know, too. How you handle both issues is an important part of your food safety program. 

Welcome to Part 1 of a two-part series on the state of the allergen and GMO control and testing programs being used by food processors. Part 1 focuses on what we heard from you about your allergen programs.

Our latest Food Safety Insights survey shows that allergen control programs are now nearly universal among respondents. These programs have a number of elements that will be familiar to a food safety professional, but analytical testing—an area we often cover here in Food Safety Insights—may be less common in many facilities than might be expected. 

We received responses from a wide range of food safety, quality, and technical professionals. About 27 percent identified as having a quality assurance/quality control (QA/QC) role, 29 percent as food safety specialists/food technologists, and nearly 10 percent as laboratory managers, microbiologists, or chemists, with the rest in regulatory, general management, and other technical roles (Figure 1).

Respondents represented a diverse set of product categories: prepared/processed foods and RTE meals (18 percent), ingredients/spices/flavors (12 percent), baked goods (10 percent), dairy and meat/poultry (about 8 percent each), and smaller shares from beverages, grains, pet foods, snack foods, and fresh-cut produce, with several "other" categories including food packaging and cleaning chemicals (Figure 2).

Geographically, roughly two-thirds of respondents were from the U.S., with other responses from Canada, Europe, Asia, and other regions.

This profile gives us a cross-section of operations that are directly handling allergens, supporting allergen-containing supply chains, or managing allergen risks as part of broader food safety programs.

Allergen Control Programs are Nearly Universal

As expected, most of the companies surveyed (96 percent) reported that they have an allergen control program in place. Their descriptions of the complexity of their programs ranged from very mature programs with multiple recognizable elements (e.g., color-coding, validated cleaning protocols, analytical testing) to minimal operations where allergens are not expected to be handled in their facility, but written procedures and training are in place anyway. A few respondents noted that financial constraints limit their ability to have a more robust program, even though they recognize the need to strengthen controls.

What is Working—And What is Not

Anticipating that there would be a range of programs and strategies employed, we also wanted to hear what survey respondents thought were the most effective elements of their programs. The most frequently mentioned elements were:

• Segregation and dedicated storage/production lines
• Production scheduling
• Cleaning and sanitation, often with verification using protein swabs, ATP, or allergen-specific tests
• Label review and approval processes and clear allergen identification on labels and visual boards
• Training and communication programs.

With the same expectations in mind that no program is perfect, and many elements of strict allergen control can be challenging, we also asked what respondents considered to be the least effective or most difficult elements of their programs. The issues most frequently mentioned were not surprising, but rather common issues that are important to understand and constitute critical areas of failure of many programs:

• People: Employee habits, including outside lunches, vending, and other food brought into the plant; turnover and inconsistent levels of training; and staff who are not engaged (or as one person mentioned, "do not seem to be interested in allergen management")
• Scheduling and changeovers: Complex changeover procedures for cleaning, validating low thresholds on multiple lines, and the readiness of proper cleaning equipment for changeover to non-allergen production
• Supply chain data: Constituents of compound ingredients; long, difficult-to-trace supply chains (especially for herbs, spices, and grains) that make getting complete allergen information from suppliers difficult; and managing allergen label inventory
• Physical environment: Control of dust and airborne contamination, shared farm and storage equipment, shared surfaces, and constraints on segregated storage space
• Cost and complexity: Costs associated with validation, complexity due to multiple allergens and proprietary blends, and limited resources for testing.

“Despite the near-universal presence of allergen control programs, only about 61 percent of respondents reported that they conduct analytical testing for allergens.”

Allergens of Greatest Concern

Respondents reported a wide range of allergens of concern, with most aligned with their particular processing categories, but several patterns stood out in our survey. When asked about "top allergens of concern," respondents most frequently cited:

• Milk, gluten/wheat, soy, and tree nuts
• Peanuts and sesame (often in combination with tree nuts and other allergens)
• Egg, fish, shellfish, and sulfites.

In a follow-up question on "other allergens of concern," about half of respondents selected wheat/gluten, and roughly one-third selected eggs, milk, soybeans, and tree nuts. Sesame, peanuts, and sulfites were mentioned by roughly 30 percent, with smaller shares for celery, mustard, fish/shellfish, lupin, and other ingredients such as rye or particular fruits. Several respondents noted that they must be prepared to manage "all U.S. Food and Drug Administration (FDA) allergens except fish and shellfish," or "all 13 [allergens] except lupin," reflecting operations that are serving export markets or needing to comply with broader international allergen lists other than the U.S. "Big 9."

Limited Analytical Testing

Despite the near-universal presence of allergen control programs, only about 61 percent of respondents reported that they conduct analytical testing for allergens. Nearly 39 percent said they do not conduct allergen testing, mainly because they do not handle allergens in their facility, rely on certificates of authenticity from suppliers, or have limited resources and a low perceived risk.

Among those who indicated that they do conduct analytical testing:

• Many use allergen testing primarily for changeover verification or program validation (e.g., quarterly gluten-free verification or post-cleaning allergen swabs)
• Several respondents mentioned using allergen-specific kit tests with specific detection limits (e.g., 20 µg) for particular allergens
• Many emphasized ATP or total protein tests as their primary verification tools, with allergen-specific testing used more selectively.

The volume of testing varied widely from those mentioning little/no testing or infrequent/periodic test collection, to operations reporting up to 60 allergen tests per week. In many facilities, allergen testing also appears to be event-driven: tests are conducted when changing products or formulations, initiating production on allergen-containing lines, or when production or customer requirements trigger testing.

In-Plant Testing

For companies that reported conducting in-plant testing, we asked which types of tests they use to support their environmental monitoring and sanitation programs. Their responses were:

• About 48 percent reported using protein residue swabs
• 27 percent use allergen-specific lateral flow immunoassay (LFA) test strips
• 27 percent use ATP tests
• Around 21 percent send samples to outside labs for sanitation-related assessments
• Only a small share reported using ELISA or PCR/qPCR for their in-plant tests.

How Facilities Test Products

For end-product samples, the story is different as respondents more commonly rely on outside laboratories. When asked how they test end-product samples for allergens, respondents said:

• Greater than 50 percent send samples to outside labs
• Approximately 26 percent use allergen-specific LFA test strips
• Around 11 percent use allergen-specific ELISA immunoassay tests
• A small number send samples to an in-house lab
• 13 percent said they do not conduct finished product testing.

Our survey results spell out what many people might expect to see: the use of a wide range of strategies tailored to processing category and allergen risk assessment. Companies also employ a broad range of technologies, with an emphasis on practical, onsite tools. For many facilities, the practical strategy of choice is to use rapid, easily deployed indicators (e.g., ATP and protein swabs) to monitor cleaning on an as-needed or daily basis, and to layer allergen-specific tests and outside lab support where risk, regulatory requirements, or customer expectations justify the added cost and complexity.

Look for Part 2 of this series in the October/November features compilation, where we will discuss the impact on the size and growth of the global allergen testing market. We will also look at how companies are managing GMOs in their products and the core elements of those programs.

References

1. Ferguson, B. "How the Food Traceability Rule will Impact Food Processors—Part 1." Food Safety Magazine February/March 2023. https://digitaledition.food-safety.com/february-march-2023/column-food-safety-insights/. 
2. Ferguson, B. "How the Food Traceability Rule will Impact Food Processors—Part 2." Food Safety Magazine April/May 2023. https://digitaledition.food-safety.com/april-may-2023/column-food-safety-insights/.
3. Ferguson, B. "What Food Safety KPIs Say About Food Safety Culture—Part 1." Food Safety Magazine December 2025/January 2026. https://digitaledition.food-safety.com/december-2025-january-2026/column-food-safety-insights/. 
4. Ferguson, B. "What Food Safety KPIs Say About Food Safety Culture—Part 2." Food Safety Magazine February/March 2026. https://digitaledition.food-safety.com/february-march-2026/column-food-safety-insights/. 
5. Ferguson, B. "Food Safety Priorities—Getting 'Back to Basics.'" Food Safety Magazine October/November 2023. https://digitaledition.food-safety.com/october-november-2023/column-food-safety-insights/.
6. Ferguson, B. "Hygienic Design: How are Processors Coping With This Essential Element of Food Safety?" Food Safety Magazine April/May 2025. https://digitaledition.food-safety.com/april-may-2025/column-food-safety-insights/. 
7. Ferguson, B. "Hygienic Design: How are Processors Coping With This Essential Element of Food Safety?—Part 2." Food Safety Magazine June/July 2025. https://digitaledition.food-safety.com/june-july-2025/column-food-safety-insights/. 
8. Ferguson, B. "Regulatory Changes Impacting Your Food Safety Program—What Should FDA's Priorities Be?" Food Safety Magazine December 2024/January 2025. https://digitaledition.food-safety.com/december-2024-january-2025/column-food-safety-insights/. 
9. Ferguson, B. "Regulatory Changes Impacting Your Food Safety Program, Part 2—What Should USDA's Priorities Be?" Food Safety Magazine February/March 2025. https://digitaledition.food-safety.com/february-march-2025/column-food-safety-insights/.

Notes

^a For chicken, the serotypes are Salmonella Enteritidis, S. Typhimurium and S. 4,[5],12:i.

^b For turkey, the serotypes are Salmonella Hadar, S. Typhimurium, and S. Muenchen.

^c These were the terms of the proposal at the time of our survey and the writing of this article. The comment period for the proposal was scheduled to end on January 17, 2025, and changes to these terms and the proposed regulation may be in process.

^d In the survey, we specifically asked the question, "If you could ask any question or make a request to USDA Deputy Under Secretary for Food Safety Sandra Eskin, what would that be?" Since the time of our survey, Sandra Eskin has left her position at USDA and, as of this writing, a successor has not yet been named.