Microbiology & infectious diseases

Gram positive bacteria

Clostridioides difficile

Editor-in-Chief: Debra L. Zynger, M.D.
Joshua A. Lieberman, M.D, Ph.D.

Last author update: 1 August 2018
Last staff update: 4 May 2023

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PubMed Search: Clostridioides difficile [title]

Joshua A. Lieberman, M.D, Ph.D.
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Cite this page: Lieberman JA. Clostridioides difficile. PathologyOutlines.com website. https://www.pathologyoutlines.com/topic/microbiologycdifficile.html. Accessed February 23rd, 2024.
Definition / general
  • Gram positive, strict anaerobe bacteria causing pseudomembranous colitis
  • Ranges from normal flora of neonates, to asymptomatic carriage in children and adults, to diarrheagenic pathogen
  • Transmissible, hand washing necessary (alcohol based sanitizers insufficient to remove spores) and contact precautions are standard
Essential features
  • Previously Clostridium difficile but phylogenetically distant from Clostridium sensu strictu and therefore renamed Clostridioides (Anaerobe 2016;40:95)
  • Jargon: C. diff
  • CDI – Clostridioides difficile infection; CDAD – Clostridioides difficile associated disease / diarrhea
  • Causes pseudomembranous colitis
ICD coding
  • A04.7: enterocolitis due to Clostridium difficile
  • Causes illness in ~ 500,000 Americans per year; 15 - 30,000 deaths per year (Clin Infect Dis 2018;66:987)
  • Incidence:
    • 147/100,000 (Clin Infect Dis 2018;66:987)
    • Highest incidence at age 65+
    • > 60% of cases are health care associated
    • Patients with inflammatory bowel disease, immunocompromise (post solid organ or bone marrow transplant) are at increased risk
  • Antibiotic use is a major risk factor due to disruption of gut microbiota (Clin Infect Dis 2018;66:987)
  • Major nosocomial pathogen; patient isolation, hand washing and proper use of gown / gloves important interventions (Clin Infect Dis 2018;66:987)
  • Rare cause of illness in children under 2 years; testing not recommended unless noninfectious and other infectious causes excluded (Clin Infect Dis 2018;66:987)
  • Colon
  • Molecular diagnostic testing is mainstay of detection; multiple assays available and perform better than cytotoxin neutralization assay or enzyme immunoassay
    • PCR assays detect either single organism versus multi organism panel
    • Example of single organism: Cepheid GeneXpert has primers to multiple targets: tcdB, tcdC, cdtA and cdtB loci with ≥ 97% sensitivity and ≥ 90% specificity (J Clin Microbiol 2010;48:4519, J Clin Microbiol 2009;47:3729)
    • Example of multiplex panel: Biofire FilmArray GI Panel detects by qPCR and also has high sensitivity (≥ 94%) and specificity (≥ 97%) for C. difficile (J Clin Microbiol 2015;53:915)
    • Molecular assays are not tests of cure as DNA can persist in stool after disease resolution
    • Institutional guidelines limiting molecular testing important to avoid overdiagnosis (e.g., detection of C. difficile in patients without diarrhea, indicating carrier state) (Clin Infect Dis 2018;66:987)
    • Minimum time for retesting after positive test (i.e., do not use as test of cure due to persistence of DNA)
    • Laboratories typically only accept nonformed stool for diagnostic testing
    • If no preset institutional nucleic acid amplification testing guidelines, recommendation is to use a stool toxin test as part of multistep algorithm
  • Gram stain and culture are rarely used in diagnosis
  • Bacteria are gram positive, albeit frequently with variable gram staining
  • Requires specific culture conditions; typically see anaerobic growth within 48 hours
  • Morphology / colonies: see gross and microscopic descriptions
Case reports
  • Insufficient data to recommend probiotics to prevent infection (Clin Infect Dis 2018;66:987)
  • Clinical images

    Contributed by Joshua A. Lieberman, M.D, Ph.D.

    C. perfringens

    Gross description
    • Colonies: gray-white, low convex, 2 - 5 mm, matte to glossy, pale green fluorescence under UV light (but traditional culture rarely employed for ID)
    Gross images

    Images hosted on other servers:

    Fluorescence under UV light

    Microscopic (histologic) description
    • Rods, box car shaped, 0.5 - 1.9 x 3 – 17 microns
    • Subterminal spores may be evident as oval, intracellular clearings
    • Occasional chains of 2 - 6 cells
    Microscopic (histologic) images

    Contributed by Joshua A. Lieberman, M.D, Ph.D.

    C. perfringens

    Electron microscopy images

    Images hosted on other servers:


    Differential diagnosis
    • Diarrheagenic E. coli
    • Viral diarrheal agents
    • Travel history, immunosuppression may point to more exotic pathogens including parasites
    Board review style question #1
    A 57 year old man with ulcerative colitis presents with 4 days of diarrhea and a leukocytosis of 14,000 cells/μL two weeks after being treated for bacterial sinusitis. The best laboratory test to diagnose his condition is:

    1. Anaerobic and aerobic bacterial culture
    2. Immunoassay for cytotoxin production
    3. Nucleic acid amplification testing (NAAT) targeted to toxin B and the CDT toxin of the suspected pathogen
    4. Stool examination for ova and parasites
    Board review style answer #1
    C. This patient has a recent history of antibiotic exposure and ulcerative colitis, both risk factors for Clostridioides difficile infection (CDI). Diarrhea with a high WBC and this history is strongly suggestive of active CDI. Nucleic acid amplification testing (NAAT) is more sensitive than cytotoxin immunoassay and faster than culture (turnaround ~1 hour). Rapid turnaround time is valuable when CDI is suspected to guide isolation practices. The description does not indicate any clear risk factors for parasitic infection.

    Comment Here

    Reference: Clostridioides difficile
    Board review style question #2
    A patient with ulcerative colitis presented with diarrhea for 4 days after antibiotic treatment for sinusitis. NAAT and culture were performed. Gram stain showed the following:

    After oral antibiotics, his diarrhea resolved, and his physicians want to repeat the NAAT as a test of cure. What do you recommend?

    1. Advocate against testing as bacterial DNA may persist after clinical symptoms resolve
    2. Advocate against testing because it is expensive
    3. Proceed with testing as a negative NAAT result can shorten the patient's antibiotic exposure
    4. Proceed with testing because a positive result should prompt fecal microbiota transplant
    Board review style answer #2
    A. This is Clostridioides difficile infection (CDI). Institutional guidelines are important to prevent repeat testing. Bacterial DNA may persist longer than symptoms, thus proving a clinical false positive result on nucleic acid amplification testing (NAAT) (albeit an analytical true positive result!). Treatment is fairly protocolized with evidence based recommendations for length of treatment. Fecal microbiota transplant is reserved for patients with at least 2 recurrences of CDI who have failed medical therapy and would not (yet) be indicated for this patient. In addition, a positive test after only a few days of treatment would NOT constitute evidence of a recurrence but most likely represents persistent C. difficile DNA in the stool.

    Comment Here

    Reference: Clostridioides difficile
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