Clostridioides difficile Infection (CDI) Tracking


Clostridioides difficile infection (CDI) is the leading cause of antibiotic-associated diarrhea and one of the most common healthcare-associated infections in the United States. The Clostridioides difficile infection surveillance program is an active population- and laboratory-based surveillance system conducted through CDC’s Emerging Infections Program (EIP) Healthcare-Associated Infections Community Interface (HAIC). Data from the EIP CDI program is used to measure the burden of CDI in the population, characterize C. difficile strains associated with disease, and to monitor trends in disease over time. The CDI surveillance program also provides an infrastructure for further public health research, including special studies aimed at identifying risk factors for C. difficile disease, populations to prioritize for vaccines, and monitoring effectiveness of prevention strategies. The EIP CDI surveillance was launched in 2009 in 7 EIP sites. Since 2011, EIP CDI surveillance has operated in selected counties in 10 EIP sites across the United States.

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Surveillance Objectives

  1. Monitor population-based CDI incidence and disease burden of community- and healthcare-associated CDI over time to assess the impact of prevention strategies and inform public health practice.
  2. Describe the molecular and microbiologic characteristics of C. difficile strains causing disease in the population under surveillance and describe changes in strain prevalence over time.
  3. Monitor changes in the epidemiology of community- and healthcare-associated CDI, including disease severity, related complications and outcomes, and relevant risk factors to help guide prevention efforts.


Surveillance Population

The table below illustrates the estimated population under surveillance for each EIP site in 2019, the most recent year for which data are available.

Surveillance Populations
Areas Under Surveillance Population
San Francisco County, CA 881,549
Adams, Arapahoe, Denver, Douglas and Jefferson Counties, CO 2,835,257
New Haven County, CT 854,757
Clayton, Cobb, DeKalb, Douglas, Fulton, Gwinnett, Newton and Rockdale Counties, GA 4,160,864
Caroline, Cecil, Dorchester, Frederick, Kent, Somerset, Talbot, Queen Anne’s, Washington, Wicomico and Worcester Counties, MD 867,271
Benton, Morrison, Olmsted*, Stearns and Todd Counties, MN 418,307
Bernalillo County, NM 679,121
Monroe County, NY 741,770
Klamath County, OR** 68,238
Davidson County, TN 694,144
Total 12,201,278

*Surveillance in Olmsted County began July 2012
**Deschutes County, OR participated in CDI surveillance during 2012-2013.

Case Definition

C. difficile infection Incident Case

A case of CDI is defined as a positive C. difficile toxin assay or a positive C. difficile molecular assay (e.g. PCR) of a stool specimen from a resident of the surveillance catchment area who is at least 1 year old. Cases with a C. difficile-positive stool specimen greater than 8 weeks after the last positive specimen are considered a new case with an incident stool specimen. Therefore, for surveillance purposes, an individual may be classified and captured as a new incident case if 8 consecutive weeks have elapsed since their last C. difficile-positive test.

Recurrent episodes

CDI cases with a positive C. difficile stool specimen between 2 to 8 weeks of the last positive specimen are considered recurrent episodes.

Duplicate episodes

CDI cases with a positive C. difficile stool specimen less than 2 weeks since the last positive specimen are considered duplicate episodes.

Case Ascertainment

CDI cases are identified based on reports of positive C. difficile toxin assay or C. difficile nucleic acid amplification assay from all clinical, reference, and commercial laboratories that serve the population in the surveillance catchment areas. Each laboratory regularly reports positive C. difficile test results to the local EIP site. Accompanying data include the patient name and local laboratory identifier, date of specimen collection, as well as any additional available information (e.g. address, date of birth, age, sex, location of stool collection). Information on additional positive specimens from the same patient is recorded for the purpose of ascertaining and tracking recurrent or duplicate episodes, as well as new cases (i.e., greater than 8 weeks after the last positive C. difficile specimen).

Data Collection and Epidemiologic Classification

Data collection is performed by surveillance epidemiologists at each EIP site. In 8 of the 10 EIP sites, a brief medical-record review is performed for each incident CDI case to gather basic demographic characteristics, location of stool collection, and healthcare exposures. In the 2 remaining EIP sites with the largest surveillance populations (Colorado and Georgia), a brief medical record review is performed on a random sample of cases. Medical record reviews are not completed on recurrent or duplicate episodes or patients determined to reside outside the surveillance area.

CDI cases are classified into 3 epidemiologic categories:

  • Healthcare facility-onset (HCFO), if the positive stool specimen was collected greater than 3 calendar days after hospital admission or in a resident of a long-term care facility
  • Community-onset healthcare facility-associated (CO-HCFA), if the positive stool specimen was collected in an outpatient setting or within 3 days after hospital admission in a person with documented overnight stay in a healthcare facility (i.e., hospitalization or long-term care facility stay) in the 12 weeks before stool specimen collection
  • Community–associated (CA), if positive stool specimen was collected in an outpatient setting or within 3 calendar days after hospital admission in a person with no documented overnight stay in a healthcare facility during the 12 weeks before the specimen was collected.

All CA and CO-HFCA cases and a random sample (10%) of HCFO cases subsequently undergo a comprehensive medical record review for clinical information and relevant risk factors.

Laboratory Characterization

A convenience sample of stool specimens from incident CDI cases with complete clinical and epidemiologic information is sent to reference laboratories for C. difficile isolation. Isolates recovered are then sent to CDC for molecular typing and characterization. Additional information can be found at Isolate Bank – C. difficile Infection Tracking.


Rates of CDI are calculated using population estimates (≥1 year of age) for the specified year. Cases with missing data (e.g., race) are multiply imputed using sequential regression imputation methods. A domain (subpopulation) analysis is performed to estimate the number of cases according to epidemiologic class and race in the 2 EIP sites where sampling was performed (Colorado and Georgia).

Response to Inaccuracies in Clostridium difficile Infection (CDI) Data

For more information on the EIP surveillance data reported from Oregon in 2010, see the Federal Register: Findings of Research Misconduct (06/01/2015)


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