Recommended Stool Studies for Diagnosing Gastrointestinal Infections
For patients with diarrhea accompanied by fever, bloody or mucoid stools, severe abdominal cramping, or signs of sepsis, stool testing should include Salmonella, Shigella, Campylobacter, Yersinia, C. difficile, and Shiga toxin-producing E. coli (STEC). 1
General Testing Recommendations
- A single diarrheal stool specimen is the optimal sample for laboratory diagnosis of infectious diarrhea 1
- If a timely diarrheal stool sample cannot be collected, a rectal swab may be used for bacterial infection detection 1
- Multiplex molecular testing is preferred over traditional stool cultures as the first-line diagnostic approach due to significantly higher sensitivity and detection rates 2, 3
Testing Based on Clinical Presentation
- Bloody or mucoid stools: Test for Salmonella, Shigella, Campylobacter, Yersinia, and STEC 1
- Recent antibiotic exposure: Test specifically for Clostridioides difficile 2
- For STEC detection: Use methods that detect Shiga toxin (or genes that encode them) and distinguish E. coli O157:H7 from other STEC serotypes 1
- For E. coli O157:H7 screening: Use sorbitol-MacConkey agar or appropriate chromogenic agar 1
Special Population Considerations
- Immunocompromised patients: Perform a broader differential diagnosis with evaluation of stool specimens by culture, viral studies, and examination for parasites 1, 4
- Patients with AIDS and persistent diarrhea: Conduct additional testing for Cryptosporidium, Cyclospora, Cystoisospora, Microsporidia, Mycobacterium avium complex, and Cytomegalovirus 1
- Infants <3 months: Consider blood cultures in addition to stool studies due to higher risk of bacteremia 5
- Travel history: Expand testing to include region-specific pathogens 6
Diagnostic Methods
- Multiplex PCR panels: These detect multiple bacterial, viral, and parasitic pathogens simultaneously with significantly higher sensitivity than traditional methods 2, 3
- Stool culture: Traditional method for identifying bacterial pathogens but less sensitive than molecular methods 1
- Toxin detection: Essential for diagnosing C. difficile and STEC infections 1
- Microscopic examination: No longer first-line for parasite detection but may be used as a confirmatory test 2
Important Considerations
- Microbial studies are generally not needed for mild symptoms that resolve within a week 2
- Clinical consideration should be included when interpreting results of multiplex molecular tests since these assays detect DNA and not necessarily viable organisms 1
- All specimens that test positive by culture-independent diagnostic testing should be cultured if isolate submission is requested or required under public health reporting rules 1
- Culture may be required in situations where antimicrobial susceptibility testing results would affect care or public health responses 1
- Serologic tests should not be used to diagnose enteric fever 1
Common Pitfalls to Avoid
- Overreliance on traditional methods: Traditional stool culture and microscopy have significantly lower sensitivity compared to molecular methods, potentially missing pathogens 3
- Delayed testing: Collection of stool samples should be done promptly as some pathogens may not remain viable for extended periods 1
- Inadequate testing in immunocompromised patients: These patients require more extensive testing as they may harbor unusual or multiple pathogens 1, 4
- Failure to consider epidemiological factors: Recent travel, food exposures, or community outbreaks should guide expanded testing 5