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Notice to Readers: New CDC Program for Rapid Genotyping of Mycobacterium tuberculosis Isolates

In January 2004, the CDC Tuberculosis Genotyping Program was initiated to enable rapid genotyping of isolates from every patient in the United States with culture-positive tuberculosis (TB). The Federal Tuberculosis Task Force recommended nationwide TB genotyping in response to the Institute of Medicine report, Ending Neglect: The Elimination of Tuberculosis in the United States (1,2). Subsequently, TB control programs in 50 states and two large cities (New York and San Diego) were approved to participate in the TB Genotyping Program, which was developed in collaboration with the National TB Controllers Association (NTCA).

The TB Genotyping Program contracts with laboratories in California and Michigan, which provide results within 10 working days from two polymerase chain reaction (PCR)-based genotyping tests: mycobacterial interspersed repetitive units (MIRU) typing (3) and spoligotyping (4). In combination, these two tests provide a highly discriminatory method to identify strains. An additional genotyping method, IS6110--based restriction fragment length polymorphism fingerprinting (5), is available to provide further discrimination between strains for isolates with identical PCR results. The mycobacteriology laboratory branch at CDC also participates in the TB Genotyping Program by performing genotyping testing for quality-control purposes.

In 2004, NTCA and CDC published the Guide to the Application of Genotyping to Tuberculosis Prevention and Control (6). TB genotyping will help TB-control programs identify recent transmission of TB, detect outbreaks sooner, identify false-positive M. tuberculosis cultures, evaluate completeness of routine contact investigations, and monitor progress toward TB elimination (6,7).


  1. CDC. Federal Tuberculosis Task Force plan in response to the Institute of Medicine Report, Ending Neglect: The Elimination of Tuberculosis in the United States. Atlanta, GA: US Department of Health and Human Services, CDC; 2003. Available at
  2. Institute of Medicine. Ending neglect: the elimination of tuberculosis in the United States. Washington, DC: The National Academies Press; 2000.
  3. Mazars E, Lesjean S, Banuls AL, et al. High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology. Proc Natl Acad Sci U S A 2001;98:1901--6.
  4. Kamerbeek J, Schouls L, Kolk A, et al. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol 1997;35:907--14.
  5. van Embden JD, Cave MD, Crawford JT, et al. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for standardized methodology. J Clin Microbiol 1993;31:406--9.
  6. National TB Controllers Association/CDC Advisory Group on Tuberculosis Genotyping. Guide to the application of genotyping to tuberculosis prevention and control. Atlanta, GA: US Department of Health and Human Services, CDC; 2004. Available at
  7. McNabb SJN, Braden CR, Navin TR. DNA fingerprinting of Mycobacterium tuberculosis: lessons learned and implications for the future. Emerg Infect Dis 2002;8:1314--9.

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