In which clinical situations (acute or persistent diarrhea, chronic diarrhea, bloody stool, iron‑deficiency anemia, colorectal cancer screening, malabsorption, immunosuppression, recent antibiotic use, recent travel, or infants/young children) should stool testing be ordered?

When to Order Stool Testing: Clinical Indications

Order stool testing in patients with chronic diarrhea (>4 weeks) after initial screening blood tests, in acute diarrhea with fever/bloody stools/severe symptoms, in immunocompromised patients, and when specific risk factors for infection or inflammation are present. 1, 2

Initial Screening Approach for Chronic Diarrhea

All patients with chronic diarrhea require basic stool testing alongside blood work as part of the initial diagnostic workup. 1

• Perform stool tests for inflammation (fecal calprotectin) and infection screening in all chronic diarrhea cases before making a diagnosis of IBS 1
• Blood tests (CBC, ESR, CRP, celiac serology, thyroid function) should be done concurrently with stool studies 1
• Fecal calprotectin is specifically recommended to exclude colonic inflammation in patients under age 40 suspected of having IBS 1

Acute Diarrhea: When Stool Testing is Mandatory

Order stool cultures and testing immediately when acute diarrhea presents with any of these features: 2

• Fever accompanying diarrhea 2
• Bloody or mucoid stools 2
• Severe abdominal cramping or tenderness 2
• Signs of sepsis 2
• Severe dehydration 3

For these presentations, test specifically for Salmonella, Shigella, Campylobacter, Yersinia, C. difficile, and Shiga toxin-producing E. coli (STEC) 2. A single diarrheal stool specimen is optimal for diagnosis 2.

Do not routinely order stool tests in self-limiting acute diarrhea without these features. 3

Special Population Requirements

Immunocompromised Patients

Perform broad stool testing including culture, viral studies, and parasite examination in all immunocompromised patients with diarrhea. 2

• For AIDS patients with persistent diarrhea, add testing for Cryptosporidium, Cyclospora, Cystoisospora, Microsporidia, Mycobacterium avium complex, and Cytomegalovirus 2
• Blood cultures are mandatory in immunocompromised patients when infection is suspected 2

Recent Antibiotic Use

Test for C. difficile toxin in any patient with diarrhea following recent antibiotic exposure. 2, 4

Recent Travel to Endemic Areas

Order stool ova and parasite (O&P) examination in patients with: 5

• Travel to endemic areas within the past several weeks 5
• Diarrhea lasting >7 days 5
• Additional risk factors: smoking, prior parasitic disease, HIV-positive status, or institutionalization 5

Avoid routine inpatient O&P testing in patients without these specific risk factors, as the yield is only 2.15%. 5

Infants and Young Children

Order stool cultures including Yersinia testing in infants and young children with: 2

• Exposure to raw or undercooked pork products 2
• Right lower quadrant abdominal pain mimicking appendicitis 2
• Fever with epidemiologic risk factors 2

Blood cultures are mandatory in all infants <3 months with suspected gastrointestinal infection 2.

Specific Clinical Scenarios Requiring Stool Testing

Bloody Stool or Iron-Deficiency Anemia

Order fecal immunochemical testing (FIT) in patients with altered bowel habit without visible rectal bleeding to guide investigation priority. 1

• Colonoscopy with biopsies takes precedence over stool testing when colorectal cancer or inflammation is suspected 1
• Test stool for Salmonella, Shigella, Campylobacter, Yersinia, and STEC in bloody diarrhea 2

Suspected Malabsorption

Order stool elastase testing when fat malabsorption is suspected. 1

• Stool studies help categorize diarrhea as watery, fatty, or inflammatory when the differential diagnosis is broad 6, 7
• Consider stool testing for Giardia in suspected malabsorptive diarrhea with weight loss 4

Persistent Symptoms Despite Normal Initial Workup

Repeat stool tests for malabsorption and infections (especially in elderly or immunocompromised) when symptoms persist after negative first-line investigations. 1

Suspected Microscopic Colitis

Colonoscopy with biopsies (not stool testing alone) is required to diagnose microscopic colitis. 1

However, fecal calprotectin may be elevated and can prompt this investigation 1.

Key Testing Pitfalls to Avoid

• Do not order routine stool cultures in immunocompetent patients with chronic diarrhea (>4 weeks), as infectious causes are uncommon. 1 Focus instead on inflammatory markers and malabsorption studies 1
• Explicitly request Yersinia testing on stool culture orders, as it is not included in standard bacterial panels. 2
• Do not rely solely on multiplex molecular tests without clinical context, as they detect DNA rather than viable organisms. 2
• Perform laxative screening early in specialist referral practice for chronic diarrhea, as factitious diarrhea becomes increasingly common. 1

Age-Based Considerations

In patients under 45 years with typical IBS symptoms and negative screening tests (including stool calprotectin), a diagnosis can be made without further stool testing. 1

Patients under 45 with atypical or severe symptoms and documented diarrhea require stool testing and further evaluation. 1