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

When a batch of spinach causes a nationwide outbreak of E. coli, how does the FDA find the exact source in time to stop more people from getting sick? The answer isn’t guesswork or old-school phone calls-it’s the Lot Number Tracking system under the FDA’s Food Traceability Rule. This isn’t just paperwork. It’s a real-time lifeline in food safety.

Why Lot Numbers Matter More Than Ever

Before 2022, tracing contaminated food often meant chasing paper trails across dozens of companies. Investigators had to call farms, packers, distributors, and retailers-sometimes for weeks-just to find where a bad batch came from. By then, hundreds could be sick, and the product was already gone from shelves.

The FDA changed that with the Food Traceability Rule, part of the Food Safety Modernization Act (FSMA). The rule targets high-risk foods that cause the most outbreaks: leafy greens, tomatoes, onions, fresh-cut fruits and veggies, nut butters, soft cheeses, eggs, and certain seafood. These make up about 15% of the U.S. food supply but cause nearly half of all foodborne illnesses.

At the heart of this system is the Traceability Lot Code (TLC). It’s not just any lot number. It’s a unique, trackable identifier assigned at three specific points: when raw agricultural commodities are first packed (like when lettuce is boxed at the farm), when seafood is first received on land, and when food is transformed (like when tomatoes are turned into salsa). Once assigned, that TLC travels with the product through every step of the supply chain.

How the TLC System Works

The TLC is the glue that connects everything. Each code links to seven Key Data Elements (KDEs): where it was assigned, what the product is, how much there is, the unit of measure, and transaction details like who sent it and when. These aren’t optional. If the FDA asks for them during an outbreak, companies must deliver them electronically within 24 hours.

Companies can use any format for their TLC-alphanumeric, Julian date + product code, or even a random string-as long as it’s unique and stays with the product. The FDA doesn’t mandate a specific system. That flexibility lets big players like Tyson Foods use their existing codes, and small farms use simple handwritten labels.

But here’s the catch: the TLC must be passed along unchanged unless the food is transformed. If a distributor repacks 100 boxes of spinach into 20 larger crates, they can’t just slap on a new code. They must keep the original TLC and link it to the new packaging. That’s how the FDA traces a single contaminated head of lettuce back to the field where it was grown-even if it passed through five different handlers.

What Happens During an Outbreak

Imagine a cluster of illnesses in Ohio, Texas, and California. The CDC spots the pattern and alerts the FDA. Instead of calling every supplier, FDA investigators pull up digital records linked to the TLC. They see that all affected products came from the same lot code: L20260115-SPN. They trace it backward: who shipped it? Who packed it? Who grew it?

Within hours, they isolate the source: a single farm in Salinas, California. That farm’s entire harvest from that day is pulled from stores. Other lots are flagged for testing. The outbreak is contained before it spreads further.

This is what the FDA says is possible: cutting outbreak response time from weeks to under 24 hours. Pilot programs showed a 20-30% drop in illness cases when traceability was fast and accurate. That’s not theoretical. It’s lives saved.

Who Has to Comply-and When

The rule applies to anyone who manufactures, processes, packs, or holds food on the Food Traceability List (FTL). That’s about 15,000 facilities across the U.S. Compliance was originally set for January 20, 2026, but in September 2023, the FDA proposed pushing that date to July 20, 2028. Why? Because many small businesses weren’t ready.

A 2023 survey found only 42% of small and medium food businesses even knew about the TLC requirements. Many are still using paper logs or outdated software. The FDA has responded with training modules, a Traceability Assistance Program, and $25 million in funding from the 2023 Farm Bill to help small farms and processors get up to speed.

Large companies like Walmart and Kroger were already ahead of the curve. Walmart started requiring blockchain-based traceability for leafy greens back in 2019. They’re not just meeting the rule-they’re exceeding it. But for smaller players, the challenge is real. Integrating TLCs into legacy ERP systems, training staff, and syncing with suppliers all take time and money. The average cost per company is around $42,500.

Challenges and Criticisms

Not everyone is thrilled. Critics say the Food Traceability List is too narrow. Melons, for example, have caused major outbreaks but aren’t included. Consumers Union called it a dangerous gap. Others worry about “tandem coding”-having to maintain both internal lot codes and TLCs. The FDA addressed this by saying: if your current lot code meets the rules, it can be your TLC. No need for two systems.

Another issue? Data silos. Even if every company has a TLC, if they don’t share data in the same format, it’s useless. Mike Taylor, former FDA deputy commissioner, called the system “necessary but insufficient” without standardized electronic formats. The FDA is working on that now, with draft standards expected in mid-2024.

And then there’s the global gap. The EU launched its Digital Product Passport in January 2023-different rules, different tech. The FDA is holding talks with international regulators to align standards. Otherwise, U.S. exporters could face barriers abroad.

What’s Next for Lot Tracking

The future of food traceability isn’t just about codes-it’s about technology. The FDA is funding pilots using blockchain, IoT sensors, and AI to automatically log temperature, location, and handling data alongside TLCs. Imagine a truck carrying spinach that logs its temperature in real time. If a batch turns contaminated, you don’t just know where it came from-you know exactly when it was exposed to unsafe conditions.

The U.S. food traceability market is expected to grow from $1.87 billion in 2022 to $4.62 billion by 2028. That’s not just tech companies making money-it’s safer food for everyone.

The bottom line? Lot number tracking isn’t about bureaucracy. It’s about stopping sickness before it spreads. The TLC system gives the FDA the tools to act fast, protect public health, and hold the right people accountable. It’s not perfect yet. But it’s the most powerful food safety tool the U.S. has ever had.