Incidence and Trends of Infections With Pathogens Transmitted Commonly Through Food and the Effect of Increasing Use of Culture-Independent Diagnostic Tests on Surveillance

Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 2013-2016

Ellyn P. Marder, MPH; Paul R. Cieslak, MD; Alicia B. Cronquist, MPH; John Dunn, DVM; Sarah Lathrop, PhD; Therese Rabatsky-Ehr, MPH; Patricia Ryan, MD; Kirk Smith, DVM; Melissa Tobin-D'Angelo, MD; Duc J. Vugia, MD; Shelley Zansky, PhD; Kristin G. Holt, DVM; Beverly J. Wolpert, PhD; Michael Lynch, MD; Robert Tauxe, MD; Aimee L. Geissler, PhD


Morbidity and Mortality Weekly Report. 2017;66(15):397-403. 

In This Article

Abstract and Introduction


Foodborne diseases represent a substantial public health concern in the United States. CDC's Foodborne Diseases Active Surveillance Network (FoodNet) monitors cases reported from 10 U.S. sites* of laboratory-diagnosed infections caused by nine enteric pathogens commonly transmitted through food. This report describes preliminary surveillance data for 2016 on the nine pathogens and changes in incidences compared with 2013–2015. In 2016, FoodNet identified 24,029 infections, 5,512 hospitalizations, and 98 deaths caused by these pathogens. The use of culture-independent diagnostic tests (CIDTs) by clinical laboratories to detect enteric pathogens has been steadily increasing since FoodNet began surveying clinical laboratories in 2010.[1] CIDTs complicate the interpretation of FoodNet surveillance data because pathogen detection could be affected by changes in health care provider behaviors or laboratory testing practices.[2] Health care providers might be more likely to order CIDTs because these tests are quicker and easier to use than traditional culture methods, a circumstance that could increase pathogen detection.[3] Similarly, pathogen detection could also be increasing as clinical laboratories adopt DNA-based syndromic panels, which include pathogens not often included in routine stool culture.[4,5] In addition, CIDTs do not yield isolates, which public health officials rely on to distinguish pathogen subtypes, determine antimicrobial resistance, monitor trends, and detect outbreaks. To obtain isolates for infections identified by CIDTs, laboratories must perform reflex culture; if clinical laboratories do not, the burden of culturing falls to state public health laboratories, which might not be able to absorb that burden as the adoption of these tests increases.[2] Strategies are needed to preserve access to bacterial isolates for further characterization and to determine the effect of changing trends in testing practices on surveillance.

FoodNet is a collaboration among CDC, 10 state health departments, the U.S. Department of Agriculture's Food Safety and Inspection Service, and the Food and Drug Administration. FoodNet personnel conduct active, population-based surveillance for laboratory-diagnosed infections caused by Campylobacter, Cryptosporidium, Cyclospora, Listeria, Salmonella, Shiga toxin-producing Escherichia coli (STEC), Shigella, Vibrio, and Yersinia for 10 sites covering approximately 15% of the U.S. population (an estimated 49 million persons in 2015). Confirmed bacterial infections are defined as isolation of the bacterium from a clinical specimen by culture. Confirmed parasitic infections are defined as detection of the parasite from a clinical specimen by direct fluorescent antibody test, polymerase chain reaction, enzyme immunoassay, or light microscopy. CIDTs detect bacterial pathogen antigen, nucleic acid sequences, or for STEC, Shiga toxin or Shiga toxin genes, in a stool specimen or enrichment broth.§ A CIDT positive–only bacterial infection is a positive CIDT result that was not confirmed by culture. Hospitalizations occurring within 7 days of specimen collection are recorded. The patient's vital status at hospital discharge (or 7 days after specimen collection if not hospitalized) is also recorded. Hospitalizations and deaths occurring within 7 days of specimen collection are attributed to the infection. FoodNet also conducts surveillance for physician-diagnosed postdiarrheal hemolytic uremic syndrome (HUS), a potential complication of STEC infection, by review of hospital discharge data through a network of nephrologists and infection preventionists. This report includes HUS cases among persons aged <18 years for 2015, the most recent year with available data.

Incidence of infection for each pathogen is calculated by dividing the number of infections in 2016 by the U.S. Census estimates of the surveillance area population for 2015. Incidence is calculated for confirmed infections alone and for confirmed or CIDT positive–only infections combined. A negative binomial model with 95% confidence intervals (CIs) was used to estimate changes in incidence of confirmed bacterial and parasitic infections and confirmed or CIDT positive–only bacterial infections in 2016 compared with 2013–2015, adjusting for changes in the surveillance population over time. For STEC, incidence is reported for all STEC serogroups combined because it is not possible to distinguish between serogroups using CIDTs. Insufficient data were available to assess change for Cyclospora. For HUS, the 2015 incidence was compared with incidence during 2012–2014.

*Connecticut, Georgia, Maryland, Minnesota, New Mexico, Oregon, Tennessee, and selected counties in California, Colorado, and New York (
Culturing of a specimen with a positive culture-independent diagnostic test (CIDT) result.
§For Shiga toxin-producing Escherichia coli, only CIDT reports that were positive at a state public health laboratory were counted.