Evaluation of two commercial amplification assays for detection of Mycobacterium tuberculosis complex in respiratory specimens

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.

Evaluation of three commercial detection systems for Mycobacterium tuberculosis where clinical diagnosis is difficult

AIMS

To assess the performance of three commercially available Mycobacterium tuberculosis detection systems employing nucleic acid amplification, when applied directly to respiratory and non-respiratory specimens from patients where the diagnosis of tuberculosis is difficult using clinical and traditional bacteriological methods.

METHODS

42 respiratory and 21 non-respiratory specimens were concentrated, examined with auramine staining, and cultured on Lowenstein-Jensen slopes. These specimens were also assayed using the Amplicor Mycobacterium tuberculosis test (AM) (Roche Diagnostic Systems), the Amplified Mycobacterium tuberculosis direct test (AMD) (Gen-Probe), and the LCx Mycobacterium tuberculosis assay (LMA) (Abbott Laboratories).

RESULTS

All three amplification systems used in this study gave specificities of 100% when used on respiratory specimens. When used on non-respiratory specimens, AM and LMA gave specificities of 100% and AMD 75%. With respiratory specimens the AM, AMD, and LMA systems gave sensitivities of 75%, 65.2%, and 79.2%, respectively. With non-respiratory specimens the sensitivities were 50%, 66.7%, and 60%, while with smear negative, culture positive specimens they were 33.3%, 66.7%, and 55.6%. Positive predictive values of 100% were seen with all specimens except non-respiratory specimens assayed using AMD where the value was 66.7%.

CONCLUSIONS

The manufacturers of these systems recommend that they should only be used for the direct analysis of respiratory specimens, and the US Food and Drug Administration has approved them for use only with smear positive specimens. This study confirms that sensitivities are lower for non-respiratory and smear negative specimens, but positive predictive values are high. Provided they are interpreted with caution, positive results with these tests in respiratory and non-respiratory specimens are useful in tuberculous patients who are otherwise difficult to diagnose. Each amplification has advantages and disadvantages compared with the others.

Clinical application of the Mycobacterium tuberculosis direct test: case report, literature review, and proposed clinical algorithm

The relatively new Mycobacterium tuberculosis direct test (MTDT) enzymatically amplifies M tuberculosis complex 16s ribosomal RNA. The sensitivity of the test ranges from 75 to 100%, with specificity of 95 to 100%, positive predictive value between 78% and 100%, and negative predictive value between 95% and 100%. Similar test characteristics have been documented in nonrespiratory specimens and in specimens that ultimately grow nontuberculous mycobacterium (NTM). This test allows for rapid identification of M tuberculosis in the smear-positive patient and may greatly improve sensitivity over acid-fast bacilli smear alone. A negative test result with a positive smear suggests infection with NTM or Mycobacterium avium complex. We present a case that illustrates the value of MTDT for analysis of tissue specimens in immunocompromised patients with suspected mycobacterial disease and review the rapidly developing literature about this test. We propose an algorithm using MTDT, acid-fast smear, and mycobacterial culture for the diagnosis and treatment of the immunocompromised patient with suspected mycobacterial infection.

Critical assessment of gene amplification approaches on the diagnosis of tuberculosis

The resurgence of tuberculosis prompted the development of a number of new options for the rapid laboratory diagnosis of Mycobacterium tuberculosis (MTB). One of the most promising and exciting methodologies has been the introduction of assays employing amplification technology to detect MTB directly in clinical specimens. Although amplification assays hold significant promise to improve the laboratory diagnosis of tuberculosis, the decision to perform or not perform these assays is complicated. The performance of in-house polymerase chain reaction (PCR) assays and two commercially-prepared assays. GenProbe's AMTD test and Roche's AMPLICOR PCR assay are reviewed. Regardless of the amplification format, all assays have decreased sensitivity with specimens that are acidfast bacilli (AFB) stain-negative. Data from these studies and others indicate possible potential pitfalls of amplification assays, those being sampling errors, the presence of substances in clinical specimens that inhibit the amplification assay, and clinical utility. In light of these findings, the possible roles for these assays in the clinical microbiology laboratory are reviewed. In addition, factors such as cost, assay performance, etc. are discussed in order to facilitate the decision-making process concerning whether an amplification assay would be appropriate in a particular laboratory setting.