Reported Incidence of Infections Caused by Pathogens Transmitted Commonly Through Food: Impact of Increased Use of Culture-Independent Diagnostic Tests — Foodborne Diseases Active Surveillance Network, 1996–2023
Increased use of culture-independent diagnostic tests (CIDTs) affects observed trends in foodborne infection incidence. 

During 2023, the incidence of eight domestically acquired infections transmitted commonly through food either increased or remained stable compared with 2016–2018, the baseline used to track progress toward disease reduction goals. Incidence of CIDT-diagnosed infection also increased during 2023. 

CIDTs allow for diagnosis of infections that previously would have been undetected; recent increases in incidence appear to be driven by increased CIDT use. Continued surveillance is needed to monitor the impact of changing diagnostic practices on disease trends. Targeted prevention efforts are needed to reduce disease incidence. 

Reducing foodborne disease incidence is a public health priority. This report summarizes preliminary 2023 Foodborne Diseases Active Surveillance Network (FoodNet) data and highlights efforts to increase the representativeness of FoodNet. During 2023, incidences of domestically acquired campylobacteriosis, Shiga toxin-producing Escherichia coli infection, yersiniosis, vibriosis, and cyclosporiasis increased, whereas those of listeriosis, salmonellosis, and shigellosis remained stable compared with incidences during 2016–2018, the baseline used for tracking progress towards federal disease reduction goals. During 2023, the incidence and percentage of infections diagnosed by culture-independent diagnostic tests (CIDTs) reported to FoodNet continued to increase, and the percentage of cases that yielded an isolate decreased, affecting observed trends in incidence. Because CIDTs allow for diagnosis of infections that previously would have gone undetected, lack of progress toward disease reduction goals might reflect changing diagnostic practices rather than an actual increase in incidence. Continued surveillance is needed to monitor the impact of changing diagnostic practices on disease trends, and targeted prevention efforts are needed to meet disease reduction goals. During 2023, FoodNet expanded its catchment area for the first time since 2004. This expansion improved the representativeness of the FoodNet catchment area, the ability of FoodNet to monitor trends in disease incidence, and the generalizability of FoodNet data. 

Reducing the incidence of foodborne and enteric diseases is a public health priority. The Healthy People 2030 (HP2030) initiative established disease reduction goals for Campylobacter, Listeria , Salmonella, and Shiga toxin-producing Escherichia coli (STEC) infections . To evaluate progress toward HP2030 goals, CDC’s Foodborne Diseases Active Surveillance Network (FoodNet) monitors infections caused by eight pathogens transmitted commonly through food. This report summarizes preliminary 2023 surveillance data and describes changes in incidence compared with average annual incidence during 2016–2018, the reference period used by HP2030 . 

Data Source FoodNet conducts active, population-based surveillance for laboratory-diagnosed Campylobacter, Cyclospora, Listeria, Salmonella, Shigella, STEC, Vibrio, and Yersinia infections and pediatric hemolytic uremic syndrome (HUS) at 10 U.S. sites; HUS is monitored because it can be a complication of STEC infection. FoodNet’s catchment area expanded during 2023 to include all of Colorado, and now represents 16% of the U.S. population (53.6 million persons); in 2023, the historic catchment area represented 15% of the U.S. population (51.0 million persons). Compared with the historic catchment area, the expansion increased representation for specific populations, including Hispanic or Latino ([Hispanic]; 8% increase), American Indian or Alaska Native (AI/AN; 8% increase), and Native Hawaiian or Pacific Islander (NH/PI; 6% increase) persons (FoodNet collects race and ethnicity as separate variables) as well as persons living in rural counties (10% increase). Laboratory Testing and Data Collection Bacterial infections were diagnosed by culture or culture-independent diagnostic tests (CIDTs). Cyclosporiasis was diagnosed by polymerase chain reaction or microscopy. Pediatric HUS surveillance is conducted through a network of nephrologists and infection preventionists and by hospital discharge data review. This report includes 2022 data on pediatric HUS cases, the most recent year for which data are available. This activity was reviewed by CDC, deemed not research, and conducted in accordance with applicable federal law and CDC policy. Statistical Methods Bayesian negative binomial models were implemented to estimate changes in incidence in the historic catchment area during 2023 compared with average annual incidence during 2016–2018 (overall, and for domestically acquired infections), using R statistical software (version 2.14.0; R Foundation). , Incidence in 2023 was considered substantially different from that during 2016–2018 if the 95% credible interval (CrI) for the incidence rate ratio (IRR) did not include 1.0. Cross-tabulations by demographic and other characteristics were also performed. 

FoodNet conducts active, population-based surveillance for laboratory-diagnosed Campylobacter, Cyclospora, Listeria, Salmonella, Shigella, STEC, Vibrio, and Yersinia infections and pediatric hemolytic uremic syndrome (HUS) at 10 U.S. sites; HUS is monitored because it can be a complication of STEC infection. FoodNet’s catchment area expanded during 2023 to include all of Colorado, and now represents 16% of the U.S. population (53.6 million persons); in 2023, the historic catchment area represented 15% of the U.S. population (51.0 million persons). Compared with the historic catchment area, the expansion increased representation for specific populations, including Hispanic or Latino ([Hispanic]; 8% increase), American Indian or Alaska Native (AI/AN; 8% increase), and Native Hawaiian or Pacific Islander (NH/PI; 6% increase) persons (FoodNet collects race and ethnicity as separate variables) as well as persons living in rural counties (10% increase). 

Bacterial infections were diagnosed by culture or culture-independent diagnostic tests (CIDTs). Cyclosporiasis was diagnosed by polymerase chain reaction or microscopy. Pediatric HUS surveillance is conducted through a network of nephrologists and infection preventionists and by hospital discharge data review. This report includes 2022 data on pediatric HUS cases, the most recent year for which data are available. This activity was reviewed by CDC, deemed not research, and conducted in accordance with applicable federal law and CDC policy. 

Bayesian negative binomial models were implemented to estimate changes in incidence in the historic catchment area during 2023 compared with average annual incidence during 2016–2018 (overall, and for domestically acquired infections), using R statistical software (version 2.14.0; R Foundation). , Incidence in 2023 was considered substantially different from that during 2016–2018 if the 95% credible interval (CrI) for the incidence rate ratio (IRR) did not include 1.0. Cross-tabulations by demographic and other characteristics were also performed. 

Incidence in 2023 Compared with Average Annual Incidence During 2016–2018 During 2023, FoodNet identified 29,607 infections, 7,234 hospitalizations, and 177 deaths overall (including domestically acquired and travel-associated infections) in the historic catchment area , compared with 31,492 infections, 7,588 hospitalizations, and 184 deaths in the expanded catchment area (Supplementary Table; https://stacks.cdc.gov/view/cdc/157822 ). In both the historic and expanded catchment areas, 15% of cases were associated with international travel. Overall, and for domestically acquired infections only, incidence of campylobacteriosis was highest, followed by salmonellosis and STEC infection. In the historic catchment area during 2023, incidences of domestically acquired campylobacteriosis, cyclosporiasis, STEC infection, vibriosis, and yersiniosis increased compared with those during 2016–2018, whereas listeriosis, salmonellosis, and shigellosis incidences remained stable. Generally, the overall percentage of infections attributable to specific Campylobacter, Shigella, Vibrio, and Yersinia species, Salmonella serotypes, and STEC serogroups was lower in 2023 than in all previous years . The overall incidence of infections for which the pathogen was not speciated, serotyped, or serogrouped increased substantially compared with incidence during 2016–2018 . During 2023, 78% of all bacterial infections were diagnosed by CIDTs in the historic catchment area, including 46% diagnosed using only CIDTs. The percentage of CIDT-diagnosed infections for which a reflex culture was attempted decreased from 71% during 2016–2018 to 68% during 2023. This decrease was largest for Yersinia , Vibrio , and STEC infections. For all illnesses except listeriosis , the percentage of reflex cultures that yielded an isolate (successful [or positive] reflex culture) was lower in 2023 than during previous years . This decrease in isolate availability has been associated with a decrease in serotyped, serogrouped, and speciated infections. For example, from 2016–2018 to 2023, the overall incidence of unspeciated infections increased substantially for Campylobacter , Shigella , Yersinia , and Vibrio ; the percentage of speciated infections declined from 33% to 26% for Campylobacter , from 65% to 41% for Shigella , from 49% to 23% for Yersinia , and from 61% to 34% for Vibrio . Although only culture-independent methods are used to diagnose cyclosporiasis, increases in CIDT-diagnosed cyclosporiasis and cyclosporiasis incidence mirror CIDT-driven increases in bacterial infection incidence. Salmonella Infections Of 8,454 total (i.e., both domestically acquired and travel-associated) Salmonella infections during 2023 in the historic catchment area, 83% yielded an isolate; 89% of isolates were fully serotyped. The incidence of nonserotyped infections increased substantially. The incidences of the most frequently reported serotypes, S. Enteritidis and S. Newport, remained stable during 2023 compared with those during 2016–2018, whereas the incidences of the next-most frequently reported serotypes, S. Typhimurium, S. Javiana, and S. I 4,[5],12:i:- decreased substantially. STEC Infections Of 3,351 total STEC infections in the historic catchment area during 2023, 57% yielded an isolate; 87% of isolates were fully serogrouped. The incidence of nonserogrouped infections increased substantially in 2023 compared with that during 2016–2018. During 2023, STEC O157 incidence decreased compared with incidence during 2016–2018, and non-O157 STEC incidence remained stable. Hemolytic Uremic Syndrome During 2022, FoodNet identified 61 cases of postdiarrheal HUS in persons aged <18 years, including 39 among children aged <5 years. The incidence of postdiarrheal HUS among persons aged <18 years (0.6 per 100,000 persons) and those aged <5 years (1.4 per 100,000) remained stable in 2022 compared with that during 2016–2018. 

During 2023, FoodNet identified 29,607 infections, 7,234 hospitalizations, and 177 deaths overall (including domestically acquired and travel-associated infections) in the historic catchment area , compared with 31,492 infections, 7,588 hospitalizations, and 184 deaths in the expanded catchment area (Supplementary Table; https://stacks.cdc.gov/view/cdc/157822 ). In both the historic and expanded catchment areas, 15% of cases were associated with international travel. Overall, and for domestically acquired infections only, incidence of campylobacteriosis was highest, followed by salmonellosis and STEC infection. In the historic catchment area during 2023, incidences of domestically acquired campylobacteriosis, cyclosporiasis, STEC infection, vibriosis, and yersiniosis increased compared with those during 2016–2018, whereas listeriosis, salmonellosis, and shigellosis incidences remained stable. Generally, the overall percentage of infections attributable to specific Campylobacter, Shigella, Vibrio, and Yersinia species, Salmonella serotypes, and STEC serogroups was lower in 2023 than in all previous years . The overall incidence of infections for which the pathogen was not speciated, serotyped, or serogrouped increased substantially compared with incidence during 2016–2018 . During 2023, 78% of all bacterial infections were diagnosed by CIDTs in the historic catchment area, including 46% diagnosed using only CIDTs. The percentage of CIDT-diagnosed infections for which a reflex culture was attempted decreased from 71% during 2016–2018 to 68% during 2023. This decrease was largest for Yersinia , Vibrio , and STEC infections. For all illnesses except listeriosis , the percentage of reflex cultures that yielded an isolate (successful [or positive] reflex culture) was lower in 2023 than during previous years . This decrease in isolate availability has been associated with a decrease in serotyped, serogrouped, and speciated infections. For example, from 2016–2018 to 2023, the overall incidence of unspeciated infections increased substantially for Campylobacter , Shigella , Yersinia , and Vibrio ; the percentage of speciated infections declined from 33% to 26% for Campylobacter , from 65% to 41% for Shigella , from 49% to 23% for Yersinia , and from 61% to 34% for Vibrio . Although only culture-independent methods are used to diagnose cyclosporiasis, increases in CIDT-diagnosed cyclosporiasis and cyclosporiasis incidence mirror CIDT-driven increases in bacterial infection incidence. 

Infections Of 8,454 total (i.e., both domestically acquired and travel-associated) Salmonella infections during 2023 in the historic catchment area, 83% yielded an isolate; 89% of isolates were fully serotyped. The incidence of nonserotyped infections increased substantially. The incidences of the most frequently reported serotypes, S. Enteritidis and S. Newport, remained stable during 2023 compared with those during 2016–2018, whereas the incidences of the next-most frequently reported serotypes, S. Typhimurium, S. Javiana, and S. I 4,[5],12:i:- decreased substantially. 

Of 3,351 total STEC infections in the historic catchment area during 2023, 57% yielded an isolate; 87% of isolates were fully serogrouped. The incidence of nonserogrouped infections increased substantially in 2023 compared with that during 2016–2018. During 2023, STEC O157 incidence decreased compared with incidence during 2016–2018, and non-O157 STEC incidence remained stable. 

During 2022, FoodNet identified 61 cases of postdiarrheal HUS in persons aged <18 years, including 39 among children aged <5 years. The incidence of postdiarrheal HUS among persons aged <18 years (0.6 per 100,000 persons) and those aged <5 years (1.4 per 100,000) remained stable in 2022 compared with that during 2016–2018. 

The current findings and previous FoodNet reports  suggest a lack of progress toward foodborne disease reduction goals; however, this outcome might reflect changing diagnostic practices such as the increased use of CIDTs rather than an actual increase in disease incidence. Increased use of CIDTs facilitates prompt clinical diagnosis and treatment but also complicates the interpretation of surveillance data and trends because CIDT adoption has varied over time, among clinical labs, and by pathogen. In addition, although CIDTs are generally considered more sensitive than are culture-based methods, some have high false-positive rates for certain pathogens (e.g., Vibrio ) . Previous studies have indicated that increased CIDT use has resulted in the diagnosis of infections that previously would have gone undetected; increased use of CIDTs has been associated with marked increases in reported incidence . Increases in CIDT-diagnosed infections are also associated with decreased rates of reflex culture, thereby reducing the number of isolates available for subtyping, whole genome sequencing, and antimicrobial resistance characterization . The impact of this reduction differs by species, serotype, and serogroup. Because an isolate is required for speciation, serotyping, and serogrouping, reduced isolate availability might result in underdetection of illnesses attributable to specific Campylobacter, Shigella, Vibrio, and Yersinia species, Salmonella serotypes, and STEC serogroups. The substantial increase in the incidence of infections for which the pathogen was not speciated, serotyped, or serogrouped is likely an artifact of changing diagnostic practices (i.e., increased CIDT use), resulting in a reduced availability of isolates for speciation and typing. Continued reductions in isolate availability might hinder outbreak identification and response (e.g., whole genome sequencing–based cluster identification and source attribution), detection of emerging antimicrobial resistance, and tracking of trends in illnesses attributable to specific species, subtypes, serotypes, and resistant strains. Increasing successful reflex culture rates after a CIDT diagnosis is a public health priority, which requires focused efforts and resources at the federal, state, and local levels. FoodNet data are used to track trends in enteric illness, monitor progress toward disease reduction goals, and guide food safety policy , . Because FoodNet is a sentinel surveillance system representing 10 sites, national extrapolation relies on strong assumptions of representativeness. Although the sites included in the FoodNet catchment area were selected nonrandomly, past analyses suggest that FoodNet’s catchment area is broadly representative of the national population . Previously, the only notable difference between FoodNet’s historic catchment area and the national population identified by these studies was that Hispanic persons were underrepresented in the catchment area relative to national representation . Investigating enteric disease epidemiology for AI/AN and NH/PI persons using FoodNet data has also been complicated by the small size of these populations in the historic catchment area. By increasing representation for these specific populations in the FoodNet catchment area, FoodNet’s expansion has helped to partially alleviate these limitations and improve the generalizability of FoodNet data. Additional expansion might be needed as national and catchment area demographics change. Limitations The findings in this report are subject to at least three limitations. First, underreporting might affect case counts because ill persons must seek care and be tested for their illness to be recorded as a case. Second, although ill persons might meet the FoodNet criteria for hospitalization or death, the underlying reason for hospitalization or death might be unknown. Deaths that occurred >1 week after specimen collection among nonhospitalized persons or after discharge for hospitalized persons might not be recorded. Finally, domestically acquired cases might be overestimated because of the inclusion of persons with unknown travel status. Implications for Public Health Practice FoodNet’s surveillance efforts are critical for tracking foodborne and enteric illnesses in the United States. During 2023, FoodNet expanded its catchment area for the first time since 2004, and it now includes all of Colorado. This expansion improved the representativeness of the FoodNet catchment area, and the ability of FoodNet to monitor trends in disease incidence, including the impact of changing diagnostic practices and the generalizability of FoodNet data. Continued surveillance is needed to monitor the impact of changing diagnostic practices on disease trends and evaluate the efficacy of prevention efforts in reducing incidence. 

The findings in this report are subject to at least three limitations. First, underreporting might affect case counts because ill persons must seek care and be tested for their illness to be recorded as a case. Second, although ill persons might meet the FoodNet criteria for hospitalization or death, the underlying reason for hospitalization or death might be unknown. Deaths that occurred >1 week after specimen collection among nonhospitalized persons or after discharge for hospitalized persons might not be recorded. Finally, domestically acquired cases might be overestimated because of the inclusion of persons with unknown travel status. 

FoodNet’s surveillance efforts are critical for tracking foodborne and enteric illnesses in the United States. During 2023, FoodNet expanded its catchment area for the first time since 2004, and it now includes all of Colorado. This expansion improved the representativeness of the FoodNet catchment area, and the ability of FoodNet to monitor trends in disease incidence, including the impact of changing diagnostic practices and the generalizability of FoodNet data. Continued surveillance is needed to monitor the impact of changing diagnostic practices on disease trends and evaluate the efficacy of prevention efforts in reducing incidence. 

