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Guide to the Application of Genotyping to Tuberculosis Prevention and Control

CDC Tuberculosis Genotyping Laboratory Procedures

Two genotyping laboratories have been funded through contracts with CDC to support the CDC Tuberculosis Genotyping Program by providing genotyping services to TB programs in the United States. TB programs can submit one isolate from each person with culture-positive tuberculosis within their jurisdictions. The genotyping laboratories will analyze isolates from current patients, but TB programs may request permission to submit selected isolates collected in the past. Isolates that are thought to be the result of false-positive cultures can be submitted, even though they may not result in a reported case. In special circumstances described in Chapter 5, Developing a Tuberculosis Genotyping Program, TB programs may submit additional isolates from the same patient.

The genotyping laboratories will use three genotyping methods: spoligotyping, MIRU analysis, and IS6110-based RFLP analysis, also known as fingerprinting. Spoligotyping and MIRU analysis are based on PCR. Together, these two methods will be referred to as the PCR genotyping tests. All submitted isolates will be analyzed by the first two methods; selected isolates will be analyzed with RFLP analysis. Descriptions of the technical aspects of these three methods were published recently (Barnes 2003).

Genotyping results will be reported to the TB program but not to the submitting laboratories, except when isolates represent suspected false-positive cultures. When the submitting laboratory suspects a false-positive culture, genotyping results from these submissions will be provided to both the TB program and the submitting laboratory.


Released October 2008
Centers for Disease Control and Prevention
National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention
Division of Tuberculosis Elimination -

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