Stool Culture

Updated: Sep 25, 2020
  • Author: Bishnu Prasad Devkota, MD, MHI, FRCS(Edin), FRCS(Glasg), FACP, FAMIA; Chief Editor: Eric B Staros, MD  more...
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Reference Range

The normal flora of the GI tract is composed of various bacteria and fungi that play a vital role in the digestion of food. They also help restrict the growth of pathogenic organisms. The use of broad spectrum antibiotics may change the balance of the normal flora, inhibiting the growth of normal flora and allowing bacteria resistant to the antibiotic to persist and overgrow. Similarly, the use of anti-neoplastic drugs can lead to bacterial overgrowth that results in abdominal pain and diarrhea.

Normal findings

Normal findings consist of normal intestinal flora. [1]



See the list below:

  • Expected results - Negative

  • Positive - Any growth of Salmonella,Shigella, Campylobacter, Yersinia, or other enteric pathogen


Collection and Panels

Specimen: Stool is obtained via rectal swab.

Container: Sterile collection containers are not required. No detergent or preservative should be present in the container. The specimen should be immediately transported to the laboratory. If transport is delayed by longer than 2 hours, transport media (eg, Cary-Blair) is recommended. [2]

Collecting 3 specimens on consecutive days increases the sensitivity of the test. Patients who are at increased risk for transmission of enteric pathogens (food handlers) or patients who are at increased risk of complications should undergo such testing. Urine-contaminated specimens from diapers or toilet paper are unacceptable for testing.

Samples must be sent in a sealed, leak-proof container marked with a biohazard sticker to comply with Occupational Safety and Health Administration (OSHA) safety requirements.

Panels: Stool culture is indicated.



The normal flora of the GI tract are composed of various bacteria and fungi that play a vital role in the digestion of food. They also help restrict the growth of pathogenic organisms. The use of broad spectrum antibiotics may change the balance of the normal flora, inhibiting the growth of normal flora and allowing bacteria resistant to the antibiotic to persist and overgrow. Similarly, the use of anti-neoplastic drugs can lead to bacterial overgrowth that results in abdominal pain and diarrhea.

Patients with acute diarrheal diseases should undergo routine stool culture. Enteric pathogens may cause nausea, vomiting, abdominal pain, and fever, in addition to frequent loose stools. Severe fluid loss may be noted, especially in small children. Cardiovascular instability and electrolyte imbalance can be associated. Most diarrheal diseases are caused by a single pathogen; however, multiple pathogens may be responsible for the illness.

Hemolytic uremic syndrome is a diarrheal illness complication arising from an infection with Escherichia coli O157:H7. This catastrophic complication is characterized by the destruction of RBCs and renal failure. It is most common in children, the elderly, and patients with compromised immune systems. E coli 0157:H7 and other toxin-producing E coli found in raw or undercooked hamburger or beef, spinach, or unpasteurized cider can cause bloody diarrhea and may cause in hemolytic uremic syndrome; however, most strains of E coli are normal flora and are not pathogenic. [3]


A direct microscopic examination of the stool may provide useful information. The presence of leukocytes in a methylene blue stain indicates the presence of an invasive organism as opposed to a toxigenic organism. Also, a Gram stain may reveal large numbers of certain organisms (eg, campylobacters, staphylococci, or clostridia). Gram staining of the stool is not typically obtained because large amounts of bacteria present in normal colon flora make interpretation difficult. [4]

Stool specimens are inoculated onto several agar media, including a nonselective medium (Sabouraud agar), mildly selective medium (MacConkey agar), and a moderately selective differential medium (Hektoen enteric agar). Some laboratories have used selective broth enrichment (Selenite broth) prior to plate inoculation; however, the cost-effectiveness has not been established. [2]

A selective, differential medium, such as MacConkey or Eosin methylene blue (EMB) agar, is used to test for Salmonella and Shigella. These media are selective; they inhibit gram-positive organisms while allowing the growth of gram-negative rods. Salmonella and Shigella do not ferment lactose; however, many other enteric gram-negative rods are lactose fermenters. If non–lactose-fermenting colonies are identified, a triple sugar iron (TSI) agar slant is indicated to differentiate Salmonella from Shigella.

Some species of Proteus resemble Salmonella on TSI agar; their differentiating point should be the enzyme urease, which is not produced by Salmonella but is produced by Proteus. Further recognition Salmonella or Shigella species should be performed using specific antisera to the organism’s cell wall O antigen in an agglutination test. This test is usually performed in hospital laboratories, but public health laboratories should identify the precise species. [4]

Unlike most intestinal pathogens, Campylobacter jejuni grows well on antibiotic-containing culture media (eg, Skirrow agar) at 42°C in an atmosphere containing 5% O2 and 10% CO2. Despite availability, stool cultures are rarely performed for Yersinia enterocolitica, Vibrio parahaemolyticus, and enteropathic or toxigenic E coli. Anaerobic cultures of stool specimens are not needed because anaerobes rarely become pathogens in the intestine, although a large number of anaerobes are observed in the stool. [4]

MacConkey-sorbitol media is used to culture the grossly blood stool specimens. Typical E coli strains ferment sorbitol and appear as red colonies; however, E coli O157 strains do not ferment sorbitol and appear colorless. [4]

Negative stool cultures usually suggest the stool culture was checked for the most common pathogens at several intervals, and none of the organisms was isolated. [3]

Indication/ Applications

Whether obtaining stool cultures from patients with acute diarrhea is cost effective remains unclear. Most surveys report a low incidence of positive stool culture findings (1.5–3% of submitted stools). However, the cost per positive culture is somewhat high (more than $1000). Acute diarrhea often resolves within 2-3 days, before stool culture results become available. In patients with diarrhea 3 or more days after hospitalization who are not immunosuppressed, stool cultures rarely provide any decision-making information.

Stool cultures should be obtained from patients with fever in excess of 102°F, severe dehydration, dysenteric stools, and stools that contain neutrophils. All immunosuppressed patients with diarrhea and patients with other severe comorbidities, including idiopathic inflammatory bowel disease (IBD), should undergo stool culture for epidemiologic purposes if an outbreak is suspected. Stool culture should also be obtained in those for whom the culture may ultimately guide therapy. [5]

Routine stool culture detects GI infections caused by enteric bacterial pathogens. Most laboratories are capable of detecting Salmonella, Shigella, and Campylobacter species; however, the organism identified by stool culture varies. If Yersinia, enterohemorrhagic E coli (EHEC), Aeromonas, or noncholera Vibrio are suspected , this should be specified in the requisition forms so proper media and culture conditions are used. [5]

Depending on local prevalence of the organisms, other pathogens (eg, shiga-toxin-producing E coli) may be isolated. However, special testing may be required for detection of other pathogens.


The most common organisms in the normal bacterial flora that inhabits the large intestine are anaerobes (Bacteroides, gram-positive rods, and gram-positive cocci), gram-negative enteric organisms, and Enterococcus faecalis. Using differential selective media and enrichment cultures, normal flora can be differentiated. Viruses, toxins (of staphylococci, clostridia, vibrios, toxigenic E coli), invasive enteric gram-negative rods, slow lactose fermenters, shigellae and salmonellae, and campylobacters cause acute gastroenteritis. The relative importance of these groups varies in different locations of the world. [6]

Shigella species may not survive broth enrichment techniques. Yersinia enterocolitica, Vibrio species, E coli (O157:H7), Aeromonas species, Clostridium difficile, or other pathogenic bacteria require special cultures. [2] Hospital inpatients older than 6 months should undergo C difficile testing as an alternative to routine enteric pathogen testing. Diarrhea caused by parasites and viruses require special testing. Stool culture findings may be negative for invasive enteric infections, including enteric fever. If systemic infection by enteric fever (development of fever in addition to diarrhea) is suggested, blood cultures are indicated.

Rectal swabs are only indicated in small infants because they collect a small amount of stool. Rapid transport of the sample is necessary for fastidious organisms such as Shigella species because they do not survive changes in stool pH.

If predominant yeast growth is noted or if Pseudomonas aeruginosa or Staphylococcus aureus is recognized by inspection of the Sabouraud agar plate, an alternative diagnosis is suggested rather than usual enteric pathogens. Oxidase testing may be done on Sabouraud agar isolated using heavy growth to screen for enteric infection caused by Plesiomonas, Aeromonas, or Vibrio species. [2]

Pathogens that cause foodborne diseases are sent to the State Public Health Laboratories to be typed using molecular methods; the results are uploaded into a national database to monitor common source outbreaks across the United States. This monitoring of pathogenic bacterial infection helps identify specific foods or food products where the infection may be located. [3]

Travelers' diarrhea is most often caused by enterotoxigenic E coli, which are the leading causes of bacterial diarrhea in travelers to Africa, Asia, and Latin America. These strains of E coli are not the same Shiga toxin-producing E Coli (0157:H7) strains that cause hemolytic uremia syndrome. [3]

Antidiarrheal medications has are not recommended in patients with infectious diarrhea because they may prolong the illness by keeping the toxin inside the body and cause other catastrophic complications like septic shock, toxic mega-colon, and perforation of colon.

A fresh stool sample is cultured to identify the cause of diarrhea and disease carriers. Most common pathogens, such as Salmonella species, Shigella, and E coli 0.157, can be grown on standard media. Yersinia and Campylobacter require a special culture medium. [7]

Most cases of nausea, vomiting, or diarrheal illnesses are caused by intolerance to food or drink, enterotoxins, drugs, or systemic illnesses and not GI tract infection. Viruses that cannot be grown in tissue culture are mostly responsible for the infectious diarrhea. Conversely, many viruses that can be grown in culture (eg, adenoviruses, enteroviruses) can multiply in the gut without producing GI symptoms. Some enteric bacterial pathogens may remain in the gut following an acute infection. Therefore, stating categorically that a bacterial or viral agent cultured from the stool is responsible for diarrhea may be difficult, especially in subacute or chronic cases. [7]

All in all, a physician should be aware of these difficulties in assigning a causative agent to the illness at hand.