Use and interpretation of enteropathogen multiplex nucleic acid amplification tests in patients with suspected infectious diarrhea

Acute diarrheal illness due to gastrointestinal infection is a significant cause of morbidity and mortality in the United States and around the world. Determining the causative organism in a timely manner assists with patient care, identifying outbreaks, providing infection control, and administering antimicrobial therapy when indicated. Traditional diagnostic modalities based on culture and immunoassays are limited by their low sensitivity and long turnaround time. Nucleic acid amplification tests (NAATs) for enteric pathogens allow for the syndromic testing of stool for multiple pathogens simultaneously and have higher sensitivity with a shorter turnaround time. However, by not isolating the organism, NAATs do not provide drug susceptibility or confirmatory identification. Furthermore, NAATs cannot distinguish between true infection and carrier states. Nevertheless, several studies have demonstrated the cost-effectiveness of multiplex NAATs by reducing the length of hospital stay and cost of isolation. Five platforms are currently approved by the US Food and Drug Administration that can detect different bacteria, parasites, and viruses. The sensitivity and specificity of each platform depends on the targeted pathogens and whether the tests are performed on fresh stool, frozen stool, or in transport media. Overall, these tests have high sensitivity and specificity of more than 90% when used in symptomatic patients. Thus, multiplex NAAT gastrointestinal platforms offer several advantages compared to traditional methods. However, the interpretation of the results requires acknowledging the limitations of the tests and exercising clinical judgment. More studies are needed to establish the cost-effectiveness of multiplex NAATs and their impact on antibiotic stewardship and clinical outcomes.