Federal investigators are working on three new foodborne illness clusters with no identified source, a multistate Salmonella outbreak tied to recalled eggs, and a set of numbers published by the CDC this spring that explains part of why those investigations are harder than they used to be.
The reason has nothing to do with the food supply. It has to do with which test a doctor orders when a patient shows up with diarrhea and cramps.
According to the CDC's FoodNet surveillance summary, 78 percent of bacterial infections tracked in 2024 were diagnosed by culture-independent diagnostic tests, up from 47 percent in the 2016 to 2018 reference period. Those tests detect a pathogen's genetic material or antigens directly from a stool sample. They are fast, sensitive, and good for the patient. They also do not produce a living bacterial sample.
The Sample Investigators Cannot Work Without
Outbreak detection in the United States runs on isolates. When a lab grows bacteria from a patient's sample, that isolate can be sequenced, and the genetic fingerprint gets compared against every other fingerprint in the national PulseNet database. That comparison is how two people who got sick in different states are connected to the same lettuce, the same eggs, the same processing plant.
A rapid panel that says "Salmonella detected" tells a doctor what to treat. It tells an epidemiologist almost nothing about which Salmonella.
The FoodNet data show the gap widening. Among patients whose samples were cultured after a positive rapid test, 59 percent yielded a result in 2024, compared with 71 percent in the earlier baseline. Cases diagnosed by rapid test only rose to 41 percent from 21 percent, while cases diagnosed by culture alone fell to 22 percent from 53 percent.
The consequences show up directly in the 2024 Salmonella figures. FoodNet sites reported 9,219 Salmonella infections. Only 7,314 of those, or 79 percent, had a positive culture, and only 6,066 isolates were fully serotyped. For Shiga toxin-producing E. coli, the gap is far wider: 3,635 infections reported, but just 1,373 with a positive culture result.
Numbers That Move Without the Disease Moving
There is a second, less obvious effect, and it cuts the other way.
Because rapid tests catch infections that older methods missed, some apparent increases in disease may reflect better detection rather than more illness. FoodNet reported that incidence in 2024 increased for Cyclospora, Shigella, STEC, Vibrio, and Yersinia compared with the baseline period, and stayed similar for Listeria and Salmonella. The agency notes that infections caused by STEC, Vibrio, and Yersinia are harder to find by traditional culture, and that before rapid tests many samples were either never tested for them or came back falsely negative.
CDC also cautions that testing changes are not the only factor, and that for some pathogens the rise in incidence appears to outpace the rise in rapid test use. The agency has not concluded that testing explains the whole picture.
This is why a headline saying a foodborne illness is climbing deserves a second look. The measuring instrument changed at the same time as the measurement.
The Practical Distance Between a Diagnosis and a Recall
For a household, the pathway runs like this. Someone gets sick after a meal. A clinician orders a stool test. If the lab performs a follow-up culture after a positive rapid result and successfully grows the organism, that isolate gets sequenced and compared nationally. If a match appears with cases elsewhere, investigators start interviewing patients about what they ate, regulators trace the product backward through the supply chain, and a recall may follow.
Every link after the first depends on that culture succeeding. When it does not, the case is still counted, the patient is still treated, but the illness becomes invisible to the system that finds the source.
The scale of what is at stake is visible in the current investigations. CDC and FDA have linked 98 Salmonella Enteritidis infections across 17 states, with 26 hospitalizations, to shell eggs from a Texas producer, and whole-genome sequencing of samples from all 98 patients revealed antibiotic resistance findings that changed treatment guidance. That analysis was only possible because isolates existed.
CDC has been direct about the fix. In its FoodNet reporting, the agency stated that "increasing successful reflex culture rates after a CIDT diagnosis is a public health priority," and its current guidance asks clinical laboratories to culture patient samples after a positive rapid result and asks test developers to design panels compatible with follow-up culture.
What Patients and Labs Can Actually Do
Most of the burden here sits with laboratories and manufacturers, not with individuals. But a few things are within reach.
If you are sick enough to see a clinician for a gastrointestinal illness, getting tested at all is the first and most useful step. Many people recover without care and are never tested, which is why CDC repeatedly notes that true outbreak sizes are larger than reported counts. A test that never happens contributes nothing to detection.
If you are told a rapid panel found a bacterial pathogen, it is reasonable to ask whether the lab will also attempt a culture. In many jurisdictions, submitting an isolate or specimen to the public health lab is required, and the answer may already be yes.
Cooperate with the interview. Public health staff who call after a positive result are building the exposure history that turns scattered cases into a traceable cluster. Those calls are often the only way a common food gets identified.
Seek prompt care for bloody diarrhea, signs of dehydration, a high fever, or symptoms that persist beyond a few days, and for any diarrheal illness in an infant, an adult over 65, someone pregnant, or someone with a weakened immune system.
FoodNet publishes preliminary data each spring and final annual figures later in the year, so the next scheduled update to these testing trends is expected in 2027. Active outbreak pages at CDC and FDA update far more frequently. MedicalDaily will continue tracking both.
The confirmed finding is that 78 percent of bacterial foodborne infections in FoodNet's 2024 data were identified by tests that do not routinely yield an isolate, and that successful follow-up culture rates have fallen. The people most affected are anyone who eats a widely distributed food product, because detection speed determines how long a contaminated item stays on shelves. The most reasonable action is to get tested when genuinely ill and to answer the public health interview. The central uncertainty is how much of the recent rise in reported infections reflects better detection rather than more disease.
Frequently Asked Questions
What is a culture-independent diagnostic test? A test that detects a pathogen's genetic material or antigens directly from a stool sample, without growing the organism. Multiplex gastrointestinal panels that check for many pathogens at once are the most common type.
Are these tests bad for patients? No. They are faster and more sensitive than traditional culture, and they detect infections that older methods missed. The problem is a surveillance one, not a treatment one.
Why do investigators need a bacterial isolate? Only a grown organism can be sequenced and serotyped in a way that produces a comparable genetic fingerprint. Those fingerprints are what link a case in one state to a case in another and, eventually, to a specific food.
How much has this changed? CDC reported that 78 percent of bacterial infections in FoodNet's 2024 data were diagnosed by rapid tests, compared with 47 percent in 2016 to 2018. Successful follow-up cultures fell to 59 percent from 71 percent.
Does this mean foodborne illness is getting worse? Not necessarily. CDC says some apparent increases likely reflect better detection rather than more disease, though it also notes that for some pathogens the rise appears to outpace testing changes.
What is CDC asking laboratories to do? Perform a follow-up culture after a positive rapid test result, and ask test developers to design panels that remain compatible with culture-based methods.
When should I see a doctor for a stomach illness? Seek care for bloody diarrhea, signs of dehydration, high fever, or symptoms lasting more than a few days, and for any diarrheal illness in an infant, an adult over 65, someone pregnant, or someone immunocompromised.
