How New Diagnostic Tests Changed the Picture of Salmonella, 2004–2024

Salmonella bacteria are a leading cause of gastrointestinal illness in the United States, spread through contaminated food or water and contact with infected people or animals. Infections are nontyphoidal (NTS) or typhoidal (TS: typhoid and paratyphoid fever). TS made up about 1% (1,496 of 107,207) of U.S. Salmonella infections from 2004 to 2024, and about 70% of those were linked to international travel. NTS, by contrast, is the second leading cause of domestically acquired bacterial foodborne illness, with an estimated 1.3 million illnesses and 12,500 hospitalizations in 2019. Healthy People 2030 aims to cut domestically acquired NTS to fewer than 11.5 infections per 100,000 people; in 2024 the rate in the Foodborne Diseases Active Surveillance Network (FoodNet) was 15.2, suggesting limited progress.

Culture and CIDTs

Salmonella infections were traditionally diagnosed by growing the bacteria in culture. Since 2013, culture-independent diagnostic tests (CIDTs), which detect a pathogen's genetic material or antigens, have been used increasingly, often in multiplex panels that can find enteric infections without a doctor suspecting a particular germ. After a positive CIDT, a lab can attempt a "reflex" culture; if it yields an isolate, the infection is culture confirmed. If no culture is tried or it fails, the infection is unconfirmed. For several enteric pathogens, rising CIDT use has pushed up reported incidence and changed the kinds of infections reported, which complicates reading trends and measuring progress. This MMWR report examined the effect on Salmonella.

The data

FoodNet has conducted active, population-based surveillance for culture-diagnosed infections since 1996 and for CIDT-diagnosed infections of eight enteric pathogens since 2012. From 2004 to 2023 its catchment area covered Connecticut, Georgia, Maryland, Minnesota, New Mexico, Oregon and Tennessee plus selected counties in California, Colorado and New York; in 2023 it expanded to all of Colorado. The analysts compared 2006–2014 with 2015–2023 — before and after the FDA approved the first multiplex panel with a Salmonella target in 2013 — and modeled trends across 2004–2024. Leaving out travelers or using the expanded area gave similar results.

What changed

Overall incidence stayed stable from 2004 to 2024, but how infections were found shifted sharply. Culture-diagnosed and culture-confirmed infections declined while CIDT-diagnosed and unconfirmed infections rose, and in 2021 CIDT diagnoses outnumbered culture diagnoses for the first time.

Trends in Salmonella incidence by diagnostic method and culture confirmation, FoodNet, 2004–2024. CDC figure.

Who was caught by which test

Demographically, CIDT- and culture-diagnosed infections were much alike. Severity was not. Infections found in blood (odds ratio 0.02) or urine (0.03), rather than stool, were far less likely to be diagnosed by CIDT; hospitalization and bloody diarrhea were also linked to lower odds, though less strongly. Outbreak-associated infections were less likely than sporadic ones to be CIDT-diagnosed (odds ratio 0.20). Geographic differences probably reflect how quickly labs serving different communities adopted CIDTs.

In other words, CIDTs catch milder, sporadic illnesses — many of which would once have gone undiagnosed — while severe and outbreak cases, such as bloodstream infections for which doctors order blood cultures, are still mostly diagnosed by culture. CIDTs have changed the range of illness detected without changing who is reported.

Why it matters

• Trends can mislead. Rising CIDT diagnoses of mild illness could hide real declines from successful prevention. The authors urged accounting for diagnostic method in analyses, for example by stratifying or including it in models.
• Isolates still matter. Culture-confirmed infections fell more slowly than culture-diagnosed ones, perhaps because Salmonella is relatively easy to culture after a positive CIDT. Isolates are needed for serotyping, whole-genome sequencing and antimicrobial susceptibility testing, and sequencing is critical for detecting outbreaks and tracing their sources, so labs should keep performing reflex cultures.

Limitations: FoodNet counts only laboratory-diagnosed infections, so changes in care-seeking and testing affect trends; CIDT-positive infections were classified as such regardless of culture results, though false positives are uncommon for Salmonella; and NTS and TS could not be analyzed separately because many infections were not serotyped — although excluding travel-associated cases (70% of TS and 8% of NTS) did not change the results.

Sources

• Tierney R, Pendley Louis R, Boxrud DJ, Houck Lamas K, Angelo KM, Weller DJ. "Effect of Diagnostic Test Type on Detection of Salmonella Infections — Foodborne Diseases Active Surveillance Network, 2004–2024." MMWR 2026;75(29).