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Acute gastroenteritis is defined as an inflammation of the intestines that causes diarrhea, abdominal cramps, nausea, loss of appetite, and other symptoms of digestive upset. Each year, an estimated 1.6 million people die from infectious gastroenteritis worldwide. There are many different viruses that can cause viral gastroenteritis including norovirus, rotavirus, adenovirus, and astrovirus. Norovirus infects people of all ages and is the most common cause, with an estimated 685 million cases each year.

Diagnosing the underlying cause of acute gastroenteritis can be difficult because symptoms are not specific to each potential pathogen. One of the most dangerous complications of the illness is dehydration from loss of fluid due to diarrhea and vomiting. Although the disease severity depends on the degree of fluid loss, accurately identifying the causative pathogen is important to determine what, if any, antimicrobial therapy may be required in addition to treatment or prevention of dehydration.

Notably, the causes of gastroenteritis can vary by geographic region and by age group. Globally, rotavirus is the most common cause of pediatric gastroenteritis among children under age two, while children older than age two are more likely to be infected with Shigella, a type of bacteria. Rotavirus used to be common in the United States, but vaccination has become relatively widespread, with 68.6% of infants receiving the entire vaccine series. Now, norovirus is the most common cause of pediatric gastroenteritis in the United States. As noted in this study, the burden of the rotavirus disease, including hospitalizations and deaths, impacts low-income settings, particularly countries in sub-Saharan Africa and south-east Asia.

The variability and range in potential causes of acute gastroenteritis creates diagnostic challenges. In an article for the International Journal of Microbiology, the authors write that, “The traditional culture and microscopy procedures are time-consuming, lack sensitivity, and require special laboratory setup and well-trained staff. However, based on the advancement in molecular diagnostics and with the introduction of commercially available tests, traditional diagnostic techniques have been continuously replaced by these newer rapid antigen detection and molecular-based methods.” 

Even these newer diagnostic methods are continuing to evolve. A paper published in the BioChip Journal noted that, “A few years ago, molecular POC [Point of Care] diagnosis was limited to testing only the most common pathogens. This lack in diagnostics capability led to further downstream tests or unnecessary prescription of antibiotics.” However, advances in technology have facilitated the expansion of testing panels, including those for gastrointestinal infections.

Utilizing a syndromic, multiplex PCR approach for diagnostic testing may be helpful to physicians, particularly in severe or complex cases of pediatric gastroenteritis. With substantially faster turn-around times than traditional methods, molecular diagnostics can help physicians make treatment decisions earlier—reducing antimicrobial overuse and saving patients’ lives.


Opinions expressed in this article are not necessarily those of bioMérieux



  • Infectious Diseases