Medical Microbiology & Diagnosis

Background: Viral gastroenteritis is a leading cause of morbidity worldwide. Evolving epidemiology, in part due to vaccines, has made identifying specific stool pathogens more relevant for clinical and public health providers. Molecular testing for gastrointestinal viruses is sensitive and effective for rapid identification of viruses from stool samples. In this study we report the prevalence of key viral pathogens in diarrheal stool specimens from a pediatric population.
Methods: From February 2014 to March 2017, remnant stool samples from patients presenting to a healthcare provider with diarrhea were examined for both bacteria (Salmonella species, Shigella species, Campylobacter species, and Shiga toxins 1 and 2) and viruses (norovirus, sapovirus, astrovirus, adenovirus, and rotavirus). Detection of targets was performed using an FDA-approved platform (BD Max™) with PCR/sequencing serving as the reference method.
Results: Of the 386 samples tested, at least one potential pathogen (viral and/or bacterial) was detected in 41.2% of specimens. 136 (35.2%) samples tested positive for at least one virus; 34 (8.8%) samples tested positive for at least one bacterium. There were 28 dual infections.
Conclusion: The most commonly detected targets were viruses. Norovirus and sapovirus were the most prevalent stool pathogens, especially in very young patients. Shigella species was the most prevalent bacteria and third most detected target overall. Rotavirus prevalence was low, but still detected in 15 (3.9%) of the samples. This may indicate that while vaccine has reduced its prevalence, it should still be considered in clinical evaluation of this population. Of note, the majority (59%) of samples were negative for viral pathogens. Providers should also consider parasites and noninfectious causes such as inflammatory bowel disease when evaluating diarrhea in a pediatric patient.