Allergen Risk Assessment: When to Use Which Test Kits

By Alex Kostin- Applications Scientist

For Quality and Food Safety Managers, one of the biggest ongoing challenges is managing risk such as cross-contact or carryover allergens that aren’t declared on the labels. Undeclared food allergen recalls are among the most frequent, and most damaging recall drivers in the food industry.

According to a joint study by the Grocery Manufacturers Association (GMA) and the Food Marketing Institute (FMI), the average cost of a food recall can reach $10 million. Allergen-related recalls may require removing thousands, or even millions, of products from shelves, retracing distribution routes, notifying customers and retailers, and reassessing sanitation procedures. In many cases, the root cause is insufficient cleaning, failure to detect residual allergen proteins, or inadequate environmental controls.

For these reasons, allergen testing may be a core pillar in a food manufacturing facility’s control strategy. The question is not “which test is best”, but when to use a broad protein screening test versus a targeted allergen assay and how allergen risk assessment guides that discussion.

What is an Allergen Risk Assessment?

An allergen risk assessment is a structured, data-driven evaluation of where allergen cross-contact could occur in your operation, how severe the risk is, and what controls (cleaning, segregation, testing) are needed to minimize that risk. Think of it as a HACCP-style hazard assessment that focuses on allergenic proteins and cross-contact rather than microbial pathogens.

Allergen risks typically include the following:

1. Ingredient risks: Identify which incoming materials contain or may contain allergens, review supplier Certificate of Analyses (CoAs), and assess potential cross contact during transport or storage.
2. Process flow risk: Map product changeovers, shared lines, rework loops, and airflow patterns to determine where allergens could transfer between runs.
3. Environmental and facility risk: Evaluate surfaces, drains, utensils, and employee traffic for opportunities of allergen residue buildup or spread.
4. Control and mitigation: Establish and validate cleaning, segregation, and scheduling controls to minimize allergen carryover.
5. Testing and verification: Define where and how often to perform environmental, ingredient, and product testing using specific or non-specific methods depending on risk level.
6. Action thresholds: Where possible, use quantitative reference doses or action levels (such as VITAL 4.0) to determine what constitutes acceptable residual allergen risk.

For quality managers, allergen control is not just an operational challenge; it is a business and regulatory priority. Conducting an allergen risk assessment helps ensure that testing and cleaning resources are deployed where they deliver the most value. Instead of testing everywhere, quality teams can focus on high-risk lines, raw materials, and changeovers. This saves time and reduces unnecessary testing costs while maintaining compliance.

In addition, undeclared allergen recalls not only disrupt production but can erode customer trust. A documented allergen risk assessment demonstrates due diligence and strengthens defensibility during audits and consumer complaints.

Check out our Handbook for Best Practices for Food Allergen Validation & Verification to better support your Allergen Control Plan.

Non-Specific (Screening) Tests

Non-specific allergen tests, also known as protein screening assays, detect total protein residues without identifying which specific allergen it came from. They are designed for speed, simplicity, and a lower cost for monitoring general residue levels for cleaning performance.

Common non-specific allergen tests are chromogenic swabs, such as Neogen’s Clean-Trace® ALLTEC60.

Since chromogenic swabs detect all proteins, not just allergens, these swabs serve as general cleaning verification tools.

When and Where to Use

Non-specific protein swabs are frequently used in post-cleaning verification. Following a sanitation procedure, a QA technician or line operator can swab critical zones (food contact surfaces, conveyor belts, nozzles) to confirm protein residues have been removed before the next production run.

Because they are fast, inexpensive, and easier to use (requiring no lab or specialized equipment), non-specific swabs are great for real-time hygiene verification.

However, it’s important to note that a positive protein swab result does not identify what protein is present or even confirm that an allergen is present. These tests provide general screening information but cannot be used as confirmatory data.

Specific or Individual Allergen Tests

A specific allergen test targets a particular allergenic protein from a defined allergen. These tests can be quantitative (measuring how much is present) or qualitative (confirming present) in a sample, such as an ingredient, surface swab, finished product or finished product.

Here are the common specific allergen tests:

Lateral Flow Devices: These are single-use test strips that use antibodies to bind the allergen and produce visible lines if the allergen is present above a certain level. They are fast (typically 5 – 15 minutes), generally qualitative tests that are useful for screening in production environments.

ELISA (Enzyme-Linked Immunosorbent Assay): These are standard laboratory immunoassays where the allergenic protein binds to an antibody, then a conjugated enzyme produces a signal. These are quantitative (or semi-quantitative), and sensitive but require lab equipment, controls, and trained personnel.

PCR (Polymerase Chain Reaction): PCR detects DNA sequences specific to the allergenic source organism (i.e. Peanut DNA). Useful in processed foods where proteins can be denatured. It can be highly specific and sensitive, but DNA presence does not always equate to allergenic protein presence.

When and Where to Use

When following your risk assessment, specific allergen tests could be used in the following situations:

• Incoming ingredients/raw material verification: Confirming supplier CoAs and verifying there hasn’t been cross-contact.
• Finished product: Especially with products with allergen-free claims or “free-from” labeling, specific tests should be used to confirm that no target allergen is present.
• Root cause investigation: If a non-specific test flags something suspect then an allergen specific test might be used in the same zone or product to detect exactly which allergen is implicated.
• Validation and verification studies: Validating a cleaning procedure (i.e. validating that a line cleaned after a peanut run meets criteria for non-detectable amount of peanut standard for the facility).
• Customer/regulatory demands: If a customer or regulatory body requires specific allergen confirmation.
  
  

Why Not Rely Only on Non-Specific Testing? Go Hybrid!

Food manufacturers may think that using a non-specific test is sufficient, but they do have their limitations:

• Sensitivity: The limit of detection may not be low enough for the allergen reference dose threshold or may not catch trace amounts of allergen that are still relevant.
• Lack of specificity: A positive protein result could come from non-allergenic proteins (i.e. non-target residue, non-food proteins).
• False negatives in denatured matrices: In heavily processed products, allergenic proteins can denature (break down or unfold) and lose immunoactivity detectable by general protein tests.
• Customer/regulatory expectations: Some customers or food safety audits expect to have specific allergen tests done and documented for verification.

In practice, allergen control within a risk assessment uses a tiered testing strategy. Non-specific testing can be used to verify cleaning efficacy in high-risk zones (zones 1 and 2) or after critical changeover. Specific allergen tests can be used to confirm the presence or absence of allergens at various stages of the process.

Conclusion

Allergen risk assessments are the foundation that enables wise allocation of testing resources in a food manufacturing facility. By mapping out where allergen cross-contact risk is the highest, you can decide where non-specific screening swabs will suffice, and where specific allergen assays are necessary.

A hybrid approach offers both efficiency and confidence in helping to prevent undeclared allergen recalls. Understanding the strengths and limitations of each test method may dramatically reduce the likelihood of an undeclared allergen recall.

Learn more about Neogen Allergen Testing Solutions or fill out the form below to connect with our team to see which test is right for you!