What Stool Culture Tests For
Stool culture is a laboratory test that specifically detects pathogenic bacteria causing infectious diarrhea, primarily targeting Salmonella, Shigella, Campylobacter, and Shiga toxin-producing E. coli (STEC), not the normal bacterial flora present in everyone's intestines. 1, 2
Primary Bacterial Pathogens Detected
Routine stool culture is designed to identify these specific disease-causing bacteria:
- Salmonella species - a common cause of bacterial gastroenteritis with fever and bloody or non-bloody diarrhea 1
- Shigella species - causes dysentery with bloody diarrhea, fever, and abdominal cramping 1
- Campylobacter species - frequently causes bloody diarrhea with fever and severe abdominal pain 1
- Shiga toxin-producing E. coli (STEC), including O157:H7 - characteristically presents with severe abdominal pain and bloody stools but minimal or no fever 1, 3, 2
Critical Distinction About E. coli
Stool cultures do NOT detect the normal commensal E. coli that lives harmlessly in everyone's intestines - they only identify specific pathogenic strains like STEC that produce disease. 2 This is a common source of confusion, as E. coli is part of normal gut flora, but only certain virulent strains cause illness.
What Stool Culture Does NOT Test For
Stool culture alone misses several important causes of gastroenteritis that require different testing methods:
- Viruses (norovirus, rotavirus, adenovirus) - require antigen detection or molecular testing 1, 4
- Parasites (Giardia, Cryptosporidium, Entamoeba) - require microscopy, antigen testing, or molecular methods 1, 5
- Clostridium difficile - requires specific toxin detection or molecular testing, not routine culture 1, 5
- Diarrheagenic E. coli pathotypes (enterotoxigenic, enteropathogenic) - require PCR detection of virulence genes 6
Modern Testing Alternatives
Culture-independent diagnostic tests (multiplex molecular panels) can simultaneously detect 15-20 bacterial, viral, and parasitic pathogens in 1 hour, compared to the 1-2 days required for traditional culture. 1, 4, 7 However, the Infectious Diseases Society of America emphasizes that positive results from molecular panels should be cultured when isolate submission is required for public health outbreak detection or when antimicrobial susceptibility testing would affect care. 1
When Stool Culture Is Indicated
The Infectious Diseases Society of America recommends stool testing in these clinical scenarios:
- Bloody or mucoid stools - suggests invasive bacterial pathogens 1, 3
- Severe abdominal cramping or tenderness - may indicate STEC or other invasive bacteria 1, 3
- Immunocompromised patients - higher risk for severe complications 1, 3
- Healthcare-associated diarrhea - though C. difficile testing takes priority 1
- Travelers with persistent diarrhea ≥14 days - though parasitic testing becomes more important 1
Critical Pitfall to Avoid
Never give empiric antibiotics to patients with bloody diarrhea while awaiting stool culture results, as this increases the risk of hemolytic uremic syndrome in STEC infections. 3 Wait for culture results to guide antimicrobial therapy, as STEC should not be treated with antibiotics.