Mycobacterium tuberculosis Genotyping

Indiana Epidemiology Newsletter
November 2007

Tina Feaster
Tuberculosis Epidemiologist

Mycobacterium tuberculosis (TB) bacteria are transmitted through airborne particles known as droplet nuclei. Depending on the frequency, duration, and environment of exposure, a person can become infected with TB. A person that is infected with TB but does not have disease is known to have latent TB infection (LTBI). Once a person has contracted LTBI, the risk for progression to disease varies. The greatest risk for progression to disease occurs within the first two years after infection, when approximately half of the 5-10 percent lifetime risk occurs (1). HIV infection is the greatest risk factor for progression to disease. Other high-risk factors include LTBI in infancy or early childhood, diabetes mellitus, apical fibronodular changes on chest radiograph, and therapeutic agents for treating autoimmune-related conditions.  Since disease may take years to develop, sometimes it is difficult to determine where transmission took place and if the transmission has stopped.

In 2004, the National Tuberculosis Controllers Association (NTCA), along with the Centers for Disease Control and Prevention (CDC) Advisory Group on Tuberculosis Genotyping, published the Guide to the Application of Genotyping to Tuberculosis Prevention and Control (2). The CDC has contracted with laboratories in California and Michigan to perform the genotyping (DNA analysis). TB control programs in 50 states and two large cities (New York and San Diego) participate in this program (3). All initial culture positive isolates of TB are sent to the program laboratories for genotyping. These data will help TB control programs identify recent transmission of TB, detect outbreaks sooner, identify false-positive M. tuberculosis cultures, and evaluate completeness of contact investigations.

The genotyping laboratories will use three methods: spoligotyping, mycobacterial interspersed repetitive units (MIRU) analysis, and IS6110-based restriction fragment length polymorphism (RFLP) analysis (2). Spoligotyping and MIRU analysis are based on the polymerase chain reaction (PCR). RFLP will be performed only if requested.  All isolates will be given a PCR type. If two PCR types match within a state, they will be given a state genotype cluster number.

Epidemiologic data, along with genotyping results, aid in contact investigations. Two patients in the same city may present with TB in the same time frame but have non-matching genotypes; it can be assumed that they were not involved in the same chain of recent transmission. Patients who belong to the same genotype cluster and share known epidemiologic links are said to belong to an epidemiologically confirmed genotype cluster. Two patients who have matching genotypes and share possible epidemiologic links will have to be re-evaluated to determine if they are involved in the same chain of recent transmission.

When the Indiana TB Control Program receives genotype results, this information is shared with the local public health nurse. If the TB Control Program is concerned about a genotype cluster or a genotype cluster has several recently new cases in the state, a conference call will be held with the TB Control Program and the counties involved to examine epidemiologic links. This involves re-interviewing the patient, re-evaluating contacts, and re-evaluating sites where transmission occurred. A major concern is high-risk congregate settings, which include health-care facilities, correctional facilities, homeless shelters, and bars. Also flagged are high-risk populations, e.g., HIV-infected persons, foreign-born, young children, and drug and excessive alcohol users who are contacts of the TB patient (1). Public health nurses and staff who have the best rapport with the patient and contacts should conduct these re-interviews, since a level of trust is needed to obtain sensitive information. The genotyping cluster information is very helpful at the state and national levels, as it helps build epidemiologic links that might not have been previously detected, especially with the mobility of patients in today’s world.

An estimated 1-3 percent of all reported cases of TB have an incorrect diagnosis for TB (2). Incorrect diagnosis can result from laboratory cross-contamination, mislabeling of patient specimens, collection errors, and reporting errors. If a patient presents with no signs or symptoms, negative chest radiograph, and improves with non-tuberculosis medications, the diagnosis should be re-evaluated. The patient might have only one specimen identified as TB positive, whereas all other specimens are negative. Genotyping may show a control strain used in the laboratory, or the specimen may have been processed near another specimen that had high numbers of TB bacillus in the sample.

What is in the pipeline for the TB Genotyping Program?  Lauren Cowan (L. Cowan, personal communication, November 5, 2007) from the CDC reports that:

  • a genotyping Web-based program will enable state TB control programs to access PCR information and manage their genotype data,

  • the Report of Verified Case of Tuberculosis (RVCT) will add PCR-type information to the report,

  • 12 more loci will be added to the MIRU analysis, which will make the test more sensitive.

The Tuberculosis Genotyping Program has improved the contact investigation of TB patients. Collaboration with the public health staff who continually interview patients for more clues in transmission has been very beneficial. The additional information enables the program to prioritize high-risk groups and populations and to find previously unknown places where transmission has occurred to facilitate locating new cases and contacts.



1. CDC. Controlling Tuberculosis in the United States, MMWR 2005; 54(No.RR-12):1-14.

2. 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; June 2004.

3. New CDC Program for Rapid Genotyping of Mycobacterium tuberculosis Isolates. JAMA 2005; 293:2086.