Lot Number Tracking: How the FDA Identifies Problem Batches in the Food Supply

The FDA doesn’t guess when a foodborne illness outbreak happens. It doesn’t wait weeks to track down contaminated food. Instead, it uses a single, powerful tool: the traceability lot code. This isn’t just a label on a box. It’s the key that unlocks the entire supply chain - from farm to store - and lets regulators find the exact source of contamination in hours, not days.

Why Lot Numbers Matter More Than Ever

Before 2022, tracing a contaminated bag of spinach or a batch of contaminated cheese could take weeks. Investigators had to call dozens of suppliers, sift through paper records, and piece together shipments like a puzzle with missing pieces. That delay meant more people got sick. In 2018, an E. coli outbreak linked to romaine lettuce took nearly three months to trace. Over 200 people were infected. Five died.

The FDA’s Food Traceability Rule, finalized in November 2022, changed all that. It didn’t just improve tracking - it forced the entire food industry to rethink how they label and track products. The rule applies to foods on the Food Traceability List (FTL), which includes high-risk items like leafy greens, tomatoes, onions, fresh-cut fruits and vegetables, nut butters, cheeses, and certain seafood. These foods make up about 15% of the U.S. food supply, but they’re responsible for a disproportionate share of outbreaks.

What Is a Traceability Lot Code (TLC)?

A traceability lot code (TLC) is an alphanumeric identifier assigned to a specific group of food products at key points in the supply chain. It’s not your company’s internal lot number - unless it meets the FDA’s rules. The TLC must be unique across the entire system, not just within one company. That means if a farm assigns TLC #2024-05-12-LG001 to a pallet of lettuce, that same code must be passed along unchanged when it’s shipped to a distributor, then to a retailer. No renumbering. No confusion.

The TLC is the anchor point. Every time the food changes hands - whether it’s packed, received, or transformed - the TLC stays with it. And it’s linked to seven other critical pieces of information, called Key Data Elements (KDEs): where the code was assigned, what the product is, how much there is, the unit of measure, who received it, when it was received, and the transaction details. Without all seven, the trace is broken.

When and Where the Code Is Assigned

The FDA doesn’t let companies assign TLCs whenever they want. There are only three legal points in the supply chain where a TLC can be created:

• When raw agricultural commodities (like lettuce or tomatoes) are first packed - unless they come from a fishing vessel
• When seafood from a fishing vessel is first received on land
• When food is transformed - like when tomatoes are turned into salsa, or spinach is washed and packaged as a salad mix

This is a big shift. Before, companies might have assigned lot codes at every step - for quality control, inventory, or internal audits. Now, the FDA says: assign it once, at the right moment, and carry it forward. If you transform the product - say, you grind almonds into butter - you must create a new TLC. But you must also keep the link to the original lot code so the FDA can trace back through every stage.

How the FDA Uses the Code During an Outbreak

Imagine a cluster of Salmonella cases pops up in Ohio, Illinois, and Texas. The CDC flags it as a possible foodborne outbreak. The FDA gets the alert. They start asking: What did all the patients eat? A common food is identified - say, pre-packaged spinach.

The FDA calls the retailer who sold the spinach and asks for the TLC on the affected packages. Within minutes, the retailer pulls up the electronic record. The TLC is #2025-11-15-LG-SPIN08. The FDA sends that code to the distributor. The distributor responds: “We received this from Farm X on November 12.” The FDA contacts Farm X. The farm’s records show: “We harvested this batch from Field 7 on November 10. We packed it on November 11.”

That’s it. In less than 24 hours - the legal deadline for responding to an FDA request - they’ve traced the contamination back to a single field. The FDA can issue a targeted recall. They can warn consumers who bought that specific batch. They can test soil samples from Field 7. And they can stop the outbreak before it spreads further.

What Happens If You Don’t Comply?

The rule isn’t optional. It’s enforceable. Companies handling FTL foods must keep electronic records of all KDEs linked to each TLC. These records must be sortable and exportable - in formats like CSV or XML - so the FDA can quickly pull data during an investigation. Paper records are allowed, but they’re slow. And slow means more people get sick.

If a company fails to provide records within 24 hours of an FDA request, the agency can take action. That could mean holding shipments, issuing warning letters, or even initiating a seizure of product. For small businesses, the cost of non-compliance isn’t just financial - it’s reputational. A single outbreak tied to poor traceability can destroy a brand.

Industry Challenges and Real-World Fixes

Not everyone was ready. A 2023 survey found that 71% of companies struggled to get their supply chain partners to use TLCs consistently. Some small farms didn’t have the software. Some distributors used different systems. Many companies ended up running two systems - their old internal lot codes and the new TLCs - just to be safe.

The FDA heard these concerns. In response, they clarified: your existing lot code can be your TLC - as long as it’s unique, passed along correctly, and linked to all seven KDEs. That’s a huge relief. Many companies simply updated their ERP systems to include the required fields. Others turned to traceability software like IBM Food Trust or SAP’s supply chain tools. A few small operators still use spreadsheets - but they’re being helped by the FDA’s Traceability Assistance Program, launched in January 2023.

The Bigger Picture: Technology and the Future

The TLC system is just the beginning. The FDA is already working on standardized electronic formats for KDEs, with a draft expected in mid-2024. They’re testing blockchain and IoT sensors to automatically log temperature, location, and handling conditions in real time. Walmart’s been using blockchain for leafy greens since 2019 - and now, the FDA’s rules are catching up.

But the biggest question is: will the list grow? Right now, melons, sprouts, and ready-to-eat meals aren’t on the FTL - even though they’ve been linked to outbreaks. FDA Commissioner Robert Califf has said these foods are under active review. If they’re added, the system’s impact will multiply.

What This Means for You

If you buy food - especially leafy greens, tomatoes, or fresh-cut produce - you’re benefiting from this system. It means fewer outbreaks. Fewer hospitalizations. Fewer deaths. It means when something goes wrong, the system doesn’t just react - it responds fast, precisely, and effectively.

For businesses, it’s a cost. For consumers, it’s safety. And for the FDA, it’s the most powerful tool they’ve had since the Bioterrorism Act of 2002. The traceability lot code isn’t just a label. It’s a lifeline.