Evaluation of Roche Amplicor PCR assay for Mycobacterium tuberculosis

A Rare Manifestation of Tuberculosis Presenting in the United States

A 64-year-old Bangladeshi female presented to her primary care physician with a tender right breast lump that had been present for 4-5 days along with subjective fevers and malaise. Initial biopsy revealed granulomas, but Ziehl-Neelsen and Gram stain were negative for TB so antibiotics were prescribed for abscess until culture came positive for tuberculosis. She was started on triple therapy for extrapulmonary tuberculosis, an exceedingly rare presentation that requires high clinical suspicion in the Western world.

Young Adult Hip: Reactivation of dormant, previously undiagnosed Mycobacterium Tuberculosis infection following intra-articular steroid injection

INTRODUCTION

Tuberculosis (TB) still remains a common problem in the UK and, with the increasing number of patients being offered arthroplasties; periprosthetic involvement is not uncommon anymore. However, the diagnosis of TB infected arthroplasties still remains difficult and misdiagnosis is common, therefore delaying treatment.

CASE REPORT

We describe a 36-years old Caucasian female with no known history of TB who presented with hip pain thought to be due to femoro-acetabular impingement (FAI). In the course of 18 months, the patient had been investigated extensively; including steroid injection, hip arthroscopy (including synovial biopsies), and eventually a total hip arthroplasty. During arthroplasty, further extensive biopsies were performed which raised the suspicion of TB on histology. Further synovial biopsies obtained arthroscopically were microbiologically positive for TB (PCR). The patient was sent to an infectious disease specialist. It appeared that the patient had TB in the past, of which she was unaware.

CONCLUSION

We hypothesise that the immunosuppressant effects of the steroid injections she received reactivated her TB.

Evaluation of in-house polymerase chain reaction assay sensitivity, can it be utilized in limited-resources settings?

BACKGROUND

Polymerase chain reaction (PCR) assay has widely used for the detection of tuberculosis (TB). This study tried to compare in-house PCR with some well-known commercial PCR kits for detection of TB agent.

METHODS

Clinical samples obtained from 620 TB suspected patients were analyzed for the diagnosis of Mycobacterium tuberculosis complex (MTC) by in-house PCR. All samples were obtained through pulmonary specimens consisted of 384 sputum, 148 bronchial aspirates and 88 pleural effusions.

RESULTS

Considering culture as a golden criterion, in which its diagnostic sensitivity and specificity of PCR assay were 87.7% and 85.6%, respectively. The findings of this study also indicate 22.1% (137/620) of the specimens were detected as MTC by PCR. Both PCR and culture confirmed presence of MTC in 57 of the samples. In comparison to culture, the diagnostic sensitivity of PCR for sputum was 87.5% (42/48), bronchial aspirates 100% (12/12), and 60% (3/5) for pleural effusions. The sensitivity of in-house PCR method is comparable with the sensitivity of Amplicor and Cobas TaqMan for MTC.

CONCLUSION

The study illustrates the in-house PCR assay for detection of MTC has high sensitivity and specificity versus approved commercial kits. This could be reliable test in the diagnosis of MTC in resource-limited countries.

The limitations of polymerase chain reaction in the setting of possible recurrent tuberculosis: 2 instructional cases

The interpretation of a positive result for Mycobacterium tuberculosis by nucleic acid amplification such as polymerase chain reaction (PCR) can be challenging. We present 2 cases that illustrate the limitations of tuberculosis PCR on respiratory secretions in previously treated patients, even years after the previous disease episode.

Tuberculosis of the breast

Tuberculosis of the breast is an uncommon disease even in countries where the incidence of pulmonary and extrapulmonary tuberculosis is high. Clinical presentation is usually of a solitary, ill-defined, unilateral hard lump situated in the upper outer quadrant of the breast. This disease can present a diagnostic problem on radiological and microbiological investigations, and thus a high index of suspicion is needed. Incorporating a highly sensitive technique like polymerase chain reaction (PCR) may be helpful in establishing the usefulness of such technology and can aid in conforming the diagnosis early. The disease is curable with antitubercular drugs, and surgery is rarely required

Rapid prediction of BACTEC MGIT 960 culture results by COBAS amplicor mycobacterium polymerase chain reaction detection

A combination of a rapid culture system, BACTEC MGIT 960 (MGIT), and a commercial polymerase chain reaction (PCR) system for the detection of Mycobacterium tuberculosis was evaluated to predict final culture results within 2 weeks. A total of 79 sputum specimens were collected from 59 tuberculosis (TB) patients before anti-TB chemotherapy. Among the 22 specimens that were smear negative and culture positive, the COBAS Amplicor nucleic amplification method for sputum resulted in 13 positives (59.1%) before culturing. In contrast, 21 liquid culture specimens (95.5%) showed positive results by COBAS Amplicor after 7 days. Similarly, 8 specimens (80%) were positive for Mycobacterium avium complex (MAC) based on COBAS Amplicor, and 10 liquid culture specimens (100%) showed positive results after 7 days. Among the 26 specimens that took more than 7 days to become positive by MGIT, 25 specimens (96.1%) were positive using COBAS Amplicor with 7-day-old cultures. Of the 26 positives, 21 were M. tuberculosis, which took 11 to 38 days to appear positive (mean, 16.6 days), and 4 were MAC, which took 8 to 10 days (mean, 8.8 days). As a result, 96.8% (31/32) of the positives could be detected by MGIT with COBAS Amplicor by day 7, and the negative predictive value was 97.9%. A combination of MGIT and COBAS Amplicor on day 7 was demonstrated as a useful method for rapid diagnosis of positives and negatives, without waiting 42 days for confirmation.

Evaluation of reverse transcription loop-mediated isothermal amplification in conjunction with ELISA-hybridization assay for molecular detection of Mycobacterium tuberculosis

Traditional culture, followed by a panel of biochemical tests for the diagnosis of tuberculosis (TB), is time-consuming, and rapid identification of Mycobacterium tuberculosis is crucial for the early administration of appropriate therapy. In this study, the reverse transcription loop-mediated isothermal amplification combined with enzyme-linked immunosorbent hybridization (RT-LAMP-ELISA-hybridization) assay has been designed for the rapid detection of 16S rRNA in clinical isolates of M. tuberculosis. This assay reproducibly detected a single copy, as opposed to 2000 copies of MTB 16S rRNA detected by conventional gel electrophoresis. Among the 150 specimens of sputum analysed, RT-LAMP-ELISA-hybridization assay had a sensitivity of 94.1% in the culture method, compared to the Amplified M. tuberculosis Direct Test (AMTD), 91.1% and the 88.2% sensitivity of acid-fast staining. Furthermore, RT-LAMP-ELISA-hybridization assay is more cost-effective when compared to the real-time TaqMan RT-PCR and AMTD assays. In conclusion, our results suggest that the RT-LAMP-ELISA-hybridization assay is a highly sensitive, low cost diagnostic tool useful for the rapid and accurate direct diagnosis of sputum specimens, and is suitable for routine clinical use.

Comparison of in-house PCR with conventional techniques and Cobas Amplicor M. tuberculosis kit for detection of Mycobacterium tuberculosis

PURPOSE

Polymerase chain reaction (PCR) assay, introduced as a fast and sensitive diagnostic method, is useful in detecting Mycobacterium tuberculosis. The purpose of this study was to evaluate the usefulness of in-house PCR assay in the detection of Mycobacterium tuberculosis by comparing PCR results with conventional diagnostic techniques and Cobas Amplicor M. tuberculosis kit.

MATERIALS AND METHODS

We retrospectively assessed the diagnostic yield of in-house PCR method employed for the amplification IS6110 sequences in 2,973 specimens. We also compared in-house PCR with Cobas Amplicor M. tuberculosis kit in 120 specimens collected from June to July 2006. Routine acid-fast stain (AFS) and culture assay were also performed and analyzed.

RESULTS

Of 2,973 cases, 2,832 cases (95.3%) showed consistent results between in house PCR, AFS and culture methods, whereas 141 (4.7%) displayed inconsistent results. The sensitivities, specificities, and positive and negative predictive values of each method were as follows: 77.5%, 99.7%, 95.5%, and 98.0%, respectively for PCR; 49.2%, 100%, 100%, and 95.7%, respectively, for AFS method; and 80.7%, 100%, 100%, and 98.3%, respectively, for culture assay. Consistent results between PCR and Cobas Amplicor M. tuberculosis kit were shown in 109 cases (90.8%). The sensitivities, specificities, and positive and negative predictive values of each method were as follows: 81.3%, 98.9%, 96.3%, and 93.5% respectively for PCR and 71.9%, 100%, 100%, and 90.7%, respectively, for Cobas Amplicor kit.

CONCLUSION

In-house PCR and Cobas Amplicor kit show high sensitivity and specificity, and are reliable tests in the diagnosis of tuberculosis.

Reactivation of ancient joint tuberculosis of the knee following total knee arthroplasty after 61 years: a case report

The prevalence of pulmonary tuberculosis is increasing and is associated with a rise in skeletal tuberculosis. Even after appropriate anti-tuberculosis therapy, reactivation of the infection may occur, even after many years. In this case report we describe a patient who had a reactivation of tuberculosis in the knee after total knee arthroplasty. At the age of 14 years, the patient had isolated tuberculosis arthritis of the left knee. Reactivation occurred after total knee arthroplasty 61 years later, at the age of 75. The patient was treated with a combined therapy; first the joint was irrigated with povidine-iodine and saline solution, and gentamicin beads were left behind. When the cultures revealed Mycobacterium tuberculosis, drug therapy of isoniazid, rifampicin, ethambutol and pyrazinamide was started and was continued for 9 months postoperatively. At a recent follow-up, the patient is doing well, with good range of motion in the knee.

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.

Use of the INNO LiPA Rif.TB for detection of Mycobacterium tuberculosis DNA directly in clinical specimens and for simultaneous determination of rifampin susceptibility

The INNO LiPA Rif.TB (Innogenetics, Ghent, Belgium) is a reverse hybridization test developed to detect genetic markers of resistance to rifampin in Mycobacterium tuberculosis complex. In the present study, this test was used directly on 3,763 clinical specimens by adopting a nested amplification of the target. The specificity of the system (98.4%) was optimal, but sensitivity (69.5%) was unsatisfactory. However, when use of the system was limited to smear-positive specimens, the sensitivity rose to 91.7%. As expected, the ability of the system to predict rifampin resistance was not influenced by its direct use on clinical specimens and confirmed the favorable results repeatedly reported in the literature.

Automatized PCR evaluation ofMycobacterium tuberculosiscomplex in respiratory and nonrespiratory specimens

In this study, Mycobacterium tuberculosis complex isolates recovered from respiratory and nonrespiratory specimens with culture were evaluated using an automatized PCR method. Specimens with suspected tuberculous disease were decontaminated and concentrated using the standard N-acetyl-L-cysteine NaOH method and were inoculated onto glycerol-supplemented Löwenstein-Jensen media and BACTEC B12 vials. Forty-one specimens with typical colonies on solid media and 127 specimens identified as M. tuberculosis complex in a BACTEC system were selected as the study group. As the control group, 46 specimens without growth on either culture media were selected. The PCR results were positive in 33 (80.5%) and 87 (68.5%) samples that were culture-positive on solid and liquid media, respectively. All (100%) culture-negative specimens within the control group were also negative in the COBAS AMPLICOR Mycobacterium tuberculosis (MTB) PCR method. In conclusion, although it is a fast method for identifying M. tuberculosis complex isolates from clinical specimens, the COBAS AMPLICOR MTB PCR method is found to be less sensitive than culture techniques, we propose therefore that it should only be used in combination with culture results in the clinical diagnosis of tuberculosis.

Comparison of the COBAS AMPLICOR MTB and BDProbeTec ET assays for detection of Mycobacterium tuberculosis in respiratory specimens

The performances of the BDProbeTec ET (Becton Dickinson) and COBAS AMPLICOR MTB (Roche) were retrospectively evaluated for detecting Mycobacterium tuberculosis complex in various respiratory specimens. The BACTEC and MGIT liquid culture system (Becton Dickinson) was used as a reference method. A total of 824 respiratory specimens, comprised of sputa, bronchoalveolar lavage fluid, and bronchial and tracheal aspirates from 580 patients, were evaluated. Out of 824 clinical specimens, 109 specimens from 43 patients were culture positive for M. tuberculosis. Of these 109 specimens, 67 were smear positive, 85 were positive by the COBAS AMPLICOR MTB test, and 94 were positive by the BDProbeTec ET. Of the 715 culture-negative specimens, 17 were positive by the auramine staining, 11 were positive by the COBAS AMPLICOR MTB test, and 12 were positive by the BDProbeTec ET. After discrepancy analysis and review of the patients' clinical data, 130 specimens from 50 patients were considered "true-positive" specimens. This resulted in the following sensitivities: microscopy, 61.5%; COBAS AMPLICOR MTB test, 78.0%; and BDProbeTec ET, 86.2%. The specificities of each system, based on the clinical diagnosis, were 99.7% for microscopy, 99.9% for the COBAS AMPLICOR MTB test, and 99.9% for the BDProbeTec ET. The data presented represent a considerable number of specimens evaluated with a considerable number of culture- and auramine-positive and culture-positive and auramine-negative results and therefore give a realistic view of how the data should be interpreted in a daily routine situation. Specifically, the data with regard to the culture-positive and auramine-negative specimens are useful, because in a routine situation, auramine-negative specimens are sometimes accepted, on clinical indications, to be analyzed by an amplification method.

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.

Evaluation of the BDProbeTec strand displacement amplification assay in comparison with the AMTD II direct test for rapid diagnosis of tuberculosis

The BDProbeTec MTB assay for direct detection of Mycobacterium tuberculosis was evaluated in comparison with the AMTD-II assay on 94 samples from different patients with clinical suspicion of tuberculosis. Using a combination of culture on Lowenstein-Jensen medium (with or without preculture in BACTEC 9000) and clinical diagnosis as the standard, BDProbeTec MTB showed high sensitivity and specificity (96.1% and 100%, respectively), similar to AMTD-II (96.1% and 97.1%, respectively), with significantly higher sensitivity than the Ziehl-Neelsen stain for acid-fast bacilli (73%, p < 0.05).

Evaluation of the BDProbeTec ET system as screening tool in the direct detection of mycobacterium tuberculosis complex in respiratory specimens

We evaluated the BDProbeTec ET System (Becton Dickinson) for the routine detection of Mycobacterium tuberculosis complex (MTC) in respiratory specimens and pleural fluids, comparing with microscopy (Ziehl Neelsen stain, ZN) and culture in liquid (BACTEC MGIT 960, MGIT) and solid (Löwenstein Jensen, LJ) media. Five hundred and two specimens, collected from 266 patients, of which 257 with suspected tuberculosis and 9 receiving anti-tuberculosis treatment, were investigated. Thirty-nine specimens were positive by any method, including false positives. Mycobacteria were isolated from 33 specimens (32 Mycobacterium tuberculosis and 1 Mycobacterium chelonae). Thirty-six specimens were BDProbeTec ET positive, 33 specimens were MGIT positive, 27 were LJ positive and 22 were ZN positive. With BDProbeTec ET, 2 specimens were false negative (culture positive), and 2 specimens from non-treated patients were false positive (culture negative). The overall sensitivity, specificity, and positive and negative predictive values for BDProbeTec ET compared to culture were 93.7, 98.7, 83.3, and 99.5%, respectively, while with smear-positive and smear-negative specimens the sensitivities were 100% and 81.5% respectively. In five treated patients the disappearance of MTC could be monitored using BDProbeTec ET in parallel with culture. The overall inhibition rate was 0.2%. BDProbeTec ET can be very useful for rapid detection of MTC, especially in smear-negative respiratory specimens.

Temperature-mediated heteroduplex analysis performed by using denaturing high-performance liquid chromatography to identify sequence polymorphisms in Mycobacterium tuberculosis complex organisms

PCR products containing sequence polymorphisms were prepared from six mycobacterial genes, denatured, mixed with reference PCR products, and reannealed; the mixtures were then examined with a denaturing high-performance liquid chromatography system (WAVE) equipped with a temperature-controlled alkalated polystyrene divinyl benzene column. Mismatching of bases in heteroduplexes of the PCR products causes elution patterns of the DNA from the column to be altered. The six mycobacterial genes studied were oxyR, in which a specific polymorphism (G(1031)A) is found only in certain species of the Mycobacterium tuberculosis complex, and five genes in which mutations associated with antituberculosis drug resistance have been found. The resistance genes (with affected drug and PCR product sizes given parenthetically) were rpoB (rifampin; 258 bp), katG (isoniazid; 205 bp), pncA (pyrazinamide; 579 bp); rpsL (streptomycin; 196 bp), and embB (ethambutol; 185 bp). Elution patterns of heteroduplexes of all 20 polymorphisms studied shifted detectably at column temperatures ranging from 65.3 to 68 degrees C and elution times of 3.5 to 6 min. These results show that temperature-mediated heteroduplex analysis is a potentially useful genotypic screen for mutations associated with antituberculosis drug resistance and for the G(1031)A polymorphism in oxyR. The method may allow users to detect novel as well as heterogeneous mutations without using expensive kits or detection labels.

Clinical evaluation of Amplicor Mycobacterium detection system for the diagnosis of pulmonary mycobacterial infection using sputum

SETTING

The Amplicor Mycobacterium detection kit was evaluated for the diagnosis of active pulmonary mycobacterial infection using sputum.

OBJECTIVE

To assess the clinical usefulness of the Amplicor Mycobacterium kit for the diagnosis of pulmonary tuberculosis and non-tuberculous mycobacterial infection in the country of medium prevalence.

DESIGN

All the patients were diagnosed with bacterial, histopathological, and clinical 'gold standard'. The sensitivity and specificity for diagnosing clinically active pulmonary tuberculosis and Mycobacterium avium and Mycobacterium intracellulare infections were evaluated comparing Amplicor results and clinical diagnosis.

RESULTS

A total of 1088 sputum specimens were collected from 780 in and out patients. Mycobacteria were recovered from 339 specimens by culture. The sensitivity and specificity of conventional culture method for the diagnosis of pulmonary tuberculosis were 60.2% and 99.8% respectively based on the number of patients. The figures for Amplicor were 61.8% and 97.4% respectively. There was no statistical significant difference between these methods. In rapidity, the Amplicor was significantly superior to the microscopy method in sensitivity.

CONCLUSION

Patients with Amplicor positive and conventional negative result had mostly mycobacteria related diseases. The Amplicor positive result indicated mostly active mycobacterial infection and was clinically useful for rapid diagnosis.

Efficacy of Amplicor PCR for the diagnosis of tuberculosis in respiratory specimens other than sputum

A total of 832 respiratory specimens not including the sputum (402 bronchial lavages, 241 bronchial brushing specimens, 136 pumping lavages, 41 pleural effusions, and 12 others) from 462 patients were assayed using the Roche Amplicor Mycobacterium tuberculosis test for amplification and identification of M. tuberculosis, M. avium and M. intracellulare (Amplicor PCR). The results were compared with those obtained using conventional microscopy and cultivation methods. Each patient had little or no sputum and showed an abnormal chest X-ray shadowing of unknown cause. No patients had previously undergone antituberculous therapy. Of the specimens obtained, 24 were both PCR and culture positive, 786 were both PCR and culture negative, 11 were PCR positive and culture negative, and 11 were PCR negative and culture positive. Based on these results, the sensitivity and specificity of Amplicor PCR were determined to be 68.67% and 98.6%, respectively, when compared with culture of respiratory specimens not including the sputum. After correcting for discrepancies due to differences in patient clinical data, the sensitivity of Amplicor PCR was found to be 68.6%, and the specificity to be 99.9%; the corresponding values for culture were 66.7% and 100%, and those for smear were 9.8% and 100%. Thus, Amplicor PCR was shown to possess a similar sensitivity to culture and to be a highly specific technique for the diagnosis of tuberculosis in the respiratory system using non-sputum specimens within hours in patients showing little or no sputum and abnormal chest X-ray shadowing of an indeterminant cause.

Accuracy and utility of commercially available amplification and serologic tests for the diagnosis of minimal pulmonary tuberculosis

Diagnosis of patients with minimal active tuberculosis (TB) is difficult, as there is no single test with high sensitivity and specificity. The yield and clinical utility of a combination of diagnostic tests were prospectively studied among 500 consecutive patients referred for sputum induction for diagnosis of possible active TB. Patients underwent sputum induction, chest X-ray, tuberculin testing, and had blood drawn for serologic testing (Detect-TB test; Biochem ImmunoSystems). Sputum was examined with fluorescent microscopy and PCR (Amplicor MTB-Roche) and cultured for mycobacteria using liquid (BACTEC) and solid media. For the diagnosis of the 60 cases of active TB, sensitivity and specificity, respectively, of the following diagnostic tests were mycobacterial culture, 73% and 100%; PCR, 42% and 100%; chest X-ray, 67-77% and 66-76%; tuberculin testing, 94% and 20%; and serology, 33% and 87%. After consideration of PCR and radiographic and clinical characteristics, a positive serologic test was independantly associated with diagnosis of active disease (adjusted odds of disease if positive, 2.6; 95% confidence limits, 1.1,6.1). No currently available test has sensitivity and specificity high enough for the accurate diagnosis of minimal pulmonary TB. Utilization of a combination of tests, together with consideration of key clinical characteristics, could improve diagnostic accuracy.

Clinical evaluation of the BDProbeTec ET system for rapid detection of Mycobacterium tuberculosis

The performance of the BDProbeTec ET system (BD Biosciences, Sparks, Md.) for direct detection of Mycobacterium tuberculosis complex (MTBC) in respiratory specimens was evaluated by comparing results to those of conventional mycobacterial culture performed with the BACTEC 460 TB system and Middlebrook 7H11 biplates. Patients known to have been on antituberculous therapy were excluded from the analysis. Of 600 evaluable specimens (4 specimens were excluded from the analysis due to failure of the internal amplification control [IAC]) from 332 patients, 57 grew mycobacteria; 16 were MTBC (from 12 patients), and 41 were nontuberculous mycobacteria. Of the 16 MTBC culture-positive specimens, 12 were smear positive and 4 were smear negative. BDProbeTec ET detected 14 of the 16 MTBC culture-positive specimens, resulting in initial overall sensitivity, specificity, and positive and negative predictive values of 87.5, 99.0, 70.0, and 99.7%, respectively. After resolution of discrepancies by review of medical records and retesting of samples yielding discordant MTBC culture and BDProbeTec ET results, the revised overall sensitivity, specificity, and positive and negative predictive values of the BDProbeTec ET were respectively 93.8, 99.8, 93.8, and 99.8% by specimen and 91.7, 99.7, 91.7, and 99.7% by patient. The BDProbeTec ET System offers the distinct advantage of including an IAC in the specimen well. These data suggest that the test performance is very good, especially for smear-positive samples. However, the number of patients with tuberculosis in our study, especially those with smear-negative disease, was small; therefore, additional studies are needed.

Polymerase chain reaction detection of Mycobacterium tuberculosis from fine-needle aspirate for the diagnosis of cervical tuberculous lymphadenitis

BACKGROUND

Despite its well-established usefulness in the diagnosis of cervical tuberculous lymphadenitis, fine-needle aspiration cytology (FNAC) has several limitations in its clinical applications, especially when the presence of acid-fast bacilli is not proven. Furthermore, fine-needle aspirate is sometimes inadequate for diagnosis, and the sensitivity and specificity of this technique for cervical tuberculous lymphadenitis has not been firmly established.

OBJECTIVE

The authors performed Mycobacterium tuberculosis polymerase chain reaction (PCR) for mycobacterial DNA sequences from the remainder of fine-needle aspirate after cytological examination and evaluated its diagnostic efficacy in clinical situations.

METHODS

Conventional diagnostic procedures including FNAC and M tuberculosis PCR were performed simultaneously in 29 cases that had been suspected to be cervical tuberculous lymphadenitis on patients' first visit. The results of FNAC and M tuberculosis PCR were compared with the clinical outcomes after several months of follow-up and pathological results from open biopsy of some cases.

RESULTS

Among the 17 cases of cervical tuberculous lymphadenitis diagnosed in clinical situations, M tuberculosis DNA was found by PCR in 13 cases (76.4%). Negative findings on PCR were achieved in 12 cases, which revealed non-granulomatous lymphadenopathy.

CONCLUSION

From these results, we conclude that M tuberculosis PCR using the remainder of aspirate for cytological examination is a very useful tool for the diagnosis of cervical tuberculous lymphadenitis, and its clinical application with FNAC could reduce the necessity for open biopsy.

Tuberculous meningitis in pregnancy--implications for mother and fetus: case report and literature review

The objective of this article is to report an illustrative case of tuberculous meningitis in pregnancy and review the recent literature outlining management and outcome of this devastating disease. A MEDLINE database search for English and French language articles dating back to 1966 was conducted and supplemented by reviewing the references of key articles and textbooks. An article was included if it described a case of tuberculous meningitis during pregnancy or explained the management of this disease. The search yielded a total of 17 articles, case reports, and reviews relating to tuberculous meningitis and/or pregnancy. Six authors describe cases and outcomes of tuberculous meningitis during pregnancy to give a total of 55 cases. Twenty-one patients died of their disease (38.2%), while 15 fetal or neonatal deaths have been reported (36.6%). Tuberculous meningitis is an insidious disease presenting a diagnostic challenge to even an astute practitioner. When recognized early and treated effectively with modern antituberculous medication, prognosis for mother and child is greatly improved.

Multicenter evaluation of the Abbott LCx Mycobacterium tuberculosis ligase chain reaction assay

Four Australian hospital laboratories evaluated the performance of the Abbott LCx Mycobacterium tuberculosis assay with 2,347 specimens (2,083 respiratory and 264 nonrespiratory specimens) obtained from 1, 411 patients. A total of 152 specimens (6.5%) were culture positive for Mycobacterium tuberculosis complex (MTBC); of these, 79 (52%) were smear positive. After resolution of discrepant data, the overall sensitivity, specificity, and positive and negative predictive values for the LCx assay were 69.7, 99.9, 99.1, and 97.7% respectively. For smear-positive respiratory specimens that were culture positive for MTBC, the values were 98.5, 100, 100, and 98.4%, respectively, while the values for smear-negative respiratory specimens were 41.5, 99.9, 96.4, and 98%, respectively. Relative operating characteristic curves were constructed to demonstrate the relationship between sensitivity and specificity for a range of possible cutoff values in the LCx assay. These graphs suggested that the assay sensitivity for respiratory samples could be increased from 70.2 to 78.6%, while the specificity would be reduced from 99.9 to 99.4% by inclusion of a grey zone (i.e., LCx assay values of between 0.2 and 0.99). An algorithm is presented for the handling of specimens with LCx assay values within this grey zone.

Clinical evaluation of the enhanced Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test for rapid diagnosis of tuberculosis in prison inmates

The reliability of the enhanced Amplified Mycobacterium Tuberculosis Direct Test (E-MTD; Gen-Probe, Inc., San Diego, Calif.) for rapid diagnosis of pulmonary tuberculosis (TB) was evaluated by testing 1, 004 respiratory specimens from 489 Texas prison inmates. Results were compared to those of mycobacterial culture (BACTEC TB 460 and Middlebrook 7H11 biplates), smear for acid-fast bacilli (AFB; auramine O), and clinical course. After chart review, three patients (nine specimens) who were on antituberculosis therapy before the study began were excluded from final analysis. Of the remaining 995 specimens, 21 were AFB smear positive: 13 grew Mycobacterium tuberculosis complex (MTBC), 6 grew nontuberculous mycobacteria, and 2 (from two patients diagnosed with TB and started on therapy after the study began) were culture negative. Twenty-eight specimens (20 patients) were positive for MTBC by culture and E-MTD. Seven specimens (seven patients) were positive by culture alone; three were from patients who had other E-MTD-positive specimens, two were false-positive cultures, and two were false-negative E-MTD results. Eight specimens were positive by E-MTD only; four specimens (four patients) were false-positive E-MTD results, and four specimens were from two patients with earlier E-MTD-positive specimens that grew MTBC. Thus, there were 22 patients with TB (10 smear positive and 12 smear negative). The sensitivity and specificity of the AFB smear for diagnosis of TB, by patient, were 45.5 and 98.9%, respectively. After resolving discrepancies, these same values for E-MTD were 90.9 and 99.1% overall, 100 and 100% for the smear-positive patients, and 83.3 and 99.1% for the smear-negative patients. Excluding the one smear-negative patient whose E-MTD-negative, MTBC culture-positive specimen contained inhibitory substances, the sensitivity of E-MTD was 95.2% overall and 90.9% in smear-negative patients. The specificity and positive predictive value of E-MTD can be improved, without altering other performance characteristics, by modifying the equivocal zone recommended by the manufacturer. These data suggest that E-MTD is a reliable method for rapid diagnosis of pulmonary TB, irrespective of the AFB smear result. Guidelines for the most appropriate use of E-MTD with smear-negative patients are needed.

Assessment of use of the COBAS AMPLICOR system with BACTEC 12B cultures for rapid detection of frequently identified mycobacteria

The use of the COBAS AMPLICOR System (Roche Molecular Diagnostics, Basel, Switzerland), the only automated system for PCR testing, was evaluated for a rapid identification of mycobacteria with positive BACTEC 12B cultures. Two hundred ninety-six specimens with a growth index of >/=30 were analyzed for the presence of Mycobacterium tuberculosis complex, Mycobacterium avium, and Mycobacterium intracellulare. Compared to traditional methods and provided that samples with PCR inhibition are retested at a 1:10 dilution, the sensitivity and specificity of the COBAS AMPLICOR System with BACTEC 12B cultures were 100 and 98%, respectively. The COBAS AMPLICOR method is rapid and reliable for identifying the most common mycobacteria in cultures.

Multicenter evaluation of two commercial amplification kits (Amplicor, Roche and LCx, Abbott) for direct detection of Mycobacterium tuberculosis in pulmonary and extrapulmonary specimens

Direct detection of Mycobacterium tuberculosis was performed in parallel with the Amplicor M. tuberculosis test (Roche Diagnostic System, USA) and the LCx M. tuberculosis (Abbott Diagnostic Division, USA) on 697 samples, collected from 481 patients, in three different Italian laboratories. Though both systems are licensed only for pulmonary specimens, 113 extrapulmonary specimens (represented mainly by pleural fluids, cerebrospinal fluids and urines) were included in the study. Amplification results were compared with acid-fast microscopy, culture, and identification of isolates. Final clinical diagnosis was used to resolve discrepant results. M. tuberculosis was detected in 105 specimens by both assays, whereas 561 were agreeing negatives; 21 and 6 of the remaining true-positive samples scored positive with LCx only and with Amplicor only, respectively. There were three false-positives with LCx and one false-positive with Amplicor. The diagnostic sensitivity of both methods was significantly better when only respiratory specimens were considered (78% versus 59% in nonrespiratory samples with Amplicor, and 88% versus 65% with LCx). Our data reveal a significantly better sensitivity of the LCx (p = 0.026) and a slight better specificity of the Amplicor assay. It is noteworthy that 16 of the 21 Amplicor-negative specimens in which LCx detected M. tuberculosis were culture negative, thus suggesting that the higher diagnostic sensitivity of the latter assay is attributable to its better analytical sensitivity. However, the majority of such samples originated from patients under antimicrobial treatment, which makes uncertain the clinical significance of such increased sensitivity. Considering true-positive for LCx and true-negative for Amplicor, the 16 culture-negative/LCx-positive/Amplicor-negative specimens resulted true-positives after the resolution of discrepancies, the final overall sensitivity and specificity values of the LCx assay were not significantly different from the ones of the Amplicor assay.

Clinical evaluation of the automated COBAS AMPLICOR MTB assay for testing respiratory and nonrespiratory specimens

We evaluated the COBAS AMPLICOR PCR system (Roche Diagnostics) for the routine detection of Mycobacterium tuberculosis complex (MTBC) in clinical specimens. Diagnostic culture, considered as the reference method, was performed with BACTEC, Löwenstein-Jensen, Stonebrink, and Kirchner media. Occasionally MB-Redox, ESP, or MGIT medium was also used. A total of 643 respiratory and 506 nonrespiratory specimens collected from 807 patients were investigated. Of the 95 culture-positive specimens, 80 were COBAS AMPLICOR MTB positive, and of the 1,054 culture-negative specimens, 1,044 were COBAS AMPLICOR MTB negative. After resolving discrepancies by review of the medical history, the overall sensitivity, specificity, and positive and negative predictive values for the COBAS AMPLICOR MTB assay, respectively, were 83.5, 98.8, 86.7, and 98.6% compared to those of diagnostic culture. In smear-positive specimens, the sensitivity of the COBAS AMPLICOR MTB assay was 96%, versus 48% for smear-negative specimens. No significant differences in the test performance between respiratory and nonrespiratory specimens were observed. The overall inhibition rate was less than 2%, excluding stool specimens. The clear advantages of the COBAS AMPLICOR PCR system are standardized procedures and reagents for specimen processing as well as an internal control for reliable monitoring of PCR inhibitors. By simplifying the work flow through a completely automated amplification and amplicon detection procedure, the COBAS AMPLICOR PCR system proved itself as a very useful component for routine diagnostic procedures.

Clinical evaluation of the BDProbeTec strand displacement amplification assay for rapid diagnosis of tuberculosis

The reliability of the BDProbeTec MTB Test (Becton Dickinson, Sparks, Md.) for direct detection of Mycobacterium tuberculosis in respiratory specimens was evaluated by comparing results to those of conventional mycobacterial culture, with the BACTEC TB 460 and Middlebrook 7H11 biplates. Patients known to have tuberculosis were excluded from analysis. Of 523 specimens from 277 patients, 53 grew a mycobacterium: 24 specimens of M. tuberculosis and 29 specimens of nontuberculous mycobacteria. After initial testing, 42 specimens were positive by the BDProbeTec, for overall sensitivity, specificity, and positive and negative predictive values of 95.8, 96. 2, 54.8, and 99.8%, respectively. After resolution of discrepancies, 28 specimens were positive by the BDProbeTec, for overall sensitivity, specificity, and positive and negative predictive values of 100, 99.2, 85.7, and 100%, respectively. These same values were 100, 80.8, 93.4, and 100%, respectively, for smear-positive samples and 100, 99.4, 75.0, and 100%, respectively, for smear-negative specimens.

Novel method for processing respiratory specimens for detection of mycobacteria by using C18-carboxypropylbetaine: blinded study

A novel method for processing respiratory specimens to improve culture and acid-fast staining of mycobacteria is introduced. This new method utilized N,N-dimethyl-N-(n-octadecyl)-N-(3-carboxypropyl)ammonium inner salt (Chemical Abstract Service no. 78195-27-4), also known as C18-carboxypropylbetaine (CB-18). In a blinded, five-center study, CB-18-based processing was compared to the standard method combining NALC and NaOH (NALC/NaOH). A total of 573 respiratory specimens were tested. Individual specimens were split approximately equally; the host institutions processed half of each specimen by the NALC/NaOH method, while the other half was processed with CB-18 at Quest Diagnostics--Baltimore. A total of 106 specimens were culture positive for acid-fast bacilli (AFB). Replacement of the primary decontamination agent with CB-18 caused changes in all diagnostic parameters. Aggregate culture sensitivity improved by approximately 43% (P < 0.01), and smear sensitivity improved by approximately 58% (P < 0.01). The sensitivity of smear relative to that of M. tuberculosis isolates exceeded 93% (P < 0.01) when specimens were processed with CB-18. The average times to a positive result were reduced by 7.3 days in liquid culture (P < 0.01) and 5.3 days on solid media (P < 0.05); however, the CB-18 method had a 20.8% contamination rate in liquid culture versus a rate of approximately 7.5% with NALC/NaOH processing. There were also unusual reductions in liquid culture sensitivity and smear specificity among CB-18-processed specimens. The characteristics of the latter parameters suggested that refinement of the CB-18 processing method should allow further improvements in culture sensitivity. This study showed that the CB-18 method has the potential to improve both smear and culture detection for these important human pathogens.

Comparison of Roche Cobas Amplicor Mycobacterium tuberculosis assay with in-house PCR and culture for detection of M. tuberculosis

The new Roche Cobas Amplicor Mycobacterium tuberculosis assay, which is a semiautomated version of the manually performed Roche Amplicor M. tuberculosis test, was compared to culture and an IS6110-based in-house PCR protocol. A total of 1,681 specimens from 833 patients, including specimen types other than sputum, were tested in parallel by both the in-house PCR and the Cobas Amplicor M. tuberculosis assay. After we resolved discrepant PCR results, the sensitivity, specificity, and positive and negative predictive values for the Cobas Amplicor M. tuberculosis assay were 66.33, 99.71, 94.36, and 97.66%, respectively. The corresponding values for the in-house PCR were 91.08, 99.85, 97.87, and 99.37%, respectively. For culture- and smear-positive specimens, the sensitivity of the Cobas Amplicor M. tuberculosis test was 96.42% (in-house PCR, 100%). If only smear-negative sputum specimens were considered, the Cobas Amplicor M. tuberculosis assay exhibited a sensitivity of 45.45% (in-house PCR, 63.63%) relative to that of culture. With a modified protocol for DNA extraction (washing of samples plus ultrasonication), both PCR methods performed better with gastric aspirates than with sputum samples (sensitivity of the Cobas Amplicor M. tuberculosis assay with smear-negative gastric aspirates, 70.00%; sensitivity of in-house PCR, 90.00%). With dithiothreitol being used for liquefaction of specimens in this study, the Cobas Amplicor M. tuberculosis assay exhibited an inhibition rate of 9.16%. In our view, the new Cobas Amplicor M. tuberculosis test (i) is well suited for typing of smear-positive specimens, (ii) may also be applied to gastric aspirates and other types of specimens if DNA extraction methods are modified appropriately, and (iii) exhibits a sensitivity with smear-negative sputum specimens which makes it recommendable that a minimum of three samples from the same patient be tested.

Diagnostic value of the Amplicor PCR assay for initial diagnosis and assessment of treatment response for pulmonary tuberculosis

We evaluated the Amplicor PCR assay as an initial diagnostic tool on the basis of clinical diagnosis, and assessed this assay as a follow-up test for patients with pulmonary tuberculosis during chemotherapy. Of the 208 specimens from 155 patients who were bacteriologically and/or clinically diagnosed with active tuberculosis before chemotherapy, 144 were Amplicor PCR-positive (sensitivity, 69.2%), which was equal to the results of culturing. Among 89 specimens which showed positive results by smear and culturing, the Amplicor PCR assay detected 87 (97.8%), whereas among 55 specimens which showed smear-negative but culture-positive results, the Amplicor PCR assay detected 46 (83.6 %)(P= 0.003). No false positive results were found in the two systems (specificity, 100%, 120/120). The Amplicor PCR assay was also evaluated as a follow-up test using 926 specimens from 207 patients receiving active tuberculosis chemotherapy. Among 433 specimens which showed Amplicor-PCR positive, 222 (51.3%) were culture-negative. On the other hand, among 233 culture-positive specimens, only 12 (5.2%) were Amplicor PCR-negative. Therefore, this assay is useful for the rapid diagnosis of tuberculosis. The duration of Amplicor PCR-positive after culture-negative conversion was significantly associated with the presence of cavitary lesion, smear-positive specimens before treatment, and smear-positive specimens with negative cultures during chemotherapy.

Two cases of chronic arthritis of the forearm due to Mycobacterium tuberculosis

In the absence of coexisting active pulmonary disease, tuberculosis is frequently not considered in the differential diagnosis of chronic inflammation of the joints. The cases of two immigrant patients with tuberculous arthritis involving the forearm are reported. In both cases non-specific arthritis or trauma was suspected, resulting in a delay between the onset of symptoms and institution of specific therapy of 21 and 24 months, respectively. Diagnosis was achieved by histological and microbiological examination of synovial biopsy material. Polymerase chain reaction for Mycobacterium tuberculosis complex was positive in only one patient. Treatment consisted of antituberculosis chemotherapy, surgical synovectomy, and debridement of the affected joints. These cases serve as a reminder that, although rare, tuberculosis can cause chronic arthritis.

Rapid diagnosis of tuberculosis in various biopsy and body fluid specimens by the AMPLICOR Mycobacterium tuberculosis polymerase chain reaction test

STUDY OBJECTIVES

This study was undertaken to determine the usefulness of the AMPLICOR Mycobacterium tuberculosis (MTB) polymerase chain reaction (PCR) test (Roche Diagnostic Systems, Inc; Branchburg, NJ) in diagnosing TB in tissue and body fluid specimens other than respiratory secretions.

DESIGN AND SETTING

Prospective analysis of clinical and laboratory data in patients with suspected TB at the four divisional hospitals of Catholic Medical Center, located in New York.

PATIENTS AND MEASUREMENTS

A total of 1,090 tissue and body fluid specimens from 1,032 patients with suspected TB were subjected to acid-fast bacillus (AFB) smear, culture, and the AMPLICOR MTB PCR test.

RESULTS

Of the 1,090 specimens, 32 grew M tuberculosis complex and 8 specimens grew isolates belonging to the Mycobacterium avium complex (MAC). The AMPLICOR MTB PCR test was positive for 24 of the 32 specimens that grew M tuberculosis. It was also positive for four additional specimens that were culture-negative for M tuberculosis or MAC. Two of these specimens were from patients with a previously recorded positive sputum culture for M tuberculosis. The AMPLICOR test was negative for all eight specimens that yielded MAC only. When AMPLICOR MTB PCR test results were compared with the confirmed clinical diagnosis of TB, the sensitivity, specificity, positive predictive value, and negative predictive value for the AMPLICOR MTB PCR test were 76.4%, 99.8%, 92.8%, and 99.2%, respectively. PCR results were available within 6.5 hours, compared with an average of 3 weeks for culture of M tuberculosis.

CONCLUSIONS

These data establish the utility of the AMPLICOR MTB PCR test for the rapid detection of M tuberculosis in tissue and body fluid specimens other than respiratory secretions.

Identification of a new DNA region specific for members of Mycobacterium tuberculosis complex

The successful use of DNA amplification for the detection of tuberculous mycobacteria crucially depends on the choice of the target sequence, which ideally should be present in all tuberculous mycobacteria and absent from all other bacteria. In the present study we developed a PCR procedure based on the intergenic region (IR) separating two genes encoding a recently identified mycobacterial two-component system named SenX3-RegX3. The senX3-regX3 IR is composed of a novel type of repetitive sequence, called mycobacterial interspersed repetitive units (MIRUs). In a survey of 116 Mycobacterium tuberculosis strains characterized by different IS6110 restriction fragment length polymorphisms, 2 Mycobacterium africanum strains, 3 Mycobacterium bovis strains (including 2 BCG strains), and 1 Mycobacterium microti strain, a specific PCR fragment was amplified in all cases. This collection included M. tuberculosis strains that lack IS6110 or mtp40, two target sequences that have previously been used for the detection of M. tuberculosis. No PCR fragment was amplified when DNA from other organisms was used, giving a sensitivity of 100% and a specificity of 100% in the confidence limit of this study. The numbers of MIRUs were found to vary among strains, resulting in six different groups of strains on the basis of the size of the amplified PCR fragment. However, the vast majority of the strains (approximately 90%) fell within the same group, containing two 77-bp MIRUs followed by one 53-bp MIRU.

Transport of digested decontaminated sputum specimens to a central laboratory for testing for M. tuberculosis by Amplicor MTB test

Rapid diagnosis of tuberculosis may improve management of infected patients and facilitate infection control procedures. The relatively slow growth rate of M. tuberculosis and the limited sensitivity and specificity of microscopy make rapid diagnosis difficult. Nucleic acid amplification techniques have been extensively studied for the detection of M. tuberculosis DNA and a number of commercial products for detection of M. tuberculosis nucleic acid in clinical specimens are now available. As performance of diagnostic PCR at central reference laboratories may be desirable, the impact of specimen transport on the performance of the Amplicor MTB PCR assay is of practical importance. We have assessed the performance of the Amplicor MTB PCR on specimens submitted and initially processed in laboratories in 3 cities and then transported to a single laboratory for PCR assay. The overall sensitivity of the PCR test was 97 per cent and the corrected specificity was 100 per cent. All of 23 culture positive specimens collected locally were PCR positive compared with 10 of 11 culture positive specimens transported from elsewhere. In this study transportation of digested decontaminated specimens to a central laboratory either frozen at -20 degrees, or overnight at room temperature had no apparent effect on the performance characteristic of the Amplicor MTB PCR assay.

Diagnosis of pulmonary tuberculosis using PCR assays on sputum collected within 24 hours of hospital admission

There have been few studies evaluating the efficacy of polymerase chain reaction (PCR) testing in front-line clinical practice. We assessed the diagnostic yield of PCR prospectively in a blinded study of patients admitted to rule out tuberculosis and compared PCR results to a culture and clinical diagnosis of tuberculosis. Specimens were sent for routine smear, culture, and PCR analysis. Sputum sediments were submitted for PCR amplification of IS6110 sequences by an in-house assay and also the Roche Amplicor PCR assay targeting 16s ribosomal RNA genes. Eighty-five patients were enrolled: 27 patients had cultures positive for tuberculosis; 12 were smear-positive. PCR by both assays on the first specimen picked up all patients smear-positive on any specimen. A positive PCR on at least one of two specimens collected in the first 24 h was 85 and 74% sensitive and 88 and 93% specific for tuberculosis by the in-house and Roche techniques, respectively. Sensitivity in smear-negative patients was 73 and 53%, respectively. The in-house PCR detected 100% and Roche detected 95% of patients with more than paucibacillary (greater than 20 colonies) tuberculosis. We conclude that PCR may be a useful tool to evaluate patients for tuberculosis within the first hospital day.

Diagnostic value of the strand displacement amplification method compared to those of Roche Amplicor PCR and culture for detecting mycobacteria in sputum samples

We compared the ability of the semiautomated BDProbeTec-SDA system, which uses the strand displacement amplification (SDA) method, with that of the Roche Amplicor-PCR system and the Septi-Chek AFB culture system to directly detect Mycobacterium tuberculosis complex (MTB) and other mycobacteria in sputum samples. A total of 530 sputum samples from 299 patients were examined in this study. Of the 530 samples, 129 were culture positive for acid-fast bacilli with the Septi-Chek AFB system; 95 for MTB, 29 for M. avium-M. intracellulare complex (MAC), and 5 for other mycobacteria. The BDProbeTec-SDA system detected 90 of the 95 samples culture positive for MTB (sensitivity, 94.7%), and the Amplicor-PCR system detected 85 of the 95 samples culture positive for MTB (sensitivity, 89.5%). The specificity of each system, based on the clinical diagnosis, was 99.8% for SDA and 100% for PCR, respectively. Among the 29 samples culture positive for MAC, the BDProbeTec-SDA system detected MAC in 24 samples (sensitivity, 82.8%), whereas the Amplicor-PCR system detected MAC in 23 samples (sensitivity, 79.3%). The specificities of the systems were 98.3 and 100%, respectively. The high degrees of sensitivity and specificity of the BDProbeTec-SDA system suggest that it should be very useful in clinical laboratories for the rapid detection of mycobacteria in sputum samples.

Comparison of two different PCR detection methods. Application to the diagnosis of pulmonary tuberculosis

The objectives are to assess the influence of the detection of the amplified DNA fragment on the sensitivity and specificity of the polymerase chain reaction (PCR). One hundred seventy-five sputum samples from 123 patients were processed. Sixty samples were taken from 60 subjects without tuberculosis, and the rest were taken from subjects with tuberculosis confirmed by culture. A fragment of the IS6110 sequence of Mycobacterium tuberculosis, which was detected using two different methods, was amplified. The detection methods used were a digoxigenin-labeled specific probe and chemiluminescent development and reamplification (nested PCR) combined with agarose gel electrophoresis. Sensitivity with probe detection was 75.65% and specificity 100%. Using the nested PCR technique, sensitivity rose to 93.04%, but specificity decreased to 96.6%. PCR is a quick and adequate way to diagnose pulmonary tuberculosis in cases where staining is negative yet there is a clinical suspicion of tuberculosis, even though a standardization process and large scale evaluation are still needed to determine its true usefulness.

Mycobacterium growth indicator tube testing in conjunction with the AccuProbe or the AMPLICOR-PCR assay for detecting and identifying mycobacteria from sputum samples

We have compared the ability of the Mycobacterium Growth Indicator Tube (MGIT) system, a new culture method with an oxygen-sensitive fluorescent sensor, to recover mycobacteria from sputum samples with the abilities of egg-based medium and the Septi-Chek AFB system. We have also assessed the clinical utility of the AccuProbe or the AMPLICOR-PCR assay to directly identify Mycobacterium tuberculosis complex and M. avium-M. intracellulare complex (MAC) from positive MGITs. From 382 sputum samples, 99 isolates of M. tuberculosis complex and 20 isolates of MAC were recovered. The MGIT system had the highest recovery rates for M. tuberculosis complex (97.0%) and MAC (100%), compared to recovery rates of 51.5 and 65.0%, respectively, with the egg-based medium and 81.8 and 85.0%, respectively, with the Septi-Chek AFB system. The shortest recovery times were also achieved with the MGIT system: 16.6 days for M. tuberculosis complex and 12.0 days for MAC, compared to 27.1 and 20.1 days, respectively, with the egg-based medium and 21.4 and 13.2 days, respectively, with the Septi-Chek AFB system. The AccuProbe identified 74 (77.1%) of the 96 M. tuberculosis complex-positive MGITs and 17 (85.0%) of the 20 MAC-positive vials. The AMPLICOR system correctly identified 94 (97.9%) of the 96 M. tuberculosis complex-positive MGITs and all 20 MAC-positive vials. Therefore, the MGIT system used in conjunction with the AMPLICOR system is a rapid and sensitive method for detecting and identifying M. tuberculosis complex and MAC isolates from sputum samples.

Gene amplification in the diagnosis of mycobacterial infections

The number of importance of infections caused by Mycobacterium tuberculosis and other mycobacterial species is increasing. Since the detection and identification of mycobacteria by conventional laboratory methods (cultivation, staining, and biochemical tests) is a slow and complex procedure, rapid diagnostic methods are urgently needed. Several amplification methods based on different techniques have been applied in the detection of mycobacteria directly from clinical specimens. Most experience has been obtained from different polymerase chain reaction (PCR) assays and their general performance is good. However, their sensitivity in the analysis of samples containing small amounts of mycobacteria or samples containing inhibitory substances has been low. Furthermore, the risk of false positives caused by contamination is high, and the clinical relevance of the results may be unclear. Thus, these gene amplification techniques are a valuable adjunct to the diagnosis of mycobacteria, but so far they cannot replace conventional microbiological methods.

Relevance of nucleic acid amplification techniques for diagnosis of respiratory tract infections in the clinical laboratory

Clinical laboratories are increasingly receiving requests to perform nucleic acid amplification tests for the detection of a wide variety of infectious agents. In this paper, the efficiency of nucleic acid amplification techniques for the diagnosis of respiratory tract infections is reviewed. In general, these techniques should be applied only for the detection of microorganisms for which available diagnostic techniques are markedly insensitive or nonexistent or when turnaround times for existing tests (e.g., viral culture) are much longer than those expected with amplification. This is the case for rhinoviruses, coronaviruses, and hantaviruses causing a pulmonary syndrome, Bordetella pertussis, Chlamydia pneumoniae, Mycoplasma pneumoniae, and Coxiella burnetii. For Legionella spp. and fungi, contamination originating from the environment is a limiting factor in interpretation of results, as is the difficulty in differentiating colonization and infection. Detection of these agents in urine or blood by amplification techniques remains to be evaluated. In the clinical setting, there is no need for molecular diagnostic tests for the diagnosis of Pneumocystis carinii. At present, amplification methods for Mycobacterium tuberculosis cannot replace the classical diagnostic techniques, due to their lack of sensitivity and the absence of specific internal controls for the detection of inhibitors of the reaction. Also, the results of interlaboratory comparisons are unsatisfactory. Furthermore, isolates are needed for susceptibility studies. Additional work remains to be done on sample preparation methods, comparison between different amplification methods, and analysis of results. The techniques can be useful for the rapid identification of M. tuberculosis in particular circumstances, as well as the rapid detection of most rifampin-resistant isolates. The introduction of diagnostic amplification techniques into a clinical laboratory implies a level of proficiency for excluding false-positive and false-negative results.