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Clostridioides difficile Diagnostic Testing

Test code(s) 91664, 16377, 92014, 4408, 34403

C difficile is an opportunistic, toxin-producing bacterial pathogen of the gastrointestinal tract that is the most common cause of healthcare-associated diarrhea. Infections are commonly seen in patients who have recently been, or are currently being, treated with antibiotics; are elderly; or are in long-term healthcare settings. C difficile causes 25% to 30% of antibiotic-associated diarrhea and >95% of pseudomembranous colitis cases. Incidence has almost doubled since 1996, and the mortality rate is rising owing to emergence of a hypervirulent strain (027/NAP1/B1). In 2011, an estimated one million infections and 29,000 deaths were attributed to C difficile.1

Disease-causing C difficile strains produce 1 or both of 2 toxins: toxin A is an enterotoxin and toxin B is a cytotoxin. Other strains produce neither toxin and are thought to colonize the colon without causing disease.

Testing should be considered for patients with recent or current antibiotic use, ≥3 episodes of non-formed stool within 24 hours, anorexia, leukocytosis, and no known ileus obstruction. For children ages 1 to 3 with diarrhea, testing can be considered but other causes (eg, viral) should be considered first. Routine testing in children <1 should be avoided given the high carriage rates of C difficile. For children >3, testing considerations are the same as for adults. Although C difficile can colonize neonates/infants, they may lack the cellular machinery to bind and process Clostridium toxins.2

Repeat testing to determine cure is not recommended.

The American College of Gastroenterology3 and the American Society for Microbiology4 guidelines recommend utilizing 2 different testing options for the detection of C difficile infection:

  • Nucleic acid amplification tests (NAAT) for C difficile toxin genes (test code 16377)
  • 2- or 3-step algorithm that includes assessment of C difficile toxin and glutamate dehydrogenase (GDH), as well as detection of the C difficile toxin B gene (test code 91664)

The Infectious Disease Society of America/The Society for Healthcare Epidemiology of America (IDSA/SHEA) guidelines, which are posted on the CDC website, recommend gene detection for confirmation when the GDH test is positive and toxin is not detected. They also recommend gene detection when the GDH test is negative and toxin is detected. PCR or another nucleic acid amplification test (NAAT) can be used.1,5

The first step is an immunoassay to simultaneously assess for toxin and GDH presence. If toxin (either A or B or both) and GDH are present, the specimen is considered positive for toxigenic C difficile infection. If both toxin and GDH are absent, then the specimen is considered negative (Figure 1).

Specimens with discordant results (ie, GDH-positive but toxin-negative or GDH-negative but toxin-positive) proceed to the second step: reflex (at additional charge and additional CPT code) to a PCR C difficile gene detection test. According to our validation studies, discordant results occur in about 6% of cases. 

If the gene is detected, results will include genotype information that indicates if the hypervirulent strain (ribotype O27/NAP1/toxinotype III) is present. Table 1 details how the results will be reported and how to interpret them.

The C difficile cytotoxicity assay has served as a historical gold standard for diagnosing clinically significant disease caused by C difficile; however, it is not timely for diagnosis. This assay is best utilized as a reference method or epidemiologic tool.3

The newer testing methods are faster than culture and have higher sensitivity and specificity than GDH testing alone. The 2-step analysis algorithm increases the sensitivity to 90.5% and the specificity to 93%.6 The sensitivity of the stand-alone NAAT is 93.4 % and the specificity is 90.9%.7

Quest Diagnostics offers multiple tests to help identify C difficile infections (Table 2). Information pertaining to test selection can be found in Questions 3 and 5.



  1. Clostridium difficile infections. Centers for Disease Control and Prevention Web site. Updated March 1, 2016. Accessed December 1, 2016.
  2. Schutze GE, Willoughby RE, Committee on Infectious Diseases, American Academy of Pediatrics. Clostridium difficile infection in infants and children. Pediatrics. 2013;131;196-200.
  3. Surawicz CM, Brandt LJ, Binion DG, et al. Guidelines for the diagnosis, treatment and prevention of Clostridium difficile infections. Am J Gastroenterol. 2013;108:478-498.
  4. American Society for Microbiology. A practical guidance document for the laboratory detection of toxigenic Clostridium difficile. Published September 21, 2010. Accessed December 21, 2016.
  5. Cohen SH, Gerding DN, Johnson S, et al. 2010. Clinical practice guidelines for Clostridium difficile infection in adults: 2010 update by the Society for Healthcare Epidemiology of America (SHEA) and the Infectious Diseases Society of America (IDSA). Infect Control Hosp Epidemiol. 2010;31:431-455.
  7. Package insert Xpert® C.difficile/EPI Assay.
  8. Chang TW, Gorbach SL, Bartlett JB. Neutralization of Clostridium difficile toxin by Clostridium sordelli antitoxins. Infect Immun. 1978;22:418-422.
  9. Kyne L, Warny M, Qamar A, et al. Association between antibody response to toxin A and protection against recurrent Clostridium difficile diarrhoea. Lancet. 2001;357:189-193.
  10. Aronsson B, Granström M, Möllby R, et al. Serum antibody response to Clostridium difficile toxins in patients with Clostridium difficile diarrhoea. Infection. 1985;13:97-101.
  11. Giannasca PJ, Warny M. Active and passive immunization against Clostridium difficile diarrhoea and colitis. Vaccine. 2004;22:848-856.
  12. Johnson S. Recurrent Clostridium difficile infection: a review of risk factors, treatments, and outcomes. J Infect. 209;58:403-410.
  13. Kyne L, Warny M, Qamar A, et al. Asymptomatic carriage of Clostridium difficile and serum levels of IgG antibody against toxin A. N Engl J Med. 2000;342:390-397.
  14. Warny M, Vaerman JP, Avesani V, et al. Human antibody response to Clostridium difficile toxin A in relation to clinical course of infection. Infect Immun. 1994;62:384-389.
  15. Viscidi R, Laughon BE, Yolken R, et al. Serum antibody response to toxins A and B of Clostridium difficile. J Infect Dis. 1983;148:93-100.

This FAQ is provided for informational purposes only and is not intended as medical advice. A clinician’s test selection and interpretation, diagnosis, and patient management decisions should be based on his/her education, clinical expertise, and assessment of the patient.

Document FAQS.136 Version: 3
Version 3 effective 06/30/2021 to present
Version 2 effective 03/03/2017 to 06/30/2021
Version 1 effective 03/24/2015 to 03/03/2017
Version 0 effective 05/28/2014 to 03/23/2015