Bacterial Gastroenteritis, PCR

Infectious gastroenteritis (IGE) is a major global health concern, contributing significantly to both morbidity and mortality. An estimated 2,195 children die each day from IGE, and the condition also contributes to serious complications such as malnutrition, stunting, and cognitive impairment. While diarrheal disease is more prevalent in developing nations, industrialized countries are not exempt. For instance, in the United States, approximately 178.8 million cases of gastrointestinal illness occur annually, resulting in 474,000 hospitalizations and 5,000 deaths. Despite this high burden, around 80% of these cases lack a specific etiologic diagnosis. Among the identified causes, norovirus and Salmonella spp. are the most common foodborne pathogens, accounting for an estimated 5.5 million and 1.0 million cases per year, respectively. Clostridium difficile is the leading cause of healthcare- and antibiotic-associated diarrhea in the U.S., with over 300,000 cases annually and estimated healthcare costs exceeding $1 billion.

The clinical presentation of IGE, predominantly diarrhea, is largely nonspecific and does not reliably indicate the causative pathogen, whether bacterial, viral, or parasitic. In developing nations, a syndromic approach based on diarrhea type (acute watery, persistent, or bloody) is commonly used for diagnosis. Conversely, industrialized countries typically employ various diagnostic tests, including antigen assays, culture, microscopy, and PCR. However, clinicians often face challenges in selecting appropriate tests, as it may not be clear which pathogens are included in each diagnostic panel. This can result in missed diagnoses, delayed results, and reliance on external reference laboratories. Consequently, the turnaround time for stool testing may span from under an hour to several days or even weeks, reducing the clinical utility of identifying the pathogen in time to influence treatment decisions.

To overcome these limitations, clinical laboratories are increasingly adopting multiplexed molecular assays that allow for the simultaneous detection of multiple gastrointestinal pathogens. These assays provide a more comprehensive and efficient diagnostic solution by targeting bacteria, viruses, and parasites directly from stool specimens collected in Cary-Blair transport media. This approach significantly improves diagnostic accuracy, reduces turnaround time, and enhances clinical and public health responses. By enabling the rapid identification of multiple etiologic agents, multiplexed testing supports better patient management, infection control measures, and the implementation of targeted public health interventions.

References

Buss SN, Leber A, Chapin K, Fey PD, Bankowski MJ, Jones MK, Rogatcheva M, Kanack KJ, Bourzac KM. Multicenter evaluation of the BioFire FilmArray gastrointestinal panel for etiologic diagnosis of infectious gastroenteritis. J Clin Microbiol. 2015 Mar;53(3):915-25. doi: 10.1128/JCM.02674-14. Epub 2015 Jan 14. PMID: 25588652; PMCID: PMC4390666.

Riddle MS, DuPont HL, Connor BA. ACG Clinical Guidelines: Diagnosis, Treatment and Prevention of Acute Diarrheal Infections in Adults. Am J Gastroenterol. 2016 May;111(5):602-622. PubMed 27068718