What are the recommended stool studies for diagnosing gastrointestinal infections?

Recommended Stool Studies for Diagnosing Gastrointestinal Infections

Stool testing should be performed for Salmonella, Shigella, Campylobacter, Yersinia, C. difficile, and Shiga toxin-producing E. coli (STEC) in patients with diarrhea accompanied by fever, bloody or mucoid stools, severe abdominal cramping or tenderness, or signs of sepsis. 1

General Testing Recommendations

• Culture-independent diagnostic testing (CIDT), including multiplex molecular panels, is preferred as the first-line approach for detecting multiple bacterial, viral, and parasitic pathogens simultaneously 2, 3
• A single diarrheal stool specimen (one that takes the shape of the container) is the optimal sample for laboratory diagnosis of infectious diarrhea 1
• If a timely diarrheal stool sample cannot be collected, a rectal swab may be used for detection of bacterial infections 1
• Diagnostic testing is not recommended for most cases of uncomplicated diarrhea that resolves within a week 2, 4

Testing Based on Clinical Presentation

Bloody or Mucoid Stools

• Test for Salmonella, Shigella, Campylobacter, Yersinia, and STEC 1
• For STEC, use methods that detect Shiga toxin (or genes that encode them) and distinguish E. coli O157:H7 from other STEC serotypes 1
• Sorbitol-MacConkey agar or appropriate chromogenic agar is recommended to screen for O157:H7 STEC 1

Persistent or Chronic Diarrhea

• Test for parasitic infections including Cryptosporidium spp., Giardia lamblia, Cyclospora cayetanensis, Cystoisospora belli, and Entamoeba histolytica 1, 5
• For travelers with diarrhea lasting 14 days or longer, evaluate for intestinal parasitic infections 1

Specific Clinical Scenarios

• Persistent abdominal pain: Test for Yersinia enterocolitica, especially in school-aged children with right lower quadrant pain mimicking appendicitis 1
• Large volume rice water stools: Test for Vibrio species, particularly with exposure to salty/brackish waters, consumption of raw/undercooked shellfish, or travel to cholera-endemic regions 1
• Recent antibiotic exposure: Test for Clostridioides difficile in patients >2 years of age with diarrhea following antimicrobial use and in those with healthcare-associated diarrhea 1, 2
• Suspected enteric fever: Perform blood cultures and stool cultures; bone marrow cultures may be particularly valuable if antimicrobials have been administered 1

Special Populations

Immunocompromised Patients

• Perform a broad differential diagnosis with evaluation of stool specimens by culture, viral studies, and examination for parasites 1, 6
• For patients with AIDS and persistent diarrhea, conduct additional testing for:
  • Cryptosporidium
  • Cyclospora
  • Cystoisospora
  • Microsporidia
  • Mycobacterium avium complex
  • Cytomegalovirus 1

Outbreak Settings

• Consider a broader set of bacterial, viral, and parasitic agents regardless of the presence of fever, bloody stools, or other markers of severe illness 1
• Selection of agents for testing should be based on host and epidemiologic risk factors, ideally coordinating with public health authorities 1
• Test specimens from people involved in an outbreak per public health department guidance 1

Infants and Children

• Obtain blood cultures from infants <3 months of age with diarrhea 1
• Consider testing for rotavirus in unvaccinated children, though incidence has decreased by up to 90% with vaccination 2

Diagnostic Methods

• Multiplex PCR panels: Provide higher sensitivity and faster turnaround time than traditional methods 2, 3
• Stool culture: Traditional method for identifying bacterial pathogens but less sensitive than molecular methods 5, 3
• Toxin detection: Essential for diagnosing C. difficile and STEC infections 5, 4
• Microscopy: Used for parasite identification but less sensitive than molecular methods 3

Important Caveats

• Clinical consideration should be included when interpreting results of multiplex molecular tests since these assays detect DNA and not necessarily viable organisms 1
• All specimens that test positive by culture-independent diagnostic testing should be cultured if isolate submission is requested or required under public health reporting rules 1
• Culture may be required in situations where antimicrobial susceptibility testing results would affect care or public health responses 1
• Serologic tests should not be used to diagnose enteric fever 1