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TB Notes 2, 2004


DTBE Announces the Tuberculosis Genotyping Program

On January 15, 2004, CDC began the Tuberculosis Genotyping Program to provide genotyping services to participating TB programs in the United States. CDC has contracted with two genotyping laboratories, one in Michigan and one in California, to provide these services. Participating TB programs may submit to a genotyping laboratory one culture-positive isolate from each patient with tuberculosis within their jurisdictions. In rare circumstances, TB programs may submit additional isolates from the same patient. The genotyping laboratories will analyze isolates from current patients, but TB programs may also request permission to submit selected isolates collected in the past. Although the implementation of universal genotyping (i.e., submitting one culture-positive isolate from every 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; they will only have to pay for the packaging and shipping costs.

Major benefits of genotyping.  The research results of the National Tuberculosis Genotyping and Surveillance Network (NTGSN) and the application of genotyping by TB programs demonstrate that genotyping holds great promise to help TB programs reduce active transmission of TB. A special November 2002 issue of the journal Emerging Infectious Diseases was devoted to NTGSN’s findings (Castro et al. 2002). The special issue of the journal is available at

NTGSN’s research findings and the application of genotyping by TB programs demonstrate that, through genotyping,

  • Contact investigations will be enhanced, expedited, and prioritized;
  • Unsuspected relationships between cases and new and unusual transmission settings will be discovered;
  • Outbreaks will be detected earlier and controlled more rapidly;
  • Transmission that occurs between patients who reside in different jurisdictions will be detected more readily;
  • False-positive cultures will be identified more easily;
  • TB programs will be able to assess distribution and prevalence of M. tuberculosis strains; and
  • TB programs will be able to evaluate completeness of routine contact investigations and progress toward TB elimination by monitoring genetic clustering as a surrogate marker of recent TB transmission.

In December 2003, Drs. Kenneth G. Castro, Director, Division of Tuberculosis Elimination, and Jonathan Kaplan, then Director, Division of AIDS, STD, and TB Laboratory Research, mailed an announcement of this new program to all TB controllers; copies were also sent to State Laboratory Directors.  Accompanying the announcement was a booklet containing guidance on developing a TB genotyping program, and a description of how the genotyping would be performed and how results would be reported. The booklet also contains instructions to TB programs about how to submit applications to participate.

The National Tuberculosis Controllers Association and the CDC have formed an Advisory Group on Genotyping and will print and distribute a Guide to the Application of Genotyping to Tuberculosis Prevention and Control to help TB programs develop procedures for effectively using genotyping results for TB prevention and control. We expect the Guide to be available in the summer of 2004.

All of the 68 TB programs in the United States that have cooperative agreements with CDC are eligible to apply to participate in the CDC Tuberculosis Genotyping Program. As of June, 43 state and big city TB programs have applied and been approved to participate in the program. Following are the steps that are required to make an application:

  • Obtain a copy of the CDC Tuberculosis Genotyping Program Application Instructions, as well as a copy of the application form, which are available on the TB WebBoard at under the folder “TB Genotyping.”
  • Read the booklet to become familiar with the Program.
  • Send the application to the CDC Tuberculosis Genotyping Program by facsimile (fax) at 404-639-8959.

Applications will be reviewed to ensure that important steps, which are described in the booklet, have been planned. If you have questions about completing your application, contact Dr. Thomas Navin or the CDC program consultant for your area. If you have laboratory questions, contact Dr. Jack Crawford at When your application is approved, you will be informed where to submit your isolates.

—Reported by Jack Crawford, PhD,
Div of AIDS, STD, and TB Laboratory Research, and
Tom Navin, MD, MPH,
Div of TB Elimination


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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