Isolate Bank – C. difficile Infection Tracking

At a glance

  • The C. difficile Isolate Bank is a collection of isolates obtained through the Emerging Infections Program's C. difficile infection (CDI) surveillance.
  • Isolates represent a convenience sample of both community- and healthcare- associated strains obtained from CDI cases in the surveillance population.
  • Researchers and public health professionals can request isolates.

Overview

The C. difficile Isolate Bank is a collection of isolates obtained through the C. difficile infection (CDI) Surveillance Program. The CDI Surveillance program is a population- and laboratory-based surveillance system operating in ten EIP sites. It draws from a population of roughly 12 million people and it launched in 2009.

How the Isolate Bank receives samples

Stool aliquots or stool swabs are sent to partner reference laboratories for culture. C. difficile isolates obtained from these cultures are sent to CDC for molecular typing and characterization by whole genome sequencing including:

  • Multilocus sequence typing (MLST).
  • Detection of tcdA, tcdB, cdtA and cdtB toxin genes.
  • Assessment of deletions in the tcdC gene.

Isolates currently available

  • C. difficile isolates from a subset of cases in EIP sites, collected since 2009.
  • A panel of highly characterized 30 C. difficile isolates that represent the top ten most prevalent PCR-ribotypes, collected in 2016. Made available through the CDC & FDA Antibiotic Resistance Isolate Bank (AR Isolate Bank).
  • A sample of C. difficile isolates (based on geographic distribution across the EIP sites) collected during 2010-2011. Made available through BEI Resources and includes the following metadata for all isolates:
    • Basic demographic information.
    • Year of specimen collection.
    • Geographical region.
    • Hospitalization.
    • Outcome.
    • Epidemiologic classification.
    • Molecular data.

Requesting isolates from EIP

Note: Request isolates from AR Isolate Bank and BEI Resources using the AR Isolate Bank ordering platform and BEI Resources ordering platform.

  1. Verify if the isolates you need are available by sending a short request (3-5 sentences) to Amy Gargis that includes:
    1. The number of isolates needed.
    2. Associated specific epidemiologic data needed.
  2. If CDC confirms availability, submit a formal request to Amy Gargis, no longer than 2 pages. This formal request should be a summary of the proposed project, on an official letterhead, which includes the following information:
    1. Objective of the project.
    2. Public health importance.
    3. Scientific methods.
    4. Authorship plans.
    5. Confidentiality.
    6. Biohazard issues.
    7. Projected timelines.
    8. Requestor's current association or affiliation and complete contact information.
    9. Number of isolates needed and associated specific epidemiologic data.
    10. Shipping account number.
  3. CDC will send a User Fee Agreement for you or other researchers to sign.
  4. Pay user fee, if applicable.

Following these steps, CDC then sends isolates to the requestor.

Requirements of use

Allowed uses of isolates

Proposed use of isolates cannot:

  • Duplicate activities already conducted as part of “core” CDI surveillance project activities.
  • Duplicate already-approved projects for which permission is granted to another investigator.

CDC ensures proper use of isolates by:

  • Sharing all isolate requests with the appropriate CDC and EIP site staff for approval by email.
  • Notifying the requestor if the request is approved or denied.
  • Requiring requestors to submit modifications to their initially proposed use of isolates for approval.

User fee agreement

CDC will send a User Fee agreement for completion. The document outlines and requires agreement on:

  • The limit on the distribution of isolates.
  • The source of these isolates.
  • The stated use of isolates detailed in the original request.
  • Standardized format when acknowledging EIP CDI surveillance: Centers for Disease Control and Prevention's Emerging Infections Program Clostridioides difficile infection (CDI) surveillance.
  • Requestor to share any abstracts or manuscripts containing EIP isolate data with CDC prior to submission to scientific conferences or peer-reviewed journals. This is to make sure that appropriate acknowledgement of the EIP CDI Surveillance Program and the presentation or publication reflects what is proposed by the requestor.
    • At least one scientist from the CDC should review the abstract or manuscript. This even includes when lead authors are not CDC or EIP site staff.

Fees for approved requests

  • For-profit institutions: $150 per isolate.
  • Non-profit institutions requesting 11 or more isolates: $50 per isolate.
  • Non-profit institutions requesting 10 or fewer isolates: free of charge.

Contacts

Print
Content Source:
National Center for Emerging and Zoonotic Infectious Diseases (NCEZID)