Routine use of the Gen-Probe MTD2 amplification test for detection of Mycobacterium tuberculosis in clinical specimens in a large public health mycobacteriology laboratory

Differential diagnostic assays for discriminating mycobacteria, especially for nontuberculous mycobacteria: what does the future hold?

Mycobacteria infections are an important medical problem, and many are regarded as emerging and re-emerging diseases. Mycobacterium tuberculosis, the causative agent of tuberculosis, remains a leading cause of human morbidity and mortality worldwide, with approximately 8.6 million cases and 1.3 million deaths in 2012. In addition, the incidence of nontuberculous Mycobacterium infection has significantly increased, especially among developed countries. Although phenotypical appearances such as culture characteristics and/or susceptibility to anti-Mycobacterium drugs are variable between different mycobacterial species, early diagnosis is crucial in terms of patient treatment and clinical outcome. In this manuscript, we describe the development of diagnostic techniques, from the classical/conventional to the most recent advances, and provide an overview of the future direction of discrimination procedures.

A clinical approach to paediatric tuberculosis in Canada

OBJECTIVE

To review clinical aspects of management of tuberculosis (TB) infection and disease in Canadian children in the context of the global TB epidemic and the rising incidence of drug-resistant TB.

DATA SOURCES

ORIGINAL AND REVIEW ARTICLES PERTINENT TO: epidemiology of TB globally and in Canada; management of latent TB infection and TB disease in children; diagnostic tests for latent TB infection and TB disease; and management of drug-resistant TB disease. Multiple Medline searches were used including combinations of the MeSH terms 'Tuberculosis*' (and its multiple subheadings), 'Child*', 'Drug Resistance', 'Mycobacterium tuberculosis*' and 'Canada/epidemiology*'. Select relevant textbooks were reviewed.

DATA SELECTION AND EXTRACTION

The articles were analyzed from the perspective of clinicians managing children in Canada today, and from our experience of managing children with TB in Southern Ontario.

DATA SYNTHESIS

TB in Canada is largely a disease of the foreign-born and their children, but continues to occur in aboriginal children. Drug resistance is increasing globally and in Canada. Most children with TB disease in Canada are asymptomatic and found through contact tracing. False positive skin tests are frequent where TB prevalence is low.

CONCLUSIONS

Obtain source case drug sensitivities when treating TB contacts and those with latent TB infection. Obtain cultures before treating TB disease and treat disease with at least four antituberculous drugs while awaiting sensitivities. Use Directly Observed Therapy for TB disease. Confine TB skin testing to children at high risk for TB infection or disease, including contacts of infectious patients and recent immigrants. A team approach and infection control measures including environmental controls are important in managing TB disease.

Commercial nucleic-acid amplification tests for diagnosis of pulmonary tuberculosis in respiratory specimens: meta-analysis and meta-regression

Background

Hundreds of studies have evaluated the diagnostic accuracy of nucleic-acid amplification tests (NAATs) for tuberculosis (TB). Commercial tests have been shown to give more consistent results than in-house assays. Previous meta-analyses have found high specificity but low and highly variable estimates of sensitivity. However, reasons for variability in study results have not been adequately explored. We performed a meta-analysis on the accuracy of commercial NAATs to diagnose pulmonary TB and meta-regression to identify factors that are associated with higher accuracy.

Methodology/Principal Findings

We identified 2948 citations from searching the literature. We found 402 articles that met our eligibility criteria. In the final analysis, 125 separate studies from 105 articles that reported NAAT results from respiratory specimens were included. The pooled sensitivity was 0.85 (range 0.36–1.00) and the pooled specificity was 0.97 (range 0.54–1.00). However, both measures were significantly heterogeneous (p<.001). We performed subgroup and meta-regression analyses to identify sources of heterogeneity. Even after stratifying by type of commercial test, we could not account for the variability. In the meta-regression, the threshold effect was significant (p = .01) and the use of other respiratory specimens besides sputum was associated with higher accuracy.

Conclusions/Significance

The sensitivity and specificity estimates for commercial NAATs in respiratory specimens were highly variable, with sensitivity lower and more inconsistent than specificity. Thus, summary measures of diagnostic accuracy are not clinically meaningful. The use of different cut-off values and the use of specimens other than sputum could explain some of the observed heterogeneity. Based on these observations, commercial NAATs alone cannot be recommended to replace conventional tests for diagnosing pulmonary TB. Improvements in diagnostic accuracy, particularly sensitivity, need to be made in order for this expensive technology to be worthwhile and beneficial in low-resource countries.

Current evidence on diagnostic accuracy of commercially based nucleic acid amplification tests for the diagnosis of pulmonary tuberculosis

BACKGROUND

Even though commercial nucleic acid amplification tests (NAATs) have become the most frequently used molecular tests for laboratory diagnosis of pulmonary tuberculosis (TB), published studies report variable estimates of their diagnostic accuracy. We analysed the accuracy of commercial NAATs for the diagnosis of pulmonary TB in smear positive and smear negative respiratory samples using culture as a reference standard.

METHODS

English language studies reporting data sufficient for calculating sensitivity and specificity of commercial NAATs on smear positive and/or smear negative respiratory samples were included. Meta-regression was used to analyse associations with reference test quality, the prevalence of TB, sample and test type. Predictive values for different levels of pre-test probability were quantified using Bayes' approach.

RESULTS

Sixty three journal articles published between 1995 and 2004 met the inclusion criteria. Pooled sensitivity and specificity were 0.96 and 0.85 among smear positive samples and 0.66 and 0.98 among smear negative samples. The number of culture media used as reference test, the inclusion of bronchial samples, and the TB prevalence were found to influence the reported accuracy. The test type had no effect on the diagnostic odds ratio but seemed to be correlated with sensitivity or specificity, probably via a threshold effect.

CONCLUSIONS

Commercial NAATs can be confidently used to exclude TB in patients with smear positive samples in which environmental mycobacteria infection is suspected and to confirm TB in a proportion of smear negative cases. The methodological characteristics of primary studies have a considerable effect on the reported diagnostic accuracy.

The diagnosis of tuberculosis

Diagnostic testing for tuberculosis has remained unchanged for nearly a century, but newer technologies hold the promise of a true revolution in tuberculosis diagnostics. New tests may well supplant the tuberculin skin test in diagnosing latent tuberculosis infection in much of the world. Tests such as the nucleic acid amplification assays allow more rapid and accurate diagnosing of pulmonary and extrapulmonary tuberculosis. The appropriate and affordable use of any of these tests depends on the setting in which they are employed.

Molecular genetic methods for diagnosis and antibiotic resistance detection of mycobacteria from clinical specimens

Mycobacteria comprise a diverse group of bacteria that are widespread in nature, some of which cause significant disease in humans. Members of the Mycobacterium tuberculosis complex (MTBC) are the most important human pathogens of the genus Mycobacterium. Traditional methods for detection and identification of mycobacteria include microscopy, culture and phenotypic tests. These methods either lack sensitivity, specificity, or are time consuming. Advances in the field of molecular biology have provided rapid diagnostic tools that have reduced the turnaround times for detecting MTBC and drug resistance in cultures and directly in clinical specimens from weeks to days. This review discusses the molecular genetic techniques for detecting and identifying MTBC as well as drug resistance of mycobacteria in clinical specimens.

New method for detection of Mycobacterium tuberculosis Direct Test inhibitors in clinical specimens

Existing protocols for the detection of Mycobacterium tuberculosis Direct Test (MDT) inhibitors require substantial quantities of specimen and cannot distinguish Mycobacterium tuberculosis complex from other mycobacteria if inhibitors are present. We describe a preliminary evaluation of a simple and practical protocol for MTD inhibitor testing that circumvents these difficulties.

Practical strategies for performance optimization of the enhanced gen-probe amplified mycobacterium tuberculosis direct test

The enhanced Gen-Probe Amplified Mycobacterium Tuberculosis Direct (MTD) test was evaluated using a combined set of 338 acid-fast smear-positive and smear-negative, respiratory and nonrespiratory clinical specimens received by the Massachusetts State Tuberculosis Laboratory from September 1999 through March 2002. Microbiological culture was used as the reference method; therefore, the sensitivity and specificity of the MTD test were calculated for culture-positive specimens only. The initial assessment indicated that the overall sensitivity, specificity, and positive and negative predictive values of the MTD test for all specimens grouped together were 62, 98, 99, and 68%, respectively. A detailed discrepancy analysis revealed that two major factors causing negative MTD results in specimens that were culture positive for M. tuberculosis complex were patient treatment with antituberculosis drugs prior to testing and the presence of inhibitory substances in the specimen. Based on these findings, a protocol for optimizing MTD test performance in this setting is proposed in which (i) specimens from patients taking antituberculosis medications are excluded from testing and (ii) all initially MTD-negative or MTD-equivocal specimens are subjected to testing for inhibitors. If this strategy was followed, the MTD test sensitivity would be at least 91%, a significant improvement over the initial sensitivity of 62%. Accordingly, the negative predictive value would increase from 68 to 91%.

Cost-effectiveness analysis of the gen-probe amplified mycobacterium tuberculosis direct test as used routinely on smear-positive respiratory specimens

A decision analysis was conducted to evaluate the cost-effectiveness of programs in which the Amplified Mycobacterium Tuberculosis Direct test (MTD) (Gen-Probe) is used to rapidly exclude Mycobacterium tuberculosis complex as a cause of disease in smear-positive respiratory specimens. MTD sensitivity, specificity, and probability of inhibition for smear-positive specimens were estimated from literature reports. Costs and laboratory performance characteristics were determined from review of records and practices at an urban hospital in the mid-Atlantic United States. In the base case, 31.4% of smear-positive specimens were assumed to be culture positive for M. tuberculosis. Under these conditions, the marginal cost of the MTD testing program was estimated as $338 per smear-positive patient, or $494 per early exclusion of tuberculosis based on negative MTD results. By comparison, the cost of respiratory isolation ($27.77/day) and drugs ($5.66/day) averted by MTD testing was estimated at $201 per early tuberculosis exclusion. MTD testing was therefore not cost-effective in this scenario. Sensitivity analysis revealed that cost-effectiveness estimates are sensitive to the number of smear-positive specimens processed annually, the relative prevalence of M. tuberculosis in smear-positive specimens, and the marginal daily cost of respiratory isolation. A decision tool is therefore presented for assessing the cost-effectiveness of MTD under various combinations of those three variables. While routine MTD testing of smear-positive specimens is not expected to be cost-saving for most individual hospitals, centralized reference laboratories may be able to implement MTD in a cost-effective manner across a wide range of situations.

Evaluation of Gen-Probe amplified mycobacterium tuberculosis direct test by using respiratory and nonrespiratory specimens in a tertiary care center laboratory

The performance of the Amplified Mycobacterium Tuberculosis Direct (AMTD) test (Gen-Probe Inc., San Diego, Calif.) was assessed in a large tertiary care mycobacteriology laboratory. Both acid-fast smear-positive and smear-negative respiratory and nonrespiratory clinical specimens were analyzed. From February 1998 to 4 October 2001, AMTD assays were performed on 391 respiratory specimens and 164 nonrespiratory specimens. The AMTD assay was compared to the "gold standard" of combined culture and clinical diagnosis. The overall sensitivity for all specimens, including those for which no smear result was available, was 91.2%. The overall sensitivities of the assay, including acid-fast smear-positive and -negative specimens, were 97.8 and 77.3% for respiratory and nonrespiratory specimens, respectively. The corresponding specificities for respiratory and nonrespiratory specimens were 99.1 and 98.5%, respectively. The overall specificity for all specimens was 98.9%. Positive and negative predictive values were 93.9 and 99.7% and 91.7 and 96.4% for respiratory and nonrespiratory specimens, respectively. The time saved by using the AMTD test for making a diagnosis of tuberculosis instead of using culture was 8.99 days. Inhibitors to the AMTD assay were found in 3.1% of respiratory specimens and 3.1% of nonrespiratory specimens. The assay, used in a general mycobacteriology laboratory setting, represents an important advance in improving the speed and accuracy of diagnosis in the management of patients with tuberculosis.

The mycobacteriology laboratory and new diagnostic techniques

Use of the most rapid and reliable laboratory tests for mycobacterial detection, identification, and susceptibility testing is important for TB control. In 1993, CDC experts made recommendations regarding optimal methods of mycobacterial testing (i.e., stains for AFB, culture, identification, and susceptibility testing of M. tuberculosis) and turnaround times for reporting results. Various technical advances have enhanced the diagnostic capability of the laboratory and/or improved laboratory efficiency since then. The commercial NAA tests for direct detection of MTBC have the greatest potential to impact patient care. To assist physicians, CDC experts have published recommendations concerning use of the NAA tests for management of patients with suspected TB, with emphasis on the MTD assay, which is approved for both AFB smear-positive and smear-negative specimens. With regard to mycobacterial culture, totally automated, nonradiometric systems are commercially available. For mycobacterial identification, various molecular techniques have been developed, but at present, they are used predominantly in research or large reference laboratories. Molecular tests also have proved useful for better understanding the epidemiology of TB and investigating episodes of suspected laboratory cross-contamination. With regard to mycobacterial susceptibility testing, use of the new automated culture systems for testing MTBC is under evaluation, but only one such system has been approved for this purpose. In addition, laboratory guidelines for susceptibility testing of MTBC and certain NTM have recently been published by the NCCLS.

Principles of molecular microbiology testing methods

Molecular testing methods have the potential to replace many conventional microbiology laboratory assays. Recent refinements in technology have resulted in more user-friendly testing platforms. These platforms are automated and have lowered risks for contamination, decreased costs, and are faster than older platforms. The success of these technologies depends on their successful application to patient care. Quality issues include appropriate specimens for analysis, performance characteristics of different analytical methods, optimal specimen processing, the effects of PCR inhibitors, and false-positive results caused by contaminating nucleic acids. Quality control guidelines for molecular microbiologic diagnostic assays are in their infancy and require further development. Additionally, the problem of "too much" sensitivity (brought on by the extreme sensitivity of these techniques coupled with the potential presence of small numbers of pathogenic organisms in asymptomatic individuals) should be considered. Potential problems when monitoring therapy (because molecular detection techniques do not generally have the ability to determine whether an organism is dead or alive) can also occur. Cost-effective test use, pathogen- or disease-targeted algorithms, and standardized methods will be necessary for the true value of these technologies to be realized. This is especially important, because, unlike traditional culture methods, most molecular microbiology methods are pathogen-specific. Clinicians familiar with the reasons why "pan-culture" (i.e., requesting all culture possibilities at once) is inadvisable should not use the same irrational approach when requesting molecular tests. The clinical usefulness of molecular testing will be maximized as targeted algorithms are developed and an understanding of molecular test ordering patterns is realized. Laboratory technicians and physicians must continue to apply and combine theories of traditional microbiology, clinical chemistry, and general medicine to the understanding and application of molecular diagnostics.

Rapid detection of Mycobacterium tuberculosis in contaminated BACTEC 12B broth cultures by testing with Amplified Mycobacterium Tuberculosis Direct Test

Contamination of broth cultures of acid-fast bacilli (AFB) by bacterial species other than Mycobacterium species frequently occurs. Many of these contaminated cultures require redecontamination and reincubation before the appropriate tests can be performed for identification, significantly affecting the turnaround time for reporting culture results. In this study, the Amplified Mycobacterium Tuberculosis Direct Test (MTD; Gen-Probe) was performed to detect the Mycobacterium tuberculosis complex (MTBC) in 125 BACTEC 12B broth cultures with positive growth indices. Among these, 41 grew non-AFB bacteria only, and all 41 were negative by the MTD. The remaining 84 bottles contained contaminated cultures that grew both AFB and other bacteria or yeasts. Repeat decontamination and reincubation of these specimens required a mean time of 13 days (range, 3 to 40 days). The MTD results were positive for 10 samples, 9 of which were MTBC culture positive and 1 of which grew Myobacterium celatum, a species known to cross-react in the MTD. All cultures growing other mycobacterial species were negative by the MTD. The results of this study demonstrate that the MTD is both sensitive and specific in detecting MTBC in contaminated broth cultures and that, when used selectively, the MTD can potentially rule in or out a diagnosis of MTBC as much as 12 days earlier than using nonamplified DNA probe testing alone can.

Clinical Evaluation of the Gen-Probe amplified mycobacterium tuberculosis direct test for rapid detection of Mycobacterium tuberculosis in select nonrespiratory specimens

The performance of the Amplified Mycobacterium Tuberculosis Direct Test (MTD; Gen-Probe, Inc., San Diego, Calif.) for rapid diagnosis of extrapulmonary tuberculosis was evaluated by testing 178 nonrespiratory specimens from 158 patients. Criteria for specimen inclusion were (i) a positive smear for acid-fast bacilli (n = 54) and (ii) the source if the smear was negative (tissue biopsies and aspirates and abscess material were tested; n = 124). Results were compared to those of mycobacterial culture; clinical history was reviewed when MTD and culture results disagreed. Forty-eight specimens (27.0%) were positive for mycobacteria, including 23 Mycobacterium tuberculosis complex specimens; of which 21 were smear positive. Twenty-five specimens were MTD positive; 20 of these grew M. tuberculosis complex. All of the five MTD-positive, M. tuberculosis complex culture-negative specimens were considered truly positive, based on review of the medical record. Of the three MTD-negative, M. tuberculosis complex culture-positive specimens, two contained inhibitory substances; one of the two was smear positive. Excluding the latter specimen from analysis, after chart review, the sensitivity, specificity, and positive and negative predictive values of the MTD were 92.6, 100, 100, and 98.7%, respectively, by specimen and 89.5, 100, 100, and 98.6% by patient. Given the few smear-negative samples from patients with extrapulmonary tuberculosis in our study, additional similar studies that include more smear-negative, M. tuberculosis complex culture-positive specimens to confirm our data are desirable.

[Clinical evaluation of the Amplified Mycobacterium Tuberculosis Direct 2 test]

OBJECTIVE

To evaluate the performance of the Amplified Mycobacterium tuberculosis Direct Test 2- Gen Probe (AMTD- 2) for direct detection of Mycobacterium tuberculosis in smear-negative samples.

PATIENTS AND METHODS

From January to December 1999, 683 specimens, 333 respiratory and 350 non-respiratory ones collected from 457 patients, were included in the study. All the samples of HIV-positive patients, the respiratory samples from patients suspected of having pulmonary tuberculosis (at least two by patient) and all non-respiratory samples were included. As diagnosis method of reference, the culture isolation was considered. Clinical data were analyzed in case of discrepant results and clinical diagnosis was considered the reference criteria. The technique was performed once a week.

RESULTS

The sensitivity, specificity, and positive and negative predictive values of this assay were 58.9%, 93.9%, 37.1% and 97.4% respectively related to the standard culture. When referred to clinical diagnosis of active tuberculosis, these values improved to 70.4%, 97.7%, 73.1% and 96.8% respectively (in respiratory samples were 67.6%, 98.6%, 86.2% and 95.9% and in nonrespiratory ones 76.5%, 96.9%, 56.5% and 98.7% respectively). The mean time of diagnosis by culture and by AMTD-2 were 20.3 days (range 10-63) and 5.7 days (range 2-20) respectively.

DISCUSSION

It is concluded that AMTD-2 is a rapid diagnosis method when clinical data are sugestive with active tuberculosis. However, due to the low positive predictive value, it would be convenient to obtain successive samples to confirm the result in patients without clinical evidence of tuberculosis.

Molecular techniques in mycobacterial detection

OBJECTIVE

To assess the clinical utility of the commercial nucleic acid amplification (NAA) tests (ie, Amplified Mycobacterium Tuberculosis Direct Test, Gen-Probe, Inc and AMPLICOR Mycobacterium tuberculosis Test, Roche Molecular Systems, Inc) for direct detection of Mycobacterium tuberculosis complex.

DATA SOURCES

Review of the English-language literature.

CONCLUSIONS

The performance of both NAA tests is excellent (sensitivity, > or = 95%; specificity, 100%) when testing respiratory specimens that are smear-positive for acid-fast bacilli (AFB). Only the Gen-Probe assay is approved for testing respiratory specimens regardless of the AFB smear result. Data from 3 studies showed that the sensitivity of the Mycobacterium Tuberculosis Direct Test in smear-negative patients ranged from 83% to 85%, and that the specificity was 99%. Both NAA tests have been used to test nonrespiratory specimens; in some studies, the performance was comparable to the performance obtained for respiratory specimens, whereas in others, it was lower. The NAA tests also appear to be reliable tools for rapid detection of M tuberculosis complex in positive broth cultures of all specimen types (except blood). The impact of the NAA tests on patient outcome varies based on the result of the AFB smear. In smear-positive patients, public health and hospital infection-control resources are predominantly affected. The potential for influencing patient outcome is much greater when the AFB smear is negative. In smear-negative patients, the NAA test could provide more rapid diagnosis of tuberculosis and subsequent initiation of therapy; eliminate the need for invasive diagnostic procedures, which are both costly and pose an added risk to the patient; and allow earlier discharge of hospitalized patients. Prospective studies concerning the cost-effectiveness of the NAA tests are needed.