Methods
Data Source
During 2004–2023, the FoodNet catchment area included Connecticut, Georgia, Maryland, Minnesota, New Mexico, Oregon, and Tennessee and selected counties in California, Colorado, and New York (i.e., the historic FoodNet catchment area). In 2023, the FoodNet catchment area expanded to include all Colorado counties (i.e., the expanded FoodNet catchment area) (2).
FoodNet has conducted active, population-based surveillance for culture-diagnosed infections since 1996 and, since 2012, for CIDT-diagnosed infections caused by eight enteric pathogens, including Salmonella, in the FoodNet catchment area† (2). After a CIDT diagnosis, infections are considered culture confirmed if reflex culture is attempted and yields an isolate. All culture-diagnosed cases are considered culture confirmed. An unconfirmed infection is an infection for which reflex culture was not attempted or failed to yield an isolate.
For each illness, FoodNet collects demographic, clinical, specimen type, and other data, including whether the illness is outbreak-associated or sporadic, and whether the person reported international travel <30 days before TS infection onset or <7 days before NTS infection onset. To diagnose a Salmonella infection, various specimens can be tested, including blood, stool, and urine. Data for all Salmonella infections reported to FoodNet during 2004–2024 (NTS and TS) were obtained for use in this report, although slightly different ranges of years were used, depending on the analysis.
Statistical Methods
All data were analyzed in R (version 4.4.1; R Foundation). Sensitivity analyses excluded persons reporting international travel and used data from the expanded FoodNet catchment area. Because these analyses produced similar results, findings from the historic FoodNet catchment area, including travel-associated cases, are included.
The demographic and clinical characteristics of infections reported during 2006–2014 and 2015–2023 were compared after stratification by diagnostic method and confirmation status. These years were selected to reflect the period immediately before and after Food and Drug Administration (FDA) approval of the first CIDT multiplex panel with a Salmonella target in 2013 and to allow for equal time periods for comparison before and after CIDT adoption.§ Demographic and clinical characteristics were not available for 2024 at the time of this analysis. For each period, the average annual incidences (number of cases per 100,000 population) were calculated using U.S. Census Bureau intercensal population estimates.¶ Incidence rate ratios (IRRs) with 95% CIs were used to compare incidences across periods and stratum. Counterfactual random forest (CFRF),** a method to quantify differences in odds of a case being diagnosed by CIDT (versus culture) for different demographic patient and clinical illness characteristics, was also conducted†† (5,7).
Bayesian splines regression§§ was used to model trends in culture-diagnosed and culture-confirmed infections during 2004–2024 and in CIDT-diagnosed and unconfirmed infections during 2011–2024¶¶ (8,9). All available data from 2004–2024 were used to identify long-term trends and improve estimate precision. This activity was reviewed by CDC, deemed not research, and conducted consistent with applicable federal law and CDC policy.***
