Stool Culture (Routine)


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Subject: Stool Culture (Routine)

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Routine stool culture should be considered for patients with acute diarrheal illness who are producing frequent, loose stools. Nausea, abdominal pain, and vomiting may be present. Fever may be present, but is not a prominent feature in uncomplicated enteric infection. Fluid loss, especially in infants and small children, may be severe and associated with complications including electrolyte imbalance and cardiovascular instability. 

Special Collection and Transport Instructions

  • Acceptable specimens: liquid stool (feces), rectal swab.

  • Sterile collection containers are not required. Specimens may be collected in clean containers. The container should be free of detergent or preservative.

  • Specimens should be transported promptly to the laboratory. If transport will be delayed >2 hours, use of a transport medium, like Cary-Blair, is recommended.

  • Three specimens, collected on consecutive days, are recommended for sensitive detection of enteric pathogens, especially for patients at risk for complication or at increased risk for transmission of enteric pathogens, like food handlers.

  • Specimens collected on toilet paper or diapers are not acceptable. Specimens contaminated by urine are not acceptable.


  • The routine stool culture is used to detect GI infections caused by enteric bacterial pathogens. The target pathogens identified by routine stool culture may vary somewhat among laboratories, but all should be capable of detecting Salmonella, Shigella, and Campylobacter species. Other pathogens may be included, like Shiga toxin–producing E. coli, depending on local prevalence. Detection of other enteric pathogens may require special testing.

  • Method: Stool specimens are typically inoculated onto several agar media, including a nonselective medium (e.g., SBA), a mildly selective differential medium (e.g., MacConkey agar), and a moderately selective differential medium (e.g., Hektoen enteric agar). Some laboratories have used selective broth enrichment (e.g., Selenite broth) prior to plate inoculation, but the cost-effectiveness of these strategies has been questioned. Selective agar media and incubation at increased temperature (42°C) and microaerophilic conditions are used for isolation of enteric Campylobacter species.

  • Turnaround time: Cultures are examined for growth at 24 and 48 hours. Suspicious colonies are isolated and confirmatory testing performed.


  • Expected results: Negative.

  • Positive results: Any growth of Salmonella, Shigella, Campylobacter or other enteric pathogen.

  • Negative results: The probability infection is decreased but is not excluded. Additional stool cultures or testing for other enteric pathogens should be considered.


  • Effective detection of enteric infection due to enterohemorrhagic E. coli (e.g., E. coli O157:H7), Yersinia enterocolitica, Vibrio species, Aeromonas species, C. difficile, or other bacterial pathogens requires special cultures for sensitive detection.

  • Diarrheal illness caused by parasitic or viral pathogens requires special test methods.

  • C. difficile testing should be considered as an alternative to routine enteric pathogen testing for inpatients.

  • Stool culture may be negative in invasive enteric infections, like typhoid fever. Blood cultures are recommended for primary gastrointestinal infections that progress to significant fever associated with signs of systemic infection.

  • Shigella species may not survive broth enrichment techniques.

  • Common pitfalls:

    • Rectal swabs can collect only a small amount of feces; their use should be restricted to infants.

    • Shigella species are fastidious and may not survive changes in stool pH that occur after passage. Rapid transport and/or the use of transport media is important for reliable isolation by culture.

Other Considerations

  • Direct detection of Campylobacter antigen in stool is an alternative to culture for diagnosis of enteric campylobacteriosis. Sensitivity of antigen testing is 80–96% with specificity approximately 98%.

  • Absence of normal fecal flora or the presence of predominant growth of yeast, S. aureus, or Pseudomonas aeruginosa can be recognized by inspection of the SBA plate, providing clinically relevant information about alternative diagnoses.

  • Oxidase testing may be performed on SBA isolated with heavy growth to screen for unexpected enteric infection caused by Vibrio, Aeromonas, or Plesiomonas species.