Allergen Testing for Food Products: What the FASTER Act Changed and How US Brands Can Stay Ahead

January 1, 2023 was a quiet deadline for most consumers. For food manufacturers, it was anything but. That’s the date the FASTER Act took effect, officially making sesame the ninth major food allergen recognized under US federal law — and instantly creating a compliance gap for thousands of products already on shelves.

The law itself (H.R. 2477) passed in April 2021, which gave the industry roughly 20 months to reformulate, relabel, and rethink allergen controls. Some brands were ready. Others discovered the hard way that “we’ve never had a complaint” isn’t a compliance program. And FDA’s enforcement posture on undeclared allergens has only sharpened since.

If you manufacture, private-label, or co-pack food products in the US, your allergen testing program needs to hold up against real scrutiny. Here’s what changed, what the regulations actually require, and how a well-designed testing protocol fits into a defensible food safety plan.

The Big 9: Why Sesame Took Decades to Get Federal Recognition

The eight allergens you’re probably already familiar with — milk, eggs, fish, shellfish, tree nuts, peanuts, wheat, and soybeans — have been federally mandated label disclosures since the Food Allergen Labeling and Consumer Protection Act (FALCPA) passed in 2004. Those eight accounted for roughly 90% of serious allergic reactions in the United States at the time, which is precisely why they made the cut.

Sesame almost joined them back then. It didn’t, largely because the food industry successfully argued that the evidence wasn’t yet robust enough to justify the regulatory burden. By the early 2020s, that argument had lost its footing. Research and advocacy — particularly from FARE (Food Allergy Research and Education) and clinical allergy specialists — documented that approximately 1.6 million Americans are allergic to sesame, with reaction severity profiles comparable to peanut and tree nut allergy.

The FASTER Act changed two things simultaneously. First, it added sesame to the official major allergen list. Second, it directed FDA to evaluate the scientific evidence for additional allergens and report back within two years. That second provision matters more than most brands realize. The Big 9 may not stay at nine — and building allergen controls that are rigid rather than adaptable is going to create problems when the list grows again.

For practical purposes right now: sesame must be declared on any food label where it is intentionally used as an ingredient, and manufacturers must account for potential cross-contact wherever sesame and non-sesame products share production lines or equipment.

What FSMA Actually Requires for Allergen Control

Many food manufacturers operate under the assumption that allergen compliance is fundamentally a labeling exercise. It isn’t — or at least, it isn’t only that. Under FDA’s Preventive Controls for Human Food rule (21 CFR Part 117), allergen control is a mandatory component of a Hazard Analysis and Risk-Based Preventive Controls (HARPC) food safety plan.

Specifically, a facility’s hazard analysis must identify allergens as known or reasonably foreseeable chemical hazards. If your facility processes any of the Big 9 — in any ingredient, processing aid, or rework stream — documented allergen preventive controls are required. Four areas need to be addressed:

Label verification: Confirming that finished product labels accurately reflect what’s in the formulation, including any allergens that may be present due to shared production equipment. This sounds straightforward; it gets complicated fast when formulas change, suppliers swap ingredients, or temporary substitutions don’t make it through the change-control process.

Supplier verification: FSMA’s Supply Chain Program requires that manufacturers verify their ingredient suppliers have adequate allergen controls in place. A COA alone doesn’t satisfy this. At minimum, a supplier questionnaire and periodic verification testing on incoming raw materials are expected.

Cross-contact prevention: Your allergen preventive controls must specifically address the risk of allergen cross-contact during processing. Production scheduling (allergen-free runs first), dedicated or color-coded utensils, and clearly defined rework protocols all play a role here.

Cleaning validation: This is the piece most small manufacturers underinvest in — and the one FDA inspectors consistently flag. Cleaning procedures for equipment that contacts allergenic ingredients must be validated, meaning you need documented evidence that the procedure actually reduces allergen levels to below detectable thresholds. A cleaning log that says “line wiped down, ready for next run” is not validation.

Cleaning validation is where third-party allergen testing from a qualified food safety testing lab becomes essentially unavoidable. The standard approach: swab equipment surfaces before and after cleaning cycles, test those swabs with quantitative ELISA, and retain the data as part of your FSMA records.

ELISA vs. PCR: Picking the Right Method for Your Matrix

Two analytical methods dominate allergen testing in food: ELISA (enzyme-linked immunosorbent assay) and PCR (polymerase chain reaction). They detect different things, and understanding that distinction helps you use each one where it actually works.

ELISA detects allergen proteins. It’s quantitative, reporting results in parts per million (ppm), with typical detection limits of 1–5 ppm depending on the kit and the allergen target. Most FDA-recognized reference methods for allergen testing are ELISA-based, and it’s the standard for finished product testing and cleaning validation swabs. For the vast majority of food products and applications, ELISA is the right starting point.

The limitation is processing. High heat, extreme pH, and certain manufacturing processes can denature allergen proteins — physically changing their shape to the point where the antibodies in an ELISA kit no longer recognize them. In heavily processed matrices like baked goods, heat-treated protein isolates, or extruded snacks, ELISA can produce false negatives even when allergenic material is genuinely present.

PCR detects allergen-encoding DNA rather than protein, and because DNA is considerably more thermally stable than protein, it can find allergenic material in processed matrices that ELISA misses. The trade-off is that PCR is qualitative — or at best semi-quantitative — which makes it less useful for risk assessments that reference specific ppm thresholds for safety determinations.

In practice: use ELISA as your primary method and confirm with PCR in any matrix where protein integrity is questionable due to processing. For cleaning validation, ELISA lateral flow rapid-test strips are widely used for real-time in-process checks, with quantitative ELISA sent to an accredited lab for formal validation records.

One non-negotiable: the food safety testing lab you use for allergen testing should hold ISO 17025 accreditation for these specific methods. Accreditation isn’t just a credential — it means the lab has documented method validation, participates in proficiency testing programs, and produces results with characterized uncertainty. All of that matters significantly if an adverse finding triggers an FDA investigation or a dispute with a retail partner.

Building a Testing Program That Holds Up Under FDA Scrutiny

A functional allergen testing program isn’t a point-in-time event; it’s a set of ongoing activities at multiple stages of the supply chain.

Incoming raw material testing: Supplier COAs are a starting point, not a finish line. Independent verification on incoming lots is particularly important for botanical extracts, shared-facility ingredients, and imported materials where supply chain traceability is harder to confirm. A lot that tests clean on paper has failed incoming testing more times than the industry likes to admit.

In-process monitoring: For facilities that run both allergenic and non-allergenic products, in-process swabs at changeover points — tested with rapid ELISA strips — catch cross-contact events before they become a finished-product problem.

Finished product testing: Quantitative ELISA on finished product confirms that declared allergens are present at the labeled levels, and that undeclared allergens are absent or below actionable thresholds. This also serves as a final check on the entire upstream control system.

Revalidation after changes: FSMA is explicit that preventive controls must be validated and revalidated when changes occur that could affect their effectiveness. New formulas, new suppliers, modified equipment, and revised cleaning procedures all trigger revalidation requirements. The documentation for each change should be retained as part of the food safety plan.

And documentation is where the discipline breaks down for many brands. FDA inspectors examining FSMA compliance during facility inspections want to see records — validation study reports, test results by lot, corrective action logs when results are out of specification. A brand that tests but doesn’t retain records in an organized, retrievable format is nearly as exposed as one that doesn’t test at all.

Undeclared allergens consistently rank as the leading cause of FDA Class I food recalls — the designation FDA uses when there’s a reasonable probability of serious adverse health consequences. Most of those recalls aren’t from brands trying to cut corners. They’re from facilities that had gaps in their allergen controls they didn’t know about until it was too late. Structured testing, with accredited methods and complete documentation, is how you find those gaps before FDA does.

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Written by Nour Abochama, Vice President of Operations, Qalitex Laboratories. Learn more about our team

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