What laboratory tests should be ordered for a stool specimen?

Laboratory Testing for Stool Specimens

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

Core Bacterial Panel (Standard Stool Culture)

The foundational stool culture should routinely detect the following pathogens 1:

• Salmonella species 1
• Shigella species 1
• Campylobacter species 1
• Yersinia enterocolitica (particularly in children with right lower quadrant pain mimicking appendicitis, or infants exposed to raw/undercooked pork) 1
• Clostridioides difficile (test in patients >2 years with diarrhea following recent antimicrobial use) 1
• STEC O157 (assessed by culture on sorbitol-MacConkey or chromogenic agar) 1
• Non-O157 STEC (detected by Shiga toxin or genomic assays) 1

Critical pitfall: Confirm with your laboratory what organisms are included in "routine stool culture," as this varies by institution—a report stating "negative" or "no enteric pathogens" is insufficient without specifying which organisms were excluded. 2

Specialized Testing Based on Clinical Context

C. difficile Testing Strategy

• Use a highly sensitive test such as glutamate dehydrogenase (GDH) as the initial screen 3
• Follow positive GDH with nucleic acid amplification test (NAAT) for toxin B or enzyme immunoassay for toxins A/B to distinguish infection from colonization 3
• Test in healthcare-associated settings (assisted-living, nursing homes) immediately, as transmission and prior antibiotic exposure are common 4

Epidemiologic Risk-Based Testing

Vibrio species should be added when patients have 1:

• Large volume "rice water" stools 1
• Exposure to salty or brackish waters 1
• Consumption of raw or undercooked shellfish 1
• Travel to cholera-endemic regions within 3 days of symptom onset 1

Parasitic Testing

Order ova and parasite examination (three specimens) when 1:

• Diarrhea persists ≥14 days 1
• Travel history suggests parasitic exposure 1
• Immunocompromised status is present 1

For persistent symptoms with negative initial O&P, add Giardia ELISA (92% sensitivity, 98% specificity) 4

In immunocompromised patients (especially AIDS), expand testing to include 1:

• Cryptosporidium 1
• Cyclospora 1
• Cystoisospora 1
• Microsporidia 1
• Mycobacterium avium complex 1
• Cytomegalovirus 1

Viral Testing

Consider viral stool studies (norovirus, rotavirus, enteric adenovirus) when 1:

• Outbreak setting with multiple affected individuals 1
• Immunocompromised host 1
• Watery diarrhea without bacterial pathogen identified 1

Blood Cultures: When to Order

Obtain blood cultures in the following scenarios 1:

• Infants <3 months of age 1
• Any age with signs of septicemia 1
• Suspected enteric fever (typhoid) 1
• Systemic manifestations of infection 1
• Immunocompromised status 1
• High-risk conditions such as hemolytic anemia 1
• Travel to or contact with travelers from enteric fever-endemic areas with unexplained fever 1

Do not routinely order blood cultures for isolated mucus-containing diarrhea without fever or systemic signs 4

Outbreak Investigation

When multiple cases occur in congregate settings (nursing homes, daycare, shared meals) 1:

• Broaden testing to include bacterial, viral, and parasitic agents regardless of individual symptom severity 1
• Coordinate with public health authorities 1, 4
• Test even in the absence of fever or bloody stools 1

Testing NOT Recommended

Avoid routine stool cultures and O&P examinations on specimens collected >3 days after hospital admission 5—only 1 of 191 positive bacterial cultures and 0 of 90 positive O&P examinations came from this group, yet these specimens contribute nearly 50% of laboratory workload 5

Do not test for uncomplicated traveler's diarrhea unless treatment is specifically indicated 1

Interpretation Cautions

Multiplex molecular panels (NAAT) detect DNA from both viable and non-viable organisms 1, 4—positive results may reflect colonization rather than active infection, requiring clinical correlation 1