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

The FDA doesn't wait for sick people to pile up before acting. When an outbreak of E. coli hits a dozen states, investigators don't start calling every farm or processor. They pick up a phone, ask for one thing: the lot number. That simple string of letters and numbers is the key to finding the source of contamination in minutes, not weeks.

What the FDA Actually Needs to Trace a Problem

Before 2026, tracing contaminated food was like following a trail of breadcrumbs in the dark. Each company kept its own records. A shipment of romaine lettuce might have one lot code from the farm, another from the packer, and a third from the distributor. If someone got sick, it could take weeks to piece together where the lettuce came from-and by then, more people were already sick.

The FDA changed that with the Food Traceability Rule, part of the Food Safety Modernization Act (FSMA) Section 204. This rule, finalized in November 2022, says: if you handle certain high-risk foods, you must assign a unique Traceability Lot Code (TLC), a descriptor-often alphanumeric-that uniquely identifies a batch throughout the entire supply chain. It’s not just any internal code. It’s the one that stays with the product from farm to store.

Which Foods Are Covered?

Not every food needs this. The FDA drew a line. They picked the ones most likely to cause outbreaks. That’s the Food Traceability List (FTL), a list of 16 high-risk foods that must carry a TLC. This includes:

• Leafy greens (like romaine, spinach)
• Tomatoes
• Onions
• Fresh-cut fruits and vegetables
• Soft cheeses (like brie, feta)
• Eggs
• Nut butters
• Specific seafood (like shrimp, tuna, and oysters)

These foods make up about 15% of the U.S. food supply by volume. But they cause nearly half of all foodborne illness outbreaks. The FDA didn’t go after everything-just the worst offenders.

When and How Is the Lot Code Assigned?

You can’t just slap a code on anytime you want. The rule says TLCs must be assigned at three specific points:

1. When raw agricultural commodities (like lettuce or tomatoes) are first packed (except seafood from fishing vessels)
2. When seafood from fishing vessels is first received on land
3. When food is transformed-meaning it’s chopped, mixed, cooked, or repackaged

Once assigned, the TLC must stay the same. If a company chops up a batch of onions and turns them into a salad mix, they can’t keep the old code. They must create a new TLC-but they must also link it back to the original. It’s like a family tree for food. Every change creates a new branch, but the root stays visible.

The Seven Key Data Elements That Tie It All Together

The TLC alone isn’t enough. The FDA needs context. For every TLC, companies must record and share seven Key Data Elements (KDEs), critical pieces of information that link the lot to its history:

• The TLC itself
• The TLC Source (where and when it was assigned)
• Product description
• Quantity
• Unit of measure (pounds, cases, pallets)
• Transaction information (who sent it, who received it)
• Location of each transfer (physical address)

If the FDA asks for this data during an outbreak, you have 24 hours to deliver it. No excuses. The records must be sortable and exportable-CSV, Excel, or similar formats. Paper logs? They’re still allowed, but they slow things down. Electronic records are the only way to meet the 24-hour window.

How Is This Different from Old Lot Codes?

Before this rule, companies used lot codes for internal quality checks. A dairy might label a batch of cheese as "CHEESE-021526" for shelf-life tracking. That’s fine for them-but useless for the FDA if the code doesn’t match up with the farm, the truck, or the distributor.

The TLC system is different. It’s not about internal control. It’s about end-to-end traceability. The code must be passed along exactly as assigned. No renumbering. No dropping the trail. And crucially, the FDA made it clear: your existing internal code can be your TLC-if it meets the requirements. You don’t need two codes. One good one is enough.

What Happens When an Outbreak Happens?

Imagine this: 12 people in three states get sick from E. coli after eating pre-packaged salad. The CDC spots the pattern. The FDA gets the alert. Within hours, they call the retailer: "What lot numbers did you get from your supplier?" The retailer pulls their records, finds the TLC, and passes it to the distributor. The distributor checks their logs and says: "We got that from GreenLeaf Farms, lot #GL-2026-047." The FDA calls GreenLeaf. They check their records: "That batch was harvested on January 12 from Field 3B, packed on January 14." Within 48 hours, they’ve isolated the source. The product is pulled. The outbreak stops.

Before this system? That process could take 40 days. Now? It’s under 5.

Who’s Affected? And What’s the Cost?

About 15,000 food facilities in the U.S. are impacted-mostly farms, processors, packers, and distributors handling FTL foods. The FDA estimates the annual cost to the industry will be $6.5 million. But the benefit? Up to $60 million a year from fewer illnesses, fewer recalls, and faster responses.

Small businesses got some relief. The FDA created the Traceability Assistance Program, a free resource offering templates, training, and technical help to small farms and processors. Many small companies are using simple spreadsheets. Larger ones are upgrading their ERP systems. A 2023 survey found 78% of produce companies had already updated their systems.

Challenges and Criticisms

Not everyone’s happy. Some say the FTL is too narrow. Melons, for example, have caused major outbreaks-but they’re not on the list. Consumers Union pointed out that this leaves a dangerous gap.

Others worry about "tandem coding"-having to run both a TLC and an internal code. But the FDA clarified: if your internal code meets the rules, it counts as the TLC. No need for double work.

The real issue? Interoperability. If one company uses a barcode, another uses a QR code, and a third uses a manual log, the system breaks. The FDA is working on standard formats for data exchange, with draft rules expected in 2024.

What’s Next?

The compliance date was originally January 20, 2026. But after industry pushback, the FDA proposed a 30-month extension-pushing it to July 20, 2028. That gives companies more time to adapt.

Looking ahead, the FDA is exploring blockchain and IoT sensors to track temperature and handling conditions in real time. They’re also considering adding melons, deli meats, and ready-to-eat foods to the FTL.

The bottom line? Lot number tracking isn’t about bureaucracy. It’s about speed. When people get sick, time is the enemy. The TLC system gives the FDA the tool they need to act fast-and that saves lives.