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Guide to the Application of Genotyping to Tuberculosis Prevention and Control

Introduction to Tuberculosis Genotyping

Overview of the CDC Tuberculosis Genotyping Program

Two genotyping laboratories, one in Michigan and one in California, are under contract with CDC to provide genotyping services to TB programs in the United States. TB programs that have been approved to participate in the CDC Tuberculosis Genotyping Program may submit to a genotyping laboratory one isolate from each culture-positive patient with TB within their jurisdictions. In rare circumstances, TB programs may submit additional isolates from the same patient. These circumstances are described in Chapter 5, Developing a TB Genotyping Program. The genotyping laboratories will analyze isolates from current patients, but TB programs may request permission to submit selected isolates collected in the past. Although the implementation of universal genotyping (i.e., submitting one isolate from every culture-positive patient with TB) has substantial benefits, a TB program does not have to submit a particular number or percentage of isolates to participate in the program.

The genotyping laboratories will use three genotyping methods: spoligotyping, mycobacterial interspersed repetitive units (MIRU) analysis, and IS6110-based restriction fragment length polymorphism (RFLP) analysis. Spoligotyping and MIRU analysis are based on the polymerase chain reaction (PCR). Together, these methods will be referred to as PCR genotyping tests. The genotyping laboratories will analyze all the submitted isolates by both PCR genotyping tests. Under certain circumstances and upon the request of the TB program, isolates that have matching genotypes by both spoligotyping and MIRU analysis can be tested by RFLP analysis. Genotyping results, under most circumstances, will be reported to the TB program but not to the submitting laboratories. The genotyping services are free to TB programs, but neither CDC nor the genotyping laboratories will pay the packaging and shipping costs.


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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