Discussion

Use of CIDTs is finding cases that were not being previously diagnosed. Among confirmed cases, the incidence of Cryptosporidium and STEC non-O157 infections in 2015 was significantly higher than the average for the previous 3 years. The increase in incidence of STEC non-O157 infections is attributable, in part or in full, to increases in diagnostic testing (2). The proportion of laboratories testing for STEC non-O157 increased to 74% in 2015, compared with 55% in 2012 (FoodNet, unpublished data). The increase in Cryptosporidium follows the pattern observed in national data since 2005 and is likely also driven by increases in diagnostic testing (3,4).

The incidence of Salmonella serotype Typhimurium infections continues to decline, and it has dropped to the third most commonly reported serotype. The use of a live attenuated Typhimurium vaccine in poultry (5), in addition to more stringent performance standards for Salmonella contamination of poultry carcasses (6) might have contributed to this decline. The significant decrease in HUS incidence in 2014 compared with the preceding 3 years (2011–2013) mirrors significant decreases in STEC O157 incidence observed during the same period (7). Efforts are still needed to decrease contamination of produce, beef, and other foods to achieve the Healthy People 2020 goal for STEC O157 of 0.6 cases per 100,000 population.¶

The percentage of infections diagnosed only by CIDTs markedly increased in 2015. Diagnostic testing practices for enteric pathogens are rapidly moving away from culture-based methods, and the impact of this change varies by pathogen. Although CIDTs are still most commonly being used for Campylobacter and STEC, the highest percentage increase in use compared with the previous 3-year average was observed for Shigella and Salmonella, most likely due to laboratories using the newly available DNA-based syndrome panels (FoodNet, unpublished data)

In FoodNet, current methods to assess trends in the incidence of illness caused by bacterial pathogens are based only on culture-confirmed infections. The ability to assess and interpret change is impeded as the number of positive CIDT reports continues to rise because of important limitations in the understanding of CIDTs and possible changes in clinician and laboratory practices surrounding them. For example, analyses need to consider the likelihood of false-positive CIDTs and of CIDTs that are more sensitive than routine culture methods; such characteristics vary among CIDTs. The availability of CIDTs might also increase testing for some pathogens. Surveillance systems need to adapt to these changes by expanding case definitions to include positive CIDT reports. Isolates are still needed for antimicrobial susceptibility testing, serotyping, subtyping, and whole genome sequencing (1); these data are critical for monitoring trends, detecting clusters of illness, and investigating outbreaks. For Salmonella, with serotypes diverse in reservoirs and sources, the inability to distinguish serotypes will prevent tracking of important changes in incidence by serotype, and markedly limit detection and investigation of outbreaks. For STEC, because identification of serogroups requires culture, it is not known which STEC-positive CIDT reports represent O157 versus non-O157.

The findings in this report are subject to at least five limitations. First, increasing use of CIDTs by clinical laboratories might affect the number of culture-confirmed infections reported; use of CIDTs might result in an increase (as seen for STEC non-O157 infections) or decrease (as fewer cases might be diagnosed by traditional methods) in reported incidence. Second, the sensitivity and specificity of CIDTs vary by test type, brand, and other factors; some CIDT reports could be false positives (1). Third, health care–seeking behaviors, access to health services, and other characteristics of the population in the surveillance area might affect the generalizability of the findings. Fourth, the proportion of illnesses transmitted by non-food routes differs by pathogen; data provided in this report are not limited to infections from food.** Finally, changes in incidence between periods can reflect year-to-year variation during those periods rather than sustained trends, and the number of infections and patterns observed might change as final data become available.

The use of CIDTs in clinical laboratories has many advantages. Illnesses can be diagnosed much faster than when culture is required. Also, some CIDTs are becoming available to detect infections caused by pathogens not routinely sought by standard laboratory methods. One of these is enterotoxigenic E. coli, an important cause of travelers’ diarrhea (8).

More work is needed to extend the benefits of CIDT to the public health sector. During this initial period when clinical laboratories are transitioning to the use of CIDTs, reflex culturing†† of specimens with positive CIDT reports should be considered for bacterial pathogens to obtain isolates needed for public health practice. For the future, expedited research and development are needed to create methods to detect the genetic sequences of pathogens directly and rapidly from stool specimens, which has the potential to benefit both clinical and public health practice, because subtype, resistance profile, and other features can be obtained from the genetic sequence.