Stool Sample: Collection and Transport

We all know microbiological specimens must be promptly transported to the laboratory within a few hours. If there is a delay, special transport media may be needed depending upon the types of specimens. In this blog post, I am sharing indications when a fecal or stool specimen is needed and the collection & transport of such specimen.

S. dysenteriae serotype 1 and V. cholerae are the two etiologic agents responsible for most epidemic diarrhea in the developing world, contributing substantially to the burden of morbidity and mortality.

Fecal specimens in the laboratory

Once specimens have arrived at the laboratory, the Microbiologist should follow standard operating procedures to isolate the suspected etiologic agent. Routine culture of the fecal specimen should include Salmonella, Shigella, and Campylobacter; specify Vibrio, Aeromonas, Plesiomonas, Yersinia, Escherichia coli O157:H7, if needed. In an outbreak situation, dysentery or cholera is usually suspected based on field reports by health personnel.

Although diarrheal illnesses can be diagnosed by the appearance of the stool to some extent, for example, it’s dysentery if the stool contains blood and mucus, and it may be cholera if it is watery. But this “bloody” versus “watery” distinction is by no means definitive. Diarrhea caused by Shigella, for example, is only bloody approximately 50% of the time, and many agents lead to watery diarrhea. 

Laboratories may also receive fecal (i.e., stool) specimens from patients suspected of typhoid fever. Stool cultures may be positive during the first week of fever and 2–3 weeks into the disease.

Caution: Do not perform routine stool cultures for patients whose length of stay in the hospital exceeds 3 days and whose admitting diagnosis was not diarrhea; these patients should be tested for Clostridium difficile.

Collection of stool

  1. Stool samples should be collected in clean, leak-proof containers without disinfectant or detergent residue and with tight-fitting, leak-proof lids.
  2. Unpreserved stool should be refrigerated, if possible, and processed within 2 hours after collection.
  3. Specimens that cannot be cultured within 2 hours of collection should be placed in a transport medium and refrigerated immediately.
Fecal specimen collecting tubes
Fecal specimen collecting tubes

Caution: Specimens should not be collected from bedpans, because the bedpans may contain residual disinfectant or other contaminants.

Transport media for fecal specimens

Media appropriate for the transport of fecal specimens that are suspected of containing Shigella, Vibrio cholerae, or Salmonella (including serotype Typhi) specimens are:

  1. Cary-Blair transport medium
    High pH (8.4)
    Medium of choice for transport and preservation of V. cholerae. Cary-Blair transport medium can transport many bacterial enteric pathogens, including Shigella, Salmonella, and Vibrio cholerae.
  2. Amies’ and Staurt’s transport media
    Acceptable for Shigella and Salmonella (including ser. Typhi), but they are inferior to Cary-Blair for transport of V. cholerae.
  3. Alkaline peptone water
    This medium may be used to transport V. cholerae, but this medium is inferior to Cary-Blair and should be used only when the Cary-Blair medium is unavailable. Alkaline peptone water should not be used if the subculture will be delayed more than 6 hours from the time of collection because other organisms will overgrow vibrios after 6 hours.
  4. Buffered glycerol saline (BGS)
    It’s a liquid medium that can be used for Shigella, but this transport medium is unsuitable for the transport of V. cholerae.

Rejection of fecal Specimens

Stool specimens are unacceptable if any of the following conditions apply;

  • The information on the label does not match the information in the requisition
  • The specimen has not been transported in the proper medium
  • The quantity of specimens is insufficient for testing


  1. Thomas, V., Clark, J., & Doré, J. (2015). Fecal microbiota analysis: an overview of sample collection methods and sequencing strategies. Future microbiology, 10(9), 1485–1504.
  2. Ahlquist, D. A., Schwartz, S., Isaacson, J., & Ellefson, M. (1988). A stool collection device: the first step in occult blood testing. Annals of internal medicine, 108(4), 609–612.

Acharya Tankeshwar

Hello, thank you for visiting my blog. I am Tankeshwar Acharya. Blogging is my passion. As an asst. professor, I am teaching microbiology and immunology to medical and nursing students at PAHS, Nepal. I have been working as a microbiologist at Patan hospital for more than 10 years.

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