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Report of Expert Consultations on Rapid Molecular Testing to Detect Drug-Resistant Tuberculosis in the United States

General considerations and principles for a molecular drug-resistance testing service

  1. 13,299 TB cases were reported to CDC in 2007 (5,17).
    1. This includes 10,590 pulmonary and 2697 extrapulmonary cases, 10426 culture confirmed cases, 762 isoniazid-resistant cases, and 125 MDR TB cases.
    2. Of the 10,590 pulmonary cases, 4864 were sputum smear positive for AFB, 4524 were smear negative and 7366 were sputum culture positive and 1878 were culture negative.
  2. Rifampin resistance is a reliable surrogate (positive predictive value >95%) for MDR TB when isolated rifampin resistance is uncommon, as it is in the United States (18–20).
  3. Molecular DR tests are useful for testing isolates and respiratory specimens directly. However, the currently available tests are highly reliable when used with AFB-smear positive specimens, but they are less reliable when used with AFB-smear negative specimens. There is little information on the performance of molecular DR tests with other types of specimens.
  4. Both ‘susceptible’ and ‘resistant’ results from molecular DR tests can be useful.
    1. The sensitivity and specificity of molecular DR tests for rifampin are sufficiently high (>97%) to use both resistant and susceptible results in case management decisions.
    2. The sensitivity of molecular DR tests for isoniazid is not sufficient to exclude isoniazid resistance based on a negative result. However, because isoniazid resistance is about 8% in the United States, the positive predictive value for isoniazid resistance is relatively high and molecular detection of isoniazid resistance can be used in case management decisions.
  5. Molecular DR testing is particularly useful for
    1. patients suspected or at high risk of having drug-resistant TB,
    2. very ill patients for whom drug-susceptibility information might alter case management decisions, such as patients who do not get better while taking standard first-line therapy,
    3. outbreak or contact investigations when drug resistance is suspected in the source case or in some severely immunocompromised persons such as HIV-infected persons or those receiving dialysis in which knowledge of drug-susceptibility would be a significant benefit and affect preventive therapy decisions,
    4. persons for whom drug-susceptibility information would influence TB Control decisions such as placing the person on a ‘Do Not Board’† list, and
    5. isolates that contain a mixture of M. tuberculosis bacteria and other mycobacteria or respiratory specimens containing only nonviable M. tuberculosis bacteria.
  6. Molecular DR testing has significant potential added value for clinicians and TB control officials.
    1. Earlier detection of resistance leads to earlier initiation of an effective treatment regimen, a reduced period of infectiousness, and improved patient outcomes.
    2. Earlier notification of drug-resistant TB cases should permit public health interventions sooner and may engage an MDR TB expert sooner in the care of the TB patient.
    3. Earlier detection of rifampin resistance should lead to earlier testing for susceptibility to other first-line and second-line anti-TB drugs.
  7. Benefits of routing requests for molecular DR tests through the TB Program include
    1. early engagement of the TB Control Program in potential TB cases,
    2. early engagement of TB laboratory in follow-up susceptibility testing,
    3. improved communications between TB clinicians, controllers, and laboratorians,
    4. reinforcement of the important role played by state and local TB Programs,
    5. engagement of a person knowledgeable about molecular DR testing for TB early in decisions regarding whether or not to request a molecular DR test, and
    6. avoidance of excessive and inappropriate ordering of the molecular DR tests – simply having a check-off box on a form often leads to inappropriate ordering.
  8. Turnaround time (TAT) must be as brief as possible to maximize benefits of molecular DR testing. The key TAT is the interval from specimen collection to time that the test result is used by the clinician for case management.
  9. It is essential that the detection of resistance immediately trigger additional (reflex) testing for susceptibility to first and second line anti-TB drugs by conventional and molecular methods.

†The CDC and the Department of Homeland Security have developed a national ‘Do Not Board list’ to prevent commercial air travel of persons with known communicable diseases that pose a serious public health threat, such as infectious tuberculosis. A person whose name appears on a “Do Not Board” list, will not be allowed to board an airplane that is inbound to the United States, outbound from the United States, or any domestic flight inside of the United States.

  1. A potential benefit of a system for providing molecular DR tests may be expanding access to NAA testing for the initial diagnosis of TB.
  2. State regulations need to be addressed as part of developing a regional approach. For example, laboratories, regardless of location, that conduct testing for patients in New York must be certified by New York State.
  3. No molecular DR test has been approved by the FDA for use in the United States, although well-characterized test kits are available in Europe and elsewhere. Several validated molecular DR tests (line-probe assays, molecular beacons, and DNA sequencing) based on analyte specific reagents, often called “home-brew” or “in-house” tests are used in the United States. Each test displays similar performance characteristics. At this time, data do not demonstrate clearly the superiority of one method over another.
    1. Tests that detect M. tuberculosis DNA and drug resistance in one step have potential advantages related to lower cost, less hands-on time, simpler testing procedure, and use of a closed system. Although the currently available one-step systems have excellent performance with AFB-smear positive specimens and cultures, they perform less well when used with AFB-smear negative specimens.
    2. A protocol that uses two methods (e.g., uses an optimized NAA assay to detect M. tuberculosis DNA (13–15) and a second assay to assess resistance) has potential advantages of increased sensitivity, particularly if AFB-smear negative specimens are tested, and the possibility of conducting more informative second tests (e.g., sequencing). Disadvantages may include a higher cost, more hands-on time, and potential end-product contamination.
  4. Specimens suitable for molecular DR testing include cultures, processed specimens (sediments), and non-processed respiratory specimens. Because of the differences in the cost of testing non-processed (processing and molecular testing) and processed specimens (only molecular testing), programs must accurately project the anticipated numbers of non-processed and processed specimens to be tested to enable the molecular DR testing laboratories to estimate the cost of the services and CDC to adequately fund the service.
    1. Advantages of processed specimens include (1) prior testing showed the sample was AFB+ and (2) it would not be necessary to process the specimen at the molecular DR laboratory which saves time and labor for the molecular DR testing laboratory. Potential disadvantages include possibly insufficient quantity of the remnant sample and possible errors introduced during processing may affect the molecular DR testing.
    2. Advantages of non-processed specimens include (1) results with this specimen would be a check or confirmation of the results from conventional testing of another specimen, (2) a processing method optimized for molecular DR testing could be used, and (3) any errors in testing the first specimen would not affect the result of molecular DR testing. Potential disadvantages include (1) increased work load and cost for the molecular DR testing laboratory, (2) lengthening of the TAT at the molecular DR testing laboratory, (3) delays for obtaining a second specimen, and (4) sometimes a follow-up specimen may be AFB-negative due to sporadic shedding of TB bacilli.
    3. Advantages of testing cultures using molecular DR test include increased sensitivity and accuracy of the molecular DR test. Potential disadvantages include the time needed to obtain an isolate and the expense of shipping viable cultures may be as much as 5-fold more than for specimens.
  5. Molecular DR tests enhance but do not replace culture or conventional drug-susceptibility testing.
    1. Molecular DR tests are not as sensitive as culture for detecting M. tuberculosis complex bacteria.
    2. Molecular DR tests are not as sensitive as culture-based proportion tests for detecting resistant bacteria in a mixture of resistant and susceptible bacteria.
    3. Molecular DR tests are most useful for rifampin, somewhat less useful for isoniazid, and not currently available for other anti-TB drugs although some are being developed.
    4. False-positive and false-negative molecular DR test results do occur.
  6. In the case of discrepancies between conventional and molecular DR test results for rifampin and isoniazid, clinicians should use the conventional DS results and clinical judgment for case management decisions until the discrepancy is resolved.
  7. Failure of molecular DR tests can be caused by the presence of inhibitors in the sample that prevent or reduce NAA. Inhibitors appear to be present in 2% to 5% of respiratory specimens tested by NAA (21). Procedures must be in place to ensure that inhibition does not cause falsely negative or non-interpretable molecular DR test results. This may include internal controls to detect inhibitors and reflex repeat testing of samples suspected to contain inhibitors with steps taken to reduce inhibition (e.g., dilution or purification of DNA).
  8. Shipping costs will be substantial. In the Florida molecular DR testing program, the contract cost of FedEx next-day shipments for specimens is $11 to $28 ($3 to $5 for shipping container plus $8 [weekday] or $23 [Saturday] for transport). The cost of U.S. Postal Service next day shipments of specimens is $16.75 plus the cost of the container. For isolates, the cost of FedEx is $97 to $115 ($12 to $15 for the container plus $85 [weekday] or $100 [Saturday] for transport). The cost of shipping isolates to the genotyping laboratories using the CDC FedEx account is $27 per shipment plus the cost of the container.
  9. Reagent costs for the currently validated molecular DR tests range from $8 to $30 per sample. It is estimated that one technician can perform 20 molecular DR tests per day. Additional operating costs include time and materials needed for processing samples; preparing samples for molecular DR testing; entering, verifying and reporting results; technical assistance and consultation; proficiency testing; quality laboratory management; equipment; information technology, and overhead.
  10. Cost efficiency, rapid turnaround time, and expertise would be enhanced by establishing high-volume regional laboratories offering molecular DR tests.
  11. New funds will be needed to cover the costs of the molecular DR testing program. Potential sources of non-CDC funds to partially offset the cost of the program include the Robert Wood Johnson Foundation, Centers for Medicare and Medicaid Services, and insurance providers.
  12. Good communication between laboratorians, clinicians, and public health officials will be critical to optimizing the benefits of molecular DR testing. Standard language or statements to include in laboratory reports of molecular DR test results are needed, such as the information in points 4a, 4b, and 16 above, to assist clinicians interpret the results.
  13. Education of laboratorians, clinicians, TB controllers, and policy makers on the appropriate use and interpretation of molecular DR tests for TB will be essential.
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