The importance of knowing the pathogens that cause infectious gastroenteritis

Infectious gastroenteritis is the inflammation of the stomach and/or intestines caused by pathogens such as viruses, bacteria, or parasites. The disease manifests mainly with diarrhea with or without vomiting, which can, in severe cases, lead to dehydration and electrolyte imbalance. Other possible complications include muscle cramps, kidney damage, and diminished urine. Depending on the pathogen causing the infection, the release of toxins can lead to secretory diarrhea, while others cause an invasive, inflammatory diarrhea.

Many pathogens that cause infectious gastroenteritis live in the intestines of animals, such as pets or domestic animals whose products are used for human consumption. Other pathogens can live in water and be present on unwashed vegetables or pre-made salads. Many can also survive on contaminated surfaces such as kitchen counters. This means that most people are at risk of contracting infectious gastroenteritis. In 2022, a reported outbreak of norovirus—one of the leading causes of infectious gastroenteritis—was linked to raw oysters harvested in the state of Texas. The outbreak left over 300 people ill with infectious gastroenteritis.*

Gastrointestinal pathogen research enables laboratories to further understand the overall infection biology of the pathogens that cause the disease. Given the multiple pathogens and high infectiousness, it is important for laboratories to build their workflows with highly sensitive assays that can detect and differentiate between multiple pathogenic targets in the same stool sample.

Infographic: Infectious gastroenteritis

This comprehensive infographic provides an overview of the causes of infectious gastroenteritis, how it spreads, its treatment, and testing technology.

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Gastrointestinal infections infographic
On-demand webinar: Advances in Diagnostic Testing for the Bacteria, Viruses, and Parasites that cause Infectious Gastroenteritis

In this webinar, Davidson Hamer, MD, from the Boston University School of Public Health and Chobanian and Avedisian School of Medicine, discusses the challenges of infectious gastroenteritis, it’s causes and different testing technologies.

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Pathogens that cause gastroenteritis

Bacteria icon


Virus icon


Parasite icon


ShigellaNorovirusCryptosporidium parvum
SalmonellaRotavirusEntamoeba histolytica
Clostridium difficileAdenovirusGiardia lamblia
CampylobacterSapovirusCyclospora cayetanensis 
Yersinia enterocolitica/Y. pseudotuberculosisAstrovirus 
Vibrio spp  
Plesiomonas shigelloides  
Escherichia coli 

Enteric pathogen infections


Infection, signs and possible causes*

Signs of infection, transmission, and possible causes*


Viral cause

Bacterial cause

Parasitic cause

Signs of infection

  • Watery diarrhea without blood or mucus
  • Vomiting
  • Intermediate onset (24–60 hr)
  • Short symptom duration (12–60 hr)
  • Diarrhea which can be bloody/mucoid
  • Fever
  • Cramping/ bloating
  • Onset <16 hr
  • Watery diarrhea that can be foul-smelling or greasy
  • Abdominal pain/cramping

Possible vehicle of transmission

  • Contaminated food and water
  • Closed communities such as daycare centers, healthcare, or long-term care facilities
  • Food contamination
  • Animal exposure
  • Closed communities such as daycare centers, healthcare, or long-term care facilities
  • Food contamination
  • Water contamination
  • Closed communities such as daycare centers, healthcare, or long-term care facilities
  • Travel
  • Animal contact

Benefits of molecular stool testing


Real-time PCR technology has significant advantages over other methods for identifying enteric pathogens. Traditional methods like culturing, immunodiagnostics, and microscopy can be inaccurate, subjective, or prone to contamination and often require repeat testing or reflex testing. Fastidious microorganisms often cannot be grown or detected using traditional methods, and long sample processing times can delay time-to-results. Molecular tests for relevant pathogens may be unavailable or lack flexibility.


Testing methods


Petri dish showing various clusters of bacterial cultures


A sample is sent to a lab where experts encourage organisms in the sample to multiply. Then they examine the dish to identify the pathogen.

An image of a COVID-19 rapid antigen test and nasal swab

Antigen (Rapid)

Sample collection swabs are agitated in a pre-mixed solution and tested on a paper strip to return results within half an hour.

Scientist performing molecular PCR testing in a laboratory

Molecular (PCR)

Genetic material from samples collected on swabs is amplified to detect genetic traces of a specific organism, even in early stages of infection.


*Shane AL, Mody RK, et al. 2017 Infectious Diseases Society of America Clinical Practice Guidelines for the Diagnosis and Management of Infectious Diarrhea. Clin Infect Dis. 2017 Nov 29;65(12):e45-e80. doi: 10.1093/cid/cix669. PMID: 29053792; PMCID: PMC5850553.

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