What is the utility of stool cultures in the emergency department for evaluating patients with acute diarrhea, particularly in high-risk populations such as the elderly, young children, or immunocompromised (immunocompromised) individuals?

Stool Cultures in the Emergency Department for Acute Diarrhea

Stool cultures should be obtained selectively in the emergency department, not routinely, and are indicated only when patients present with fever, bloody or mucoid stools, severe abdominal cramping or tenderness, signs of sepsis, or belong to high-risk populations (infants <3 months, immunocompromised patients, or those with specific epidemiologic exposures). 1

When to Order Stool Testing

Clear Indications for Stool Culture (Strong Evidence)

Order stool testing for Salmonella, Shigella, Campylobacter, Yersinia, C. difficile, and STEC when patients present with:

• Fever (documented temperature ≥38.5°C) 1, 2
• Bloody or mucoid stools 1
• Severe abdominal cramping or tenderness 1
• Signs of sepsis (tachycardia, hypotension, altered mental status) 1, 2

High-Risk Populations Requiring Testing

Always obtain stool cultures in these groups, even with less dramatic presentations:

• Infants <3 months of age 1
• Immunocompromised patients (HIV, chemotherapy, transplant recipients) requiring broad evaluation including bacterial culture, viral studies, and parasitic examination 1
• Patients with hemolytic anemia or other high-risk conditions 1
• Suspected enteric fever (travel to endemic areas, febrile illness) 1

Specific Epidemiologic Triggers

Order targeted testing based on exposure history:

• Yersinia enterocolitica: School-aged children with right lower quadrant pain mimicking appendicitis, or infants exposed to raw/undercooked pork 1
• Vibrio species: Large volume rice-water stools, exposure to brackish water, raw shellfish consumption, or travel to cholera-endemic regions within 3 days 1
• STEC: When clinical history suggests Shiga toxin-producing organisms; use methods detecting Shiga toxin and distinguishing E. coli O157:H7 from other STEC 1
• Outbreak settings: Multiple people with diarrhea sharing common meal or sudden rise in cases, coordinating with public health authorities 1

When NOT to Order Stool Cultures

Avoid routine stool cultures in:

• Uncomplicated acute watery diarrhea without fever, blood, or severe symptoms in immunocompetent adults 1
• Most cases of traveler's diarrhea unless treatment fails 1
• ICU patients with diarrhea starting >48 hours after admission (yield only 0.1% for bacterial pathogens other than C. difficile) 3

The evidence strongly supports this selective approach: among hospitalized adults with acute gastroenteritis, only 4% of stool cultures yielded pathogenic bacteria 4, and in ICU patients, the yield was even lower at 0.1% 3. However, in pediatric emergency departments with complete microbiologic evaluation, nearly half of specimens yielded pathogens when appropriately selected 5.

Critical Testing Considerations

C. difficile Testing Priority

Test for C. difficile in patients with:

• Recent antibiotic use within 8-12 weeks 6, 7
• Healthcare-associated diarrhea 6

Note that C. difficile had an 8.1% positivity rate in ICU patients versus 0.1% for other bacterial pathogens 3, and 6.6% prevalence in hospitalized patients 3, making it the highest-yield test in hospital settings.

STEC-Specific Approach

When STEC is suspected (bloody diarrhea without fever):

• Use Sorbitol-MacConkey agar or chromogenic agar to screen for O157:H7 1
• Detect Shiga toxin or genomic assays for non-O157 STEC 1
• Never give empiric antibiotics while awaiting results in immunocompetent patients, as this increases hemolytic uremic syndrome risk 7

Blood Cultures

Obtain blood cultures when:

• Infants <3 months with diarrhea 1
• Any age with signs of septicemia 1
• Suspected enteric fever 1
• Immunocompromised patients 1

Common Pitfalls to Avoid

Critical errors that worsen outcomes:

1. Giving antibiotics before testing in suspected STEC increases hemolytic uremic syndrome risk 7
2. Ordering cultures in ICU patients with hospital-acquired diarrhea (>48 hours after admission) wastes resources with 0.1% yield 3
3. Missing C. difficile testing in patients with recent antibiotic exposure, despite absence of fever or bloody stools 6, 7
4. Failing to test for parasites in immunocompromised patients with persistent diarrhea, especially those with AIDS requiring evaluation for Cryptosporidium, Cyclospora, Cystoisospora, microsporidia, and others 1
5. Not considering viral pathogens in appropriate clinical contexts, as rotavirus and norovirus are common causes 5, 8

Practical Algorithm for ED Decision-Making

Step 1: Assess severity markers

• Fever ≥38.5°C, bloody/mucoid stools, severe cramping, or sepsis signs → Order stool culture 1, 2

Step 2: Identify high-risk populations

• Age <3 months, immunocompromised, hemolytic anemia → Order stool culture 1

Step 3: Evaluate epidemiologic exposures

• Travel, outbreak, specific food exposures → Order targeted testing 1

Step 4: Consider C. difficile

• Recent antibiotics (8-12 weeks) or healthcare exposure → Test for C. difficile 6, 7

Step 5: If none of above apply

• Uncomplicated watery diarrhea in immunocompetent adult → No stool culture needed 1, 3

The 2017 IDSA guidelines provide the strongest framework 1, emphasizing that selective testing based on clinical and epidemiologic factors is more efficient than routine testing, which has consistently shown low yield in multiple studies 3, 4, 9. Physician clinical judgment, when informed by these criteria, performs nearly as well as prediction models 5.