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U.S. Department of Health and Human Services


Guide to the Application of Genotyping to Tuberculosis Prevention and Control

Applying Genotyping Results to Tuberculosis
Control Practices

Evaluating Nonmatching Genotypes

The previous discussion focused on genotyping matches. The following discussion will describe possible action steps for isolates that have nonmatching genotypes. If the genotyping laboratory reports that an isolate has a unique genotype that does not match any other isolates from the TB programís jurisdiction, no further genotyping tests are required to conclude that the isolate is genetically distinct. Specifically, there is no reason to request RFLP if PCR tests have shown that an isolate has a unique genotype pattern.

Nonmatching Genotypes with Known Epidemiologic Links

Results from the NTGSN study show that patients with nonmatching genotypes often had known epidemiologic links identified during previous contact investigations. In these cases, three possibilities exist: a) the genotypes changed slightly over time, b) the previously identified epidemiologic links are misleading and do not reflect recent transmission, or c) the genotyping results are erroneous or misleading. Although there is little information available about the relative frequencies of these three possibilities, the standardized nature of the genotyping tests and the ambiguities involved in conducting contact investigations suggest that misleading epidemiologic links are much more common than incorrect genotyping results.

The possibility that genotypes have changed slightly over time is easy to evaluate. Isolates that match in all but one digit in the MIRU type or that have spoligotypes that differ in one region (as a result of loss of one or more spacers) should be considered closely related.  Programs should consult with the genotyping laboratory or CDC to determine if RFLP typing of such isolates is warranted. RFLP patterns can also change slightly over time. In these cases, the RFLP patterns will differ by only a single band.

There are two common characteristics of patients identified with known epidemiologic links and nonmatching genotypes; if either of these characteristics is present, the probability that the epidemiologic links are incorrect or misleading is even higher. As discussed in Chapter 4, Combining Genotyping and Epidemiologic Data to Improve Our Understanding of Tuberculosis Transmission, epidemiologic links that have later been shown to be inconsistent with genotyping results have occurred when the presumed secondary case-patient was born in a foreign country or when the presumed source case-patient was culture-positive but sputum smear-negative. If either of these characteristics is present, these epidemiologic links presumably do not indicate recent transmission.

Incorrect or misleading genotyping results are not common. They can, however, occur under unusual circumstances. Persons can be infected with more than one strain of M. tuberculosis at the same time. If an infection with two strains of M. tuberculosis is suspected, the TB program should consult with the genotyping laboratory about testing additional isolates from that person. Finally, a genotyping laboratory error can occur. A specimen might be mislabeled, an isolate might be contaminated, or there might be an error in reporting. If any of these are suspected, the genotyping laboratory should be consulted.

Nonmatching Genotypes and No Known Epidemiologic Links Identified

If a particular isolate shows a unique genotype pattern that has not been reported from a jurisdiction in the past, and if the contact investigation of the person with the non-matching genotype did not reveal any epidemiologic links with other cases or only possible epidemiologic links, there is insufficient evidence of recent transmission to support additional investigations. Although future genotyping reports might identify new patients with matching genotypes (and if they do, additional investigations might be required at that point), at this point in the decision analysis there is little additional work that is necessary, except to ensure that routine TB control measures have been taken.

Concluding Remarks on Decision Analysis

At this point in the decision analysis, genotyping data have been combined with information about possible epidemiologic links in order to determine what specific action steps are needed. The following sections describe the goals, steps, and the expected outcome of those action steps.


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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