BACKGROUND: The use of culture-independent diagnostic tests (CIDTs), specifically multiplex PCR gastrointestinal panels for stool specimens is increasing rapidly. We summarize Colorado’s experience with the changing diagnostic testing practices and the impact on surveillance for enteric pathogens. We also discuss challenges in interpretation of results and case reporting, isolate recovery, and adapting case investigation and exclusion.
METHODS: Colorado regularly surveys clinical laboratories on the use of CIDTs and collects information about the type and brands of tests performed. We also conduct ongoing surveillance to detect changes in laboratory practices and perform outreach to ensure correct case reporting. Colorado encourages clinical laboratories to perform reflex culture for all bacterial enteric pathogens, and requires submission of isolates or clinical material for Salmonella, Shigella, Shiga toxin-producing E. coli (STEC), Vibrio and Yersinia. Two data sources were examined: a survey of clinical laboratories conducted during spring 2016 and surveillance data from 2014–2016.
RESULTS: Prior to 2014, one clinical laboratory in Colorado was using a multiplex PCR panel to identify enteric pathogens. By spring 2016, 15 (of 50) clinical laboratories adopted multiplex PCR panels. Eight clinical laboratories perform reflex culture for Salmonella and Shigella, 2 culture for STEC, 2 culture for Campylobacter, 1 cultures for Vibrio, and 0 culture for Yersinia. During 2014-2015, 16% (569/3623) of Campylobacter, Salmonella, Shigella, STEC, Vibrio, and Yersinia cases reported were tested using PCR. In 2016, the percent of cases tested using PCR for those same pathogens increased to 42% (1003/2404). During 2016, reflex culture was performed for 90% of PCR-positive cases of Salmonella, Shigella, and STEC. Of those, isolates were recovered from 92% of PCR-positive Salmonella cases, 66% of PCR-positive Shigella cases and 62% of PCR-positive STEC cases. Reflex culture was performed for 16% of PCR-positive Campylobacter cases at clinical laboratories.
CONCLUSIONS: The percent of bacterial enteric infections detected by CIDTs is increasing. We continually perform outreach to ensure correct interpretation of results and accurate case reporting; some panels report results for multiple pathogens with similar names, but not all are reportable. Although we encourage labs to perform reflex culture, a large burden falls to the SPHL. We continue to adapt our case investigation and exclusion guidance to account for the detection of multiple pathogens and non-viable organisms. Outreach with hospital infection preventionists, laboratories, and local public health partners has been key in addressing many of the challenges posed by the rapid adoption of CIDTs in Colorado.