Collection and Transport of Stool Specimens

Last updated on June 7th, 2021

We all know that microbiological specimens must be promptly transported to the laboratory preferably within 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 talking about indications when fecal specimen is needed and 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 fecal specimen should include Salmonella, Shigella, and Campylobacter; specify Vibrio, Aeromonas, Plesiomonas, Yersinia, Escherichia coli O157:H7, if needed. In an outbreak situation, usually, either dysentery or cholera is suspected on the basis of field reports of 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 the stool 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 there are many agents that lead to watery diarrhea. 

Laboratories may also receive fecal (i.e., stool) specimens from patients who are suspected to have typhoid fever. Stool cultures may be positive during the first week of fever and may be positive 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. Stools 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 a maximum of 2 hours after collection.
  3. Specimens that cannot be cultured within 2 hours of collection should be placed in transport medium and refrigerated immediately.

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 to contain 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 be used to 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 Cary-Blair medium is not available. 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 specimen is insufficient for testing
About Acharya Tankeshwar 474 Articles
Hello, thank you for visiting my blog. I am Tankeshwar Acharya. Blogging is my passion. I am working as an Asst. Professor and Microbiologist at Department of Microbiology and Immunology, Patan Academy of Health Sciences, Nepal. If you want me to write about any posts that you found confusing/difficult, please mention in the comments below.


  1. For ordinary routine test sample these days collected by testing hospitals, how long the stool in particular and in general other test samples need to be preserved. Because in some cases rechecking may be required.
    Is there a standard practice or Medical council notification on preservation of such samples?

  2. hello Prof.
    thanks so much for your blogging, i enjoy reading them – so helpful in my studies and i am learning a lot.
    Can you kindly clear out and outline the stages + procedures in lab stool processing (such what comes 1st gram staining, ZN staining culture …) and probably the interpretation

  3. Hi all, I am new. I searcing if any screening guidline for assessing laboratory/institution who can do stool testing: such as collection, packaging-keeping, transporation, storage, test types..etc? I am really appreciated in advance for your help on this. regards

  4. Thank you for this! What medium can I use to transport fecal sample when not using swab stick? I want a direct sample

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