Which stool tests should be performed to evaluate a patient with suspected infectious diarrhea?

Stool Testing for Infectious Diarrhea

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

Core Testing Strategy

The 2017 IDSA guidelines provide clear direction on when and what to test:

Standard Bacterial Panel

Test for the following pathogens when clinical indicators are present:

• Salmonella species
• Shigella species
• Campylobacter species
• Yersinia enterocolitica
• C. difficile
• STEC O157 (by culture) and non-O157 STEC (by Shiga toxin or genomic assays)

The optimal specimen is a diarrheal stool sample that takes the shape of the container 1. If timely diarrheal stool cannot be collected, a rectal swab may be used for bacterial detection, though molecular techniques are generally more sensitive and less dependent on specimen quality 1.

Testing Methods Available

Modern laboratories offer two main approaches 1:

Traditional Methods

• Routine stool culture for Salmonella, Shigella, Campylobacter
• Sorbitol-MacConkey agar or chromogenic agar for STEC O157:H7
• Shiga toxin immunoassay for non-O157 STEC
• C. difficile: NAAT or GDH antigen with toxin detection

Multiplex Nucleic Acid Amplification Tests (MP-NAAT)

These gastrointestinal panels can detect multiple pathogens simultaneously and distinguish between Shiga toxins 1 and 2. However, interpret MP-NAAT results with clinical consideration because these assays detect DNA, not necessarily viable organisms 1.

Special Circumstances Requiring Additional Testing

Yersinia enterocolitica

Test specifically when 1:

• Persistent abdominal pain (especially school-aged children with right lower quadrant pain mimicking appendicitis)
• Fever with epidemiologic risk (infants with exposure to raw/undercooked pork products)

Vibrio species

Test when patient has 1:

• Large volume rice water stools, OR
• Exposure to salty/brackish waters, OR
• Consumption of raw/undercooked shellfish, OR
• Travel to cholera-endemic regions within 3 days of symptom onset

Immunocompromised Patients

A broad differential diagnosis is essential 1. Test for:

• Standard bacterial pathogens (culture)
• Viral studies
• Parasites (ova and parasite examination)

For AIDS patients with persistent diarrhea, add testing for 1:

• Cryptosporidium
• Cyclospora
• Cystoisospora
• Microsporidia
• Mycobacterium avium complex
• Cytomegalovirus (CMV)

Traveler's Diarrhea

Diagnostic testing is NOT recommended for most uncomplicated cases 1. Test only when:

• Diarrhea lasts ≥14 days (evaluate for parasites)
• Recent antimicrobial use within 8-12 weeks (test for C. difficile)
• Fever, bloody diarrhea, severe dehydration, or prolonged course >5 days

Parasitic Testing

For parasitic infections, perform ova and parasite examination with permanent stained smear or NAAT 1. Specific tests include:

• E. histolytica: Species-specific immunoassay or NAAT
• Giardia lamblia: EIA or NAAT
• Cryptosporidium: Direct fluorescent immunoassay, EIA, or NAAT
• Cyclospora, Cystoisospora: Modified acid-fast stain on concentrated specimen

Critical Pitfalls to Avoid

1. Do NOT use fecal leukocyte examination or stool lactoferrin detection to establish the cause of acute infectious diarrhea 1. These tests lack diagnostic utility.

2. For positive MP-NAAT results, culture confirmation is required when isolate submission is needed for public health reporting or when antimicrobial susceptibility testing would affect care 1.

3. STEC O157 requires BOTH culture AND Shiga toxin testing because O157 is the most consistently virulent STEC in the United States, and early identification aids clinical management and public health control 1.

4. Bloody stools are NOT an expected manifestation of C. difficile infection 1. If bloody diarrhea is present, prioritize testing for other bacterial pathogens.

When NOT to Test

Do not perform stool testing for 1:

• Uncomplicated watery diarrhea in immunocompetent adults without fever, blood, or severe symptoms
• Most cases of uncomplicated traveler's diarrhea
• Follow-up testing after symptom resolution (except when required by public health authorities for return to work/childcare) 1

Outbreak Situations

In suspected outbreaks (multiple people with diarrhea sharing a common meal or sudden rise in cases), test for a broader set of bacterial, viral, and parasitic agents regardless of symptom severity 1. Coordinate testing selection with public health authorities.