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What Does a Stool Culture Test For?
Updated on September 21, 2023
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What Does a Stool Culture Test For?
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Stool cultures are a diagnostic method used to detect a range of microorganisms present in stool samples.1

There are several reasons why a stool culture is done. These reasons include:

  • Identify diseases in the digestive tract
  • Screen for colon cancer
  • Search for parasites such as pinworms or Giardia
  • Search for bacteria, fungus, or a virus that is causing infection
  • Check the absorption of nutrients in the digestive tract

Through stool cultures, healthcare professionals can uncover valuable information regarding gastrointestinal infections and disorders.

What Stool Cultures Test For

Stool cultures identify various microorganisms present in a stool specimen. These microorganisms include bacteria, parasites, viruses, and other infectious agents.1

Here's an overview of what stool cultures are used to identify:

  • Bacteria – Stool cultures help identify the presence of pathogenic bacteria cultures. Examples include shigella, salmonella, and Escherichia coli (E. coli).2 These bacteria can cause illnesses like bloody diarrhea, gastroenteritis, and extraintestinal infections.3
  • Parasites – Stool cultures can also detect parasites. A few examples include Giardia lamblia, Cryptosporidium, and Entamoeba histolytica.4 These parasites are responsible for conditions like giardiasis, cryptosporidiosis, and amoebiasis. These can all lead to diarrhea, abdominal pain, and other gastrointestinal symptoms.5
  • Other Microorganisms – Stool cultures may also identify other microorganisms. These microorganisms can include viruses, fungi, and yeast. These microorganisms can contribute to infectious diseases and other health issues.

“This involves taking a properly collected stool sample and examining which specific organisms (including strain) it contains. Chronic, persistent, gastrointestinal symptoms may require a stool culture,” explains our in-house medical expert, Dr. Rizza Mira.

The Role of Bacteria in Stool Testing

Bacterial analysis is an essential component of stool cultures. The presence of certain bacteria in a stool specimen can provide valuable diagnostic information.

Here's why bacteria are tested for in stool cultures and what their presence may indicate:

  • Infection – Salmonella, shigella, and campylobacter are bacteria that can cause severe gastrointestinal infections.2 Detecting these bacteria in stool samples helps diagnose and treat the underlying infection.
  • Foodborne illnesses – Contaminated food can introduce harmful bacteria into the body. This can cause food poisoning.6 Stool cultures help identify the specific bacteria responsible for the illness. Targeted treatment and transmission prevention can be informed through stool cultures.
  • Antibiotic resistance – Stool cultures can also provide insights into antibiotic resistance patterns of bacteria. This information helps healthcare providers prescribe appropriate antibiotics that effectively target the identified bacteria.

“Most doctors request for stool cultures to find an effective treatment that will target the specific organism,” explains Dr. Mira.

Other Organisms Identified in Stool Cultures

In addition to bacteria, stool cultures can identify various other organisms. Here's a closer look at these microorganisms:

  • Viruses – Certain viruses can be identified in stool samples. Examples include norovirus7 and rotavirus.8 However, they are less commonly tested using stool cultures. These viruses are often responsible for viral gastroenteritis.8 Their detection can help determine appropriate treatment measures.
  • Fungi and yeast – Stool cultures may also reveal the presence of fungi9 and yeast.10 This can cause gastrointestinal infections. People who don’t have healthy immune systems are most at risk.11 Identifying these organisms can guide appropriate antifungal treatment.

“Stool cultures help differentiate diarrhea that necessitates antibiotic use from those that don't,” says Dr. Mira.

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How is a Stool Culture Performed?

Performing a stool culture involves several steps. These steps begin with the collection of the sample and end with laboratory testing.

There is no special preparation for a stool culture process.

However, before beginning the stool culture process, inform your doctor of the following:

  • If you are on any antibiotic treatment
  • Drank untreated water
  • Traveled abroad
  • Took a test with contrast material such as barium swallow

Stool Sample Collection

To ensure accurate results, collecting the stool sample correctly is essential. Here's a step-by-step guide on how to collect a stool.12,13

  1. Obtain a sterile container –  You will be provided with a sterile container for your stool sample. These containers come with a lid, a scoop, or a spoon-like attachment for easy and hygienic sampling.
  2. Urinate before sample collection – Make sure to urinate before sample collection. You should collect a fresh stool sample that hasn't come into contact with urine or toilet water. Do not urinate while collecting the sample.
  3. Collect the sample – Make sure you are wearing gloves before you handle your stool. Use the scoop or spoon attached to the container lid to collect a pea-sized amount of stool. Avoid touching the inside of the container. Avoid contaminating the sample with toilet water, toilet paper, urine, or other substances.
  4. Secure the lid – Once the sample is collected, fasten the lid of the container securely. This is to prevent leakage or exposure to the environment.
  5. Label the container – Write your name, date, and any additional information requested by your healthcare provider on the container label. This ensures proper identification and reduces the risk of sample mix-ups.
  6. Submit the sample to your healthcare provider – After securing the sample, submit it to your healthcare provider as instructed.

When collecting your stool sample, you can collect either solid or liquid stool.13 Here are other notes to remember:

  • Do not collect the sample from the toilet bowl or diapers. Your healthcare provider may provide you with tissue or wax paper for the stool to be collected. A rectal swab may be done for those who cannot move their bowels.
  • Do not mix the stool sample with toilet paper, water, or soap.
  • If you have diarrhea, your healthcare provider may suggest using a plastic bag over the toilet bowl. This will help ease the collection process.
  • The procedure is painless, but you may experience some pain if you are constipated. To ease the process, consume more fiber-rich foods before the stool sample collection.
  • Make sure to wash your hands after the procedure to prevent cross-contamination and spread of disease.

Laboratory Testing Process

Once the stool sample reaches the laboratory, it undergoes a series of testing procedures. 

Laboratory analysis of a stool culture involves microscopic examination, chemical tests, and microbiologic tests.1

The technician will smear the stool sample on sterile plates that contain a gel-like substance.14 The plates are stored at certain temperatures to promote the growth of targetted germs and bacteria.2

The stool is examined based on color, consistency, and mucus, if present.1

The stool can also be examined for the following: 

  • Hidden or occult blood
  • Fat
  • Undigested meat fibers
  • Bile
  • White blood cells
  • Reducing substances or sugars
  • Worms or parasites that are widely seen

Other laboratories can also measure the pH of the stool.

The laboratory technician may also conduct other tests to determine possible courses of treatment.

Interpreting Stool Culture Results

Interpreting stool culture results is essential to understanding the presence of microorganisms in the stool sample.

“This is best interpreted by a healthcare professional. Other measures to prevent the recurrence of gastrointestinal infections will also be determined by your doctor,” says Dr. Mira.

Results are typically available within 2-3 days, depending on the nature of the cultures.13 For example, results for fungus and parasite cultures may take weeks.

Here's an explanation of what negative and positive test results could mean:15

  • Negative result – A negative stool culture result means that no abnormal bacteria or other microorganisms were detected in the stool sample. This confirms the absence of pathogens or infectious agents commonly associated with gastrointestinal infections. 
  • Positive result – A positive stool culture result indicates the sample contains bacteria, parasites, or viruses. These microorganisms are likely the cause of any present infection. Healthcare professionals will diagnose the underlying infection or condition and determine the appropriate treatment.

In some cases, a false-negative result may occur. This indicates that the test missed certain bacteria.

“Antibiotic use prior to collection may contribute to a false-negative result,” explains Dr. Mira.

If you continue to experience any gastrointestinal infection symptoms, additional tests may be required. This will help determine the cause of these symptoms.

Understanding Bacterial Presence in Stool Culture

Bacteria are a significant focus of stool culture testing.

Stool culture testing differentiates bacteria that are normally found in the gut flora from pathogenic or disease-causing bacteria.16

If pathogenic bacteria are identified, stool culture testing determines whether it is causing symptoms of gastrointestinal infection.

Understanding the types of bacteria typically found in stool is crucial. 

Here's a breakdown of bacterial presence in stool culture:

Normal bacteria

The gastrointestinal tract naturally contains a diverse community of bacteria. This community of bacteria is known as the gut microbiota.17

Common organisms found in stool culture include anaerobes, gram-negative enteric organisms, and Enterococcus faecalis.18 The presence of these bacteria in small amounts in stool is considered normal. They do not typically indicate an infection or disease.

Harmful bacteria

Stool cultures identify pathogenic bacteria that can cause gastrointestinal infections or diseases. Examples of harmful bacteria include shigella, salmonella, and E. coli.2

The presence of these bacteria in stool may indicate an active infection. This will require prompt medical attention and appropriate treatment.

“The strains and colony count are also important to take note of. Some gram-negative enteric organisms are considered harmful at certain levels,” clarifies Dr. Mira.

How is a Positive Result Treated?

The treatment of a positive stool culture result depends on the identified microorganism and the specific infection or condition it causes. Here are some potential treatment options or next steps:

  • Antibiotics – Antibiotics may be prescribed to eliminate the infection.19,20 The choice of antibiotics depends on the specific bacteria and their susceptibility to different drugs. It's important to complete the full course of antibiotics as your healthcare provider prescribes.
  • Antiparasitic Medications – In cases where parasites are identified, antiparasitic medications may be recommended.21 These medications target and eliminate the parasites responsible for the infection.
  • Supportive Care – Supportive care measures may be advised to manage symptoms and aid recovery. This may include ensuring hydration21 or taking probiotics for certain conditions like diarrhea.22 Supportive care may be advised together with other medications.
  • Further Testing – In some cases, additional tests may be required to gather more information about the infection.15 These tests may include further stool analysis, blood tests, or consultations with specialists.

It's crucial to follow your healthcare provider's instructions closely. They will provide guidance tailored to your specific situation to ensure effective management and recovery. Make sure to communicate any changes or concerns during the treatment process. 

The Importance of Stool Culture Testing in Digestive Health

Stool culture testing serves as an invaluable tool in digestive health. It plays a crucial role in diagnosing and managing gastrointestinal disorders. 

Moreover, stool culture testing provides valuable insights into microorganism presence in the gastrointestinal tract.

Stool culture testing helps healthcare professionals accurately diagnose infections, identify pathogens, and guide appropriate treatment strategies. 

The significance of stool culture testing can be summarized in the following key points:

  • Accurate diagnosis – Stool culture testing accurately identifies microorganisms responsible for gastrointestinal conditions. Healthcare providers can tailor treatment plans by pinpointing the specific cause of symptoms.16
  • Targeted treatment – Identifying microorganisms in stool helps determine the most effective treatment options.14 Antibiotics, antiparasitic medications, or other targeted therapies can be prescribed. This will help increase the likelihood of successful treatment outcomes.
  • Infection control – Stool culture testing not only aids in individual patient care but also contributes to public health. Healthcare authorities can identify and track specific pathogens responsible for outbreaks of foodborne illnesses. They can implement measures to control and prevent the spread of infections in communities.23
  • Differential diagnosis – Stool culture testing is an essential tool for diagnosing gastrointestinal disorders.24 It helps differentiate between infectious and non-infectious causes of symptoms.16 Moreover, it provides guidance for healthcare providers to determine the appropriate treatments.
  • Monitoring treatment efficacy – Stool culture testing is valuable in monitoring treatment efficacy.25 Repeat stool cultures can be performed. This will ensure the eradication of the identified pathogens. Moreover, it will confirm the success of therapeutic approaches.
  • Proactive management – Stool culture testing can also be used proactively to screen anyone considered at-risk. This helps identify asymptomatic carriers of pathogens. Additionally, healthcare authorities can implement appropriate preventive measures to minimize the spread of infections.

Stool culture testing is a crucial diagnostic tool to evaluate and manage gastrointestinal health. 

Stool culture testing identifies infections, directly targets treatments, and tracks the effectiveness of treatments. This is achieved by precisely detecting the presence of microorganisms.

Moreover, stool culture testing is crucial in fostering digestive health and general well-being. This is because of its use in differential diagnosis, infection control, and proactive management.

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Updated on September 21, 2023
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25 sources cited
Updated on September 21, 2023
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  2. Stool Test: Bacteria Culture”. Nemours KidsHealth
  3. Chapter 283. Salmonella, Shigella, and Escherichia Coli“. Access Pediatrics.
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  5. Amoebiasis, cryptosporidiosis and giardiasis”. Wiley Online Library.
  6. Food Poisoning”. Cleveland Clinic.
  7. Specimen Collection”. Centers for Disease Control and Prevention.
  8. Acute Gastroenteritis”. National Library of Medicine.
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  10. Candida Test UK”. The IBS & Gut Disorder Centre.
  11. Yeast Infections”. Urology Care Foundation.
  12. How should I collect and store a poo (stool) sample?”. National Health Service.
  13. Stool Culture”. HealthLink BC.
  14. Fecal culture”. MedlinePlus.
  15. Stool Culture”. University of Rochester Medical Center. 
  16. Stool Culture”.
  17. Gut Microbiome”. ScienceDirect.
  18. Stool Culture”. Medscape.
  19. Shigella – Shigellosis”. Centers for Disease Control and Prevention.
  20. Infectious diarrhea: when to test and when to treat”. National Library of Medicine.
  21. Ova and Parasite Test”. MedlinePlus.
  22. Diarrhea”. Mayo Clinic.
  23. CDC and Food Safety”. Centers for Disease Control and Prevention.
  24. The importance of stool tests in diagnosis and follow-up of gastrointestinal disorders in children”. National Library of Medicine.
  25. Performance of the Kato-Katz method and real time polymerase chain reaction for the diagnosis of soil-transmitted helminthiasis in the framework of a randomised controlled trial: treatment efficacy and day-to-day variation”. BioMed Central.
Angela Natividad
Angela Natividad
Content Contributor
Angela Natividad is the content manager and editor for KnowYourDNA. She loves learning about the latest in DNA.
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