What laboratory tests should be ordered for a stool sample?

Laboratory Tests for Stool Samples

For optimal diagnostic yield, 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

Optimal Specimen Collection

• The optimal specimen for laboratory diagnosis of infectious diarrhea is a diarrheal stool sample that takes the shape of the container 1
• Fresh stool is preferred for detection of viral and protozoal agents, and C. difficile toxin 1
• For bacterial infections only, if a timely diarrheal stool sample cannot be collected, a rectal swab may be used as an alternative, though with reduced sensitivity 1, 2
• Molecular techniques are generally more sensitive and less dependent on specimen quality than traditional culture methods 1

Core Diagnostic Tests Based on Clinical Presentation

1. Patients with Fever, Bloody Diarrhea, or Severe Symptoms

• Standard bacterial pathogens:

  • Salmonella, Shigella, Campylobacter (routine stool culture or NAAT)
  • Yersinia (specialized culture or molecular assay)
  • STEC (culture for E. coli O157:H7 and Shiga toxin testing)
  • C. difficile (NAAT, GDH antigen with toxin detection)

• Testing methods:

  • STEC O157 should be assessed by culture
  • Non-O157 STEC should be detected by Shiga toxin or genomic assays
  • Sorbitol-MacConkey agar or chromogenic agar is recommended to screen for O157:H7 STEC 1

2. Patients with Persistent Diarrhea (>14 days)

• Parasitic testing:
  • Ova and parasite examination including permanent stained smears or NAAT
  • Specific tests for:
    • Giardia lamblia (EIA or NAAT)
    • Cryptosporidium (Direct fluorescent immunoassay, EIA, or NAAT)
    • Cyclospora, Cystoisospora (Modified acid-fast stain, UV fluorescence microscopy, or NAAT)
    • Entamoeba histolytica (species-specific immunoassay or NAAT) 1

3. Special Circumstances

• Immunocompromised patients:

  • Broader testing for bacterial, viral, and parasitic agents
  • Additional testing for Cryptosporidium, Cyclospora, Cystoisospora, microsporidia, Mycobacterium avium complex, and cytomegalovirus 1

• Recent travel or outbreak settings:

  • Test for Vibrio species in patients with rice water stools or shellfish consumption
  • Consider broader testing based on epidemiologic risk factors 1

Advanced Diagnostic Approaches

Molecular Testing Options

• Multiplex PCR panels can simultaneously detect multiple enteric pathogens with higher sensitivity than conventional methods 3, 4
• These panels typically include:
  • Bacterial pathogens: Salmonella, Shigella, Campylobacter, C. difficile, STEC, Vibrio, Yersinia
  • Viral pathogens: Norovirus, Rotavirus, Adenovirus
  • Parasites: Giardia, Cryptosporidium, Entamoeba 3

Blood Culture Indications

• Blood cultures should be obtained from:
  • Infants <3 months of age
  • Patients with signs of septicemia
  • Suspected enteric fever
  • Immunocompromised patients
  • Patients with certain high-risk conditions (e.g., hemolytic anemia)
  • Travelers from enteric fever-endemic areas with febrile illness 1

Common Pitfalls and Practical Considerations

1. Avoid over-testing:

   • Multiple stool specimens for ova and parasite examination have low incremental yield; a single comprehensive examination is sufficient in most cases 5
   • Implement the "3-day rule" - specimens from patients with diarrhea developing after 3 days of hospitalization have very low yield when cultured for standard bacterial pathogens 1

2. Consider test limitations:

   • Rectal swabs have limited sensitivity (65.6%) compared to stool samples, especially for viral pathogens and parasites 2
   • Molecular techniques may detect pathogens at levels below clinical significance 6

3. Correlation with clinical findings:

   • In Campylobacter infections, fecal inflammatory markers (calprotectin) correlate with bacterial load and positive culture results 6
   • Consider the clinical context when interpreting positive molecular test results in the absence of positive cultures

4. Testing for C. difficile:

   • Testing should be considered in patients >2 years of age with history of diarrhea following antimicrobial use
   • A single diarrheal stool specimen is sufficient for detection of toxin or toxigenic C. difficile strain
   • Multiple specimens do not increase yield 1

By following these evidence-based recommendations, clinicians can optimize the diagnostic yield of stool testing while minimizing unnecessary tests and costs.