CDC MMWR - Incidence of Foodborne Infections 2022

CDC released its report on the incidence of foodborne infections.  Interesting items from this report:

• During 2022, FoodNet identified 25,479 cases of infection, 5,981 hospitalizations, and 170 deaths
• Campylobacter and Salmonella are the leading causes of bacterial enteric infections transmitted commonly by food. 
• During 2022, FoodNet identified higher incidences of Shiga toxin-producing Escherichia coli, Yersinia, Vibrio, and Cyclospora infections compared with 2016–2018. Campylobacter, Salmonella, Shigella, and Listeria incidences did not change [from 2016–2018].
• Many COVID-19 pandemic-related factors influencing enteric disease transmission, detection, and reporting (3,4) ended by 2022. The incidence of infections caused by pathogens transmitted commonly through food during 2022 generally returned to levels observed during the pre-pandemic period, 2016–2018.

https://www.cdc.gov/mmwr/volumes/72/wr/mm7226a1.htm

Preliminary Incidence and Trends of Infections Caused by Pathogens Transmitted Commonly Through Food — Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 2022

Weekly / June 30, 2023 / 72(26);701–706

Summary

What is already known about this topic?
Campylobacter and Salmonella are the leading causes of bacterial enteric infections transmitted commonly by food. Reported incidence of enteric infections was lower during the COVID-19 pandemic (2020–2021) compared with previous years.

What is added by this report?
During 2022, FoodNet identified higher incidences of Shiga toxin-producing Escherichia coli, Yersinia, Vibrio, and Cyclospora infections compared with 2016–2018. Campylobacter, Salmonella, Shigella, and Listeria incidences did not change.

What are the implications for public health practice?
Progress in reducing enteric infection incidence was not observed during 2022, as influences of the COVID-19 pandemic subsided. Collaboration among food growers, processors, retail stores, restaurants, and regulators is needed to reduce pathogen contamination during poultry slaughter and to prevent contamination of leafy greens.

Article
Each year, infections from major foodborne pathogens are responsible for an estimated 9.4 million illnesses, 56,000 hospitalizations, and 1,350 deaths in the United States (1). To evaluate progress toward prevention of enteric infections in the United States, the Foodborne Diseases Active Surveillance Network (FoodNet) conducts surveillance for laboratory-diagnosed infections caused by eight pathogens transmitted commonly through food at 10 U.S. sites. During 2020–2021, FoodNet detected decreases in many infections that were due to behavioral modifications, public health interventions, and changes in health care–seeking and testing practices during the COVID-19 pandemic. This report presents preliminary estimates of pathogen-specific annual incidences during 2022, compared with average annual incidences during 2016–2018, the reference period for the U.S. Department of Health and Human Services’ Healthy People 2030 targets (2). Many pandemic interventions ended by 2022, resulting in a resumption of outbreaks, international travel, and other factors leading to enteric infections. During 2022, annual incidences of illnesses caused by the pathogens Campylobacter, Salmonella, Shigella, and Listeria were similar to average annual incidences during 2016–2018; however, incidences of Shiga toxin-producing Escherichia coli (STEC), Yersinia, Vibrio, and Cyclospora illnesses were higher. Increasing culture-independent diagnostic test (CIDT) usage likely contributed to increased detection by identifying infections that would have remained undetected before widespread CIDT usage. Reducing pathogen contamination during poultry slaughter and processing of leafy greens requires collaboration among food growers and processors, retail stores, restaurants, and regulators.

CDC, 10 state health departments, the U.S. Department of Agriculture’s Food Safety and Inspection Service (FSIS), and the Food and Drug Administration (FDA) collaborate to conduct active population-based surveillance of the FoodNet catchment area,* which included an estimated 51 million persons in 2022 (approximately 15% of the U.S. population). Laboratories diagnose bacterial infections by culture or CIDT and Cyclospora infections by microscopy or polymerase chain reaction.† Infection incidence was calculated by dividing the number of infections during 2022 by 2021 U.S. Census Bureau population estimates for the surveillance area and is reported as infections per 100,000 persons. A Bayesian, negative binomial model with penalized thin plate splines adjusting for state-specific trends and population changes§ was used to estimate incidence changes during 2022 compared with the average annual incidence during 2016–2018 using the brms package (version 2.14.0) in R software (version 3.6.2, R Foundation).¶ Incidence was described as increased or decreased relative to the reference period if the 95% credible interval (CrI) for the incidence rate ratio (IRR) did not cross the null value of 1. Incidence changes were also estimated using this method for the subset of infections that were domestically acquired.** Frequencies of hospitalizations, deaths, outbreak-associated infections, and international travel-associated infections were calculated overall and by pathogen.†† The proportion of infections that were diagnosed by CIDT§§ and diagnosed only by CIDT (meaning the specimen had a negative culture result or was not cultured), the proportion of infections diagnosed by CIDT for which a culture was performed, and the proportion of those cultures yielding an isolate were calculated by pathogen for bacterial infections.

A network of nephrologists and infection preventionists conducts surveillance for diagnosed pediatric post-diarrheal hemolytic uremic syndrome (HUS), a complication of STEC infection that most commonly occurs among young children; additional HUS data are collected by hospital discharge review.¶¶ This report includes HUS cases and incidence per 100,000 children and adolescents aged <18 years detected during 2021, the most recent year with available data. This activity was reviewed by CDC and conducted consistent with applicable federal law and CDC policy.***

During 2022, FoodNet identified 25,479 cases of infection, 5,981 hospitalizations, and 170 deaths (Table 1). Infection incidence was highest for Campylobacter (19.2 cases per 100,000 population), followed by Salmonella (16.3). Compared with pathogen-specific average annual incidences during 2016–2018, STEC, Yersinia, Vibrio, and Cyclospora infection incidences were higher during 2022. Overall infection incidence was stable for Campylobacter, Salmonella, Shigella, and Listeria. However, when limited to domestically acquired infections, Campylobacter incidence was higher during 2022 (IRR = 1.07, 95% CrI = 1.01–1.14), as were incidences for Yersinia, Vibrio, and Cyclospora. Compared with 2016–2018, similar percentages of infections during 2022 resulted in hospitalization (23.5% in 2022 versus 23.8%) and death (0.7% versus 0.5%) or were associated with outbreaks (4.3% versus 3.9%) or international travel (12.4% versus 12.8%). However, 62 Salmonella infections (0.7%) resulted in death during 2022, compared with an annual average of 37 (0.4%) during 2016–2018. Serotypes and characteristics of Salmonella infections resulting in death were similar to those during 2016–2018 (FoodNet, unpublished data, 2023).†††

Among 7,032 Salmonella infections with positive culture results during 2022, 6,345 isolates (90%) were fully serotyped. The five most common serotypes were Enteritidis (2.7 cases per 100,000 population), Typhimurium (1.6), Newport (1.4), Javiana (0.9), and I 4,[5],12:i:- (0.6), which have been the five most common serotypes each year since 2010. The incidences of two of these serotypes were lower during 2022 compared with those during 2016–2018: Enteritidis (IRR = 0.88, 95% CrI = 0.79–0.97) and I 4,[5],12:i:- (IRR = 0.69, 95% CrI = 0.56–0.86).

Among 2,882 STEC infections, specimens for 2,401 (83%) were cultured; 1,298 (54%) of those cultured yielded an isolate. The O antigen was determined for 1,187 (91%) of the cultured isolates; among those, serogroup O157 was most common (301; 25%), followed by O103 (164; 14%), O26 (155; 13%), and O111 (149; 13%). During 2021, 72 cases of post-diarrheal HUS among persons aged <18 years were reported (0.7 cases per 100,000) (IRR relative to 2016–2018 = 0.96, 95% CrI = 0.82–1.13), including 41 (57%) among persons <5 years old (1.5 per 100,000) (IRR = 0.95, 95% CrI = 0.79–1.18).

The percentage of bacterial infections diagnosed using CIDT increased from 49% during 2016–2018 to 73% in 2022 (Table 2). The percentage of bacterial infections diagnosed using only CIDT increased from 26% during 2016–2018 to 41% in 2022, and, by pathogen, was highest for Yersinia (77%), Vibrio (56%), and STEC (55%). The overall proportion of reflex cultures that yielded an isolate was similar during 2016–2018 (65%) and 2022 (62%), but decreased for Salmonella, STEC, Shigella, Vibrio, and most markedly for Yersinia (from 48% to 24%).

Discussion

Many COVID-19 pandemic-related factors influencing enteric disease transmission, detection, and reporting (3,4) ended by 2022. The incidence of infections caused by pathogens transmitted commonly through food during 2022 generally returned to levels observed during the pre-pandemic period, 2016–2018. Concerted efforts are needed now to implement strategies to reach national prevention targets and lower the prevalence of enteric infections.

This report highlights lack of progress in reducing enteric infection incidence. The incidence of Salmonella infections during 2022 was above the Healthy People 2030 target.§§§ Also during 2022, the incidence of the most common domestically acquired infections, those caused by Campylobacter (17.4 per 100,000 population), was above the Healthy People 2030 target of 10.9. Poultry meat has been the most commonly identified source of Campylobacter infections in many countries for many years (5) and is also estimated to be the most common U.S. source of Salmonella infections (6).

Further efforts to reduce contamination during poultry slaughter and processing are needed to reduce the incidence of Campylobacter, Salmonella, and other foodborne pathogens (7). In 2021, FSIS published new guidelines for poultry slaughter and processing establishments to control Campylobacter in raw poultry.¶¶¶ Recommendations aim to reduce the incidence of pathogen colonization in birds (e.g., poultry vaccination and use of prebiotics and probiotics) and minimize contamination of poultry water, feed, and bedding. In 2022, FSIS proposed a new regulatory framework to control Salmonella in poultry products,**** guided by recommendations from the National Advisory Committee on Microbiological Criteria for Foods. In 2023, FSIS released a proposed notice of determination to declare Salmonella an adulterant in not-ready-to-eat breaded and stuffed chicken products.†††† Reducing leafy green contamination by improving agricultural water safety, as promoted by FDA§§§§ and the Food Safety Modernization Act,¶¶¶¶ could also reduce Salmonella, STEC, Listeria, and other pathogens that cause foodborne illnesses.

In 2022, 73% of infections detected by FoodNet surveillance had a CIDT result (ranging from 24% to 100% by pathogen). These rapid, highly sensitive assays permit prompt clinical diagnoses from a broad range of potential etiologies, enhancing detection of infections that would have otherwise remained undetected. However, CIDT adoption and the routine usage of culture methods has varied by time, pathogen, and market forces (8,9). These factors and the different sensitivity and specificity of CIDTs complicate the interpretation of surveillance data. Furthermore, having a lower proportion of cases with an isolate obtained by reflex culture limits public health response by reducing the number of isolates having sequenced genomes, which can hinder identification of outbreaks of genetically related infections and the determination of genes coding for antibiotic resistance.

The results of this analysis are subject to at least three limitations. First, the number of reported infections might be undercounted because some ill persons might not seek care, and recommended testing of ill persons might not always be conducted; conversely, false-positive results might cause some overcounting. Second, persons meeting FoodNet criteria for hospitalization or death are included in this report, although underlying reasons for hospitalization or death might be unknown.***** Finally, deaths associated with enteric infections occurring >1 week after specimen collection among patients not hospitalized, and occurring after discharge among those hospitalized (e.g., in hospice care), might have been omitted.

The incidences of infections caused by certain pathogens reported during 2022 were higher than during the prepandemic period 2016–2018, and substantial progress toward Healthy People 2030 objectives was not evident. Prevention measures targeted at reducing food contamination, including the FSIS-proposed Salmonella regulatory framework for reducing illnesses from poultry, are needed to mitigate the prevalence of disease and to meet Healthy People 2030 targets. Better understanding of reasons for decreased incidence of foodborne infections during the COVID-19 pandemic (2020–2021) that were not sustained during 2022 could help guide the creation of additional mitigation strategies.