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Most foodborne illness clusters and outbreaks start with a sick person or people who go to their doctor to check out their symptoms. For example, someone with diarrhea, vomiting, cramps, fever or other G.I.  symptoms go to their doctor urgent care. The clinician examines the patient and might collect a stool sample, which they send to a lab.

If the lab finds a reportable foodborne germ in the specimen, the results are sent back to the doc but also (electronically) sent to the county/state health departments. An astute clinician might also alert call the county health department, especially if the illness is unusual or they’ve seen several patients w/ similar symptoms.

The next steps in finding whether the diagnosis is part of a cluster or outbreak happen at the county health department.

The County Investigation

A county health department epidemiologist then interviews the patient(s) – probably by phone. The epi asks the patient about symptoms, travel, restaurants, grocery purchases, social events and everything they might have eaten during the likely exposure period. Easier said than done.

Think about how difficult that is. What did you eat for lunch 11 days ago? Was there lettuce on your taco? Where did the restaurant buy it? Was the cilantro in the salsa fresh? Did you save the receipt? Where are all the other places you ate – including what you ate at home that you made yourself from groceries.

Investigators might also use restaurant records, shopper-card histories, receipts, food packaging and leftovers from the patient’s refrigerator.

If the evidence points toward a local restaurant, grocery store or food processor, environmental health sanitarians (also from the county) get involved. They can inspect the facility, interview employees, review food-handling and employee-illness records, collect samples and look for problems such as inadequate refrigeration, poor handwashing, cross-contamination or an ill food worker.

Sometimes they find a smoking gun. Often they don’t.

Connecting the Laboratory Results

Folks at the state and county health departments then look to see whether there are other reports of the same illness around the same time. If there is they’ll look at other county investigations to see whether there looks like there might be a common thread. One of the cluse they can use is to look at the genetics of the bacteria or parasite. The lab work is so good now they can often see whether it’s the same strain of the organism, which provides a good clue about whether the cases might be linked to the same food source.

Those results are uploaded into PulseNet, CDC’s national laboratory network.

When patients in several states have bacteria with nearly identical genetic fingerprints, investigators might figure out that illnesses which looked unrelated are actually part of the same outbreak – even among multiple states.

Cyclospora is among the more difficult outbreaks to identify. Routine stool tests don’t always include it. Detecting it in food is hard and investigators don’t yet have the same mature genetic-fingerprinting system used for many bacteria.

From One County to Several States

The state may set up a “case definition”—a standard set of laboratory, symptom and timing criteria used to decide which patients belong in the outbreak. They might alert clinicians and laboratories to watch for more cases (in AZ we call these HAN’s or Health Alert Network notices), review emergency-department records and ask neighboring states if they’re seeing anything similar.

When the evidence suggests a multistate outbreak (as has been the case with the current Cyclosporiasis outbreak), CDC can start a national epidemiologic investigation.

Investigators create an epidemic curve showing when illnesses began and map where patients live. They give states a common questionnaire so everyone in all the states/counties ask the same detailed questions.

Following the Food Backward

Once they have an idea about what the source might be (from the food histories, lab results and sanitarian inspections) they can start traceback work. That’s what happened with the current Cyclo outbreak in several states.

Traceback starts with the places where patients ate or bought the suspected food. The federal/state team finds food invoices, shipping records, lot numbers, delivery dates and supplier information for the suspected products. They work backward from restaurants and stores to distributors, processors, packing facilities and farms.

Investigators might also collect leftover food and environmental samples. They may sample food-processing equipment, water sources, soil, irrigation systems or other parts of the growing and packing environment.

Note: At the national level FDA generally regulates produce and most other foods. USDA’s Food Safety and Inspection Service regulates meat, poultry and processed egg products. CDC manages the interstate epidemiological investigations.

Stopping a Multistate Outbreak

Investigators don’t always wait for perfect laboratory proof before acting, including during the current outbreak. When the combined epidemiologic and traceback evidence is clear and convincing, several interventions can happen even if they haven’t isolated the germ from the food – as has been the case so far with the multi-state Cyclosporiasis outbreak.

Distributors can (or be asked or compelled) to place suspected products on hold or recall them. A company can, and usually does, voluntarily recall food already in stores and warehouses. FDA can issue public warnings, increase inspections or screening at the border and work with retailers to find where the food was shipped.

If the source looks like it’s from a farm or processor they can examine irrigation water, sewage exposure, worker sanitation, harvesting equipment, wash water, sanitary packing practices etc.

After the product is removed, investigators keep watching the epidemic curve. Because of incubation periods and reporting delays, illnesses might continue to be reported for several weeks even after the contaminated food is gone.

The Current Cyclospora Investigation

That’s what we’re seeing in the current Cyclospora outbreak.

As of right now CDC/states/counties have found 1,644 laboratory-confirmed cases with exposure to iceberg lettuce in Taco Bell products mostly in Indiana, Kentucky, Michigan, Ohio and West Virginia. For example, Michigan epi’s found that of their 190 patients, 90%  ate at Taco Bell, eating food with iceberg lettuce.

The handful of cases in AZ over the last few weeks don’t appear to be part of the big national outbreak.

FDA traced the lettuce supplied to the Taco Bell locations to shredded iceberg lettuce from Taylor Farms de Mexico that was sourced from central Mexico.

Even though the parasite hasn’t been found in any lettuce so far, all the county health department and laboratory gumshoe work still leads back to the same lettuce producer: Taylor Farms’ source in Mexico.

Because the epi data were compelling, Taylor Farms recalled iceberg lettuce from that farm in Mexico.  Taco Bell has stopped using that lettuce. Mexican health and agricultural authorities also began inspections and traceback work.

There will still be lots more cases reported I the next couple weeks even though the source is likely gone – because the incubation period for the parasitic illness can be up to 10 days or 2 weeks.

Did Federal Staffing Cuts Cause the Outbreak?

Several journalists have asked me whether the federal staffing cuts caused this outbreak.

I can’t say that for sure, but it’s possible.

Why? Because DOGE and Kennedy’s firings at FDA and CDC in 2025 weakened parts of the food-safety system. FDA inspector firings, including all the probationary employees and other mass firings led to a lot fewer FDA inspectors posted in other countries and also to suspend laboratory quality-control work… including proficiency testing to detect Cyclospora in produce.

Those cuts didn’t necessarily cause this outbreak. But fewer inspectors, laboratory scientists, epidemiologists and support staff mean fewer opportunities to prevent contamination and detect illnesses earlier.

Summary

Foodborne illness investigations are slow, complicated and built on hundreds of small pieces of information collected by county/state/federal epidemiologists, doctors, labs, sanitarians and regulators.

The current Cyclospora outbreak highlights how those pieces can point to a likely source even when the organism hasn’t been isolated from the food itself. It also shows why a strong public health and food-safety workforce matters… from preventing contamination to finding illnesses and tracing the food backward.

We’ll never know whether the DOGE/Kennedy firings led to this outbreak, but weakening the system at the federal level makes outbreaks like this harder to prevent.