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Isolate Bank - C. difficile Infection Tracking


The C. difficile isolate bank is a collection of isolates obtained through the Emerging Infections Program’s C. difficile Infection (CDI) Surveillance. This population- and laboratory-based surveillance system operates in ten states, drawing from a population of approximately 11 million people. Isolates represent a convenience sample of both community- and healthcare facility- associated strains obtained from cases of C. diff infection in the population under surveillance.

Stool aliquots or stool swabs are sent to partner reference labs for toxigenic culture and then sent to CDC for molecular investigation including pulsed-field gel electrophoresis (PFGE), polymerase chain reaction (PCR), toxinotyping and mutation analysis.

On this website you will find further information about the available isolates, as well as the proper procedure for requesting them.


Isolates Currently Available

  • Isolates from 9 US States; California, Colorado, Connecticut, Georgia, New York, Maryland, Minnesota, Tennessee and Oregon


Guidelines for Requesting Isolates

  1. Request for EIP C.difficile Isolates:

    Requests for C. difficile isolates should come directly to CDC by interested institutions.

    Initiating a Request:

    • Requestor will be required to prepare a short request (3-5 sentences) which states the number of isolates needed and associated specific epidemiologic data requested. The request should be sent to Kamile Rasheed by email, Data linked to isolates available to requestors include year of isolation, PFGE type, age group, state.
    • C. diff Infection Surveillance staff will notify requestor if the isolates are available.
    • If isolates are available; requestor will submit a formal request using official letterhead with the following information:

      Brief summary of the proposed project, no longer than 2 pages, which includes the following:
      • Objective of the project
      • Public health importance
      • Scientific methods
      • Authorship plans
      • Confidentiality
      • Biohazard issues
      • Projected timelines
      • Requestor’s current association/affiliation and complete contact information
      • Number of isolates needed and associated specific epidemiologic data
      • Shipping account number

    CDC Evaluation:

    In order to avoid duplication, the scientific work proposed must not already be part of 'core' C. diff infection surveillance project activities or contained within a proposal for which permission was already granted to another investigator.CDC will ensure this through the following process:

    • All requests will be shared with C. diff infection Pathogen Group for approval by email (within 14-21 days of receipt of formal request).
    • C. diff Infection Surveillance staff will notify the requestor as to the outcome of the request (within 14 days of approval/refusal).
    • Any modifications to the initially proposed use of isolates by receiving institutions should be submitted for approval by the C. diff Infection Pathogen Group.

    User Fee Agreement:

    • If the request is approved, for-profit institutions will be charged $150 per isolate requested and non-profit institutions will be charged $50 per isolate requested if over 10 isolates are requested. Isolates will be free of charges for non-profit institutions requesting ≤ 10 isolates. CDC will send a User Fee agreement for completion. The document requires a limit on dissemination of isolates and includes an agreement to acknowledge the source of these isolates and to limit isolate use to what was proposed in the original request. Acknowledgment for C. diff Infection Surveillance will be in the following standardized format: Clostridium difficile Infection (CDI) surveillance/Emerging Infections Programs (EIP) Network. In addition, requestor will be required to share any abstracts or manuscripts containing EIP isolates data with CDC prior to submission to scientific conferences or peer-review journals to ensure that source of isolates have been appropriately acknowledged and that the presentation/publication reflects what was proposed by the requestor.

      Note:At least one scientist from the C. diff Infection Pathogen Group should review the abstract or manuscript , even when lead authors are not members of the C. diff Infection Pathogen Group (refer to C. diff Infection Authorship Guidelines).


    • Shipping questions should be directed to: Kamile Rasheed (email:
    • All other questions should be directed to: Fernanda Lessa (email:

Click here to download and print guidelines for requesting Isolates [PDF - 154 KB]



  1. Impact of North American Pulsed-field Type 1 (NAP1) Clostridium difficile Strain on Disease Severity and Outcome
  2. Epidemiology of Community-associated Clostridium difficile infection (CA-CDI), Emerging Infections Program, 2009-2011. Abstract presented at the 2012 Anaerobe Meeting, June 29-July 1,San Francisco, CA [PDF - 142 KB]


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