What stool cultures and additional tests should be ordered for a patient with diarrhea, considering travel history, immunosuppression, recent antibiotic use, and severity of symptoms?

What Stool Cultures to Order for Diarrhea

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

Standard Testing Panel

The core bacterial pathogens to test in acute diarrhea include:

• Salmonella, Shigella, Campylobacter, and Yersinia should be included in routine stool culture orders for patients meeting clinical criteria 1
• C. difficile toxin testing is essential if the patient has antibiotic exposure within the preceding 8-12 weeks 2
• STEC detection must use methods that detect Shiga toxin (or genes encoding them) and distinguish E. coli O157:H7 from other STEC serotypes 1
• Yersinia testing must be specifically requested because it is not included in standard bacterial stool culture panels—this is a critical pitfall to avoid 1

Clinical Triggers for Testing

Order stool cultures when patients have any of the following:

• Fever with diarrhea 1
• Bloody or mucoid stools 1, 3
• Severe abdominal cramping or tenderness 1
• Signs of sepsis or systemic illness 1, 3
• Persistent diarrhea lasting weeks even without fever 2

Special Population Considerations

Immunocompromised Patients

• Perform a broad differential diagnosis including bacterial culture, viral studies, and parasitic examination 1
• For AIDS patients with persistent diarrhea, add testing for Cryptosporidium, Cyclospora, Cystoisospora, Microsporidia, Mycobacterium avium complex, and Cytomegalovirus 1

Travel History

• Test for parasitic infections (Cryptosporidium, Giardia, Cyclospora, Cystoisospora, Entamoeba histolytica) in patients with travel to endemic areas and persistent diarrhea 2
• Consider enteric fever testing (blood cultures, not serology) only when a febrile patient has traveled to endemic areas or consumed foods prepared by people with recent endemic exposure 2

Pediatric Considerations

• School-aged children with right-lower-quadrant pain mimicking appendicitis warrant Yersinia testing 1
• Infants and young children with exposure to raw or undercooked pork products require Yersinia testing 1
• Blood cultures should be obtained in all infants younger than 3 months regardless of presentation 1, 3

Specimen Collection

• A single diarrheal stool specimen is optimal for laboratory diagnosis 1, 2
• If timely diarrheal stool cannot be collected, a rectal swab may be used for bacterial detection 1

Testing Methods: Traditional vs. Molecular

The evidence shows a significant advantage for molecular methods:

• Molecular multiplex PCR panels detect pathogens with 100% sensitivity compared to 52.9-76.9% for traditional culture 4
• Molecular screening increases total detection rates from 6.4% to 19.2% compared to conventional methods 5
• Results are available within a single working day versus several days for culture 5

However, there are important caveats:

• All positive culture-independent tests should be followed by culture if isolate submission is required for public health reporting or antimicrobial susceptibility testing would affect care 1
• Molecular tests detect DNA, not necessarily viable organisms, so clinical context is essential when interpreting results 1
• Avoid over-testing with multiplex panels in hospitalized patients to prevent overtreatment and increased costs 6

Critical Pitfalls to Avoid

• Never forget to specifically request Yersinia testing—it is routinely omitted from standard panels 1
• Do not order typhoid-specific tests in afebrile patients—fever is nearly universal in enteric fever 2
• Do not rely on serological tests (Widal, Typhidot) for enteric fever diagnosis—blood cultures are the gold standard 2
• Avoid antibiotics in STEC O157 and Shiga toxin 2-producing STEC due to hemolytic uremic syndrome risk 3
• Do not overlook parasitic causes in persistent diarrhea without fever 2

Additional Testing Based on Presentation

For Bloody Diarrhea

• Prioritize testing for Salmonella, Shigella, Campylobacter, Yersinia, and STEC 1
• Use sorbitol-MacConkey agar or chromogenic agar to screen for O157:H7 STEC 1

For Persistent/Chronic Diarrhea

• Parasitic infections are the most likely cause when diarrhea persists for weeks without fever 2
• Test for Cryptosporidium, Giardia, Cyclospora, Cystoisospora, and Entamoeba histolytica 2

For Recent Antibiotic Use

• C. difficile testing is mandatory with antibiotic exposure in the preceding 8-12 weeks 2