Evaluation of two different cell lysis methods for releasing mycobacterial nucleic acids in the INNO-LiPA mycobacteria test

The INNO-LiPA Mycobacteria Test (Innogenetics, N.V., Belgium) is a PCR-based reverse hybridization assay for the simultaneous identification of several mycobacterial species. We evaluated two simplified lysis methods for mycobacterial DNA release for application in the INNO-LiPA Mycobacteria Test. The two methods were based on either (i) heat treatment or (ii) sonication. Both methods were performed directly on 45 positive liquid cultures (MB-BacT, BioMérieux, Marcy l'Etoile, France) containing 17 different mycobacterial species. These two simple lysis procedures demonstrated similar effectiveness (100%) to that recommended by the manufacturer. They also significantly shortened the time required for mycobacterial DNA release.

Comparison of the sodium dodecyl sulfate-sodium hydroxide specimen processing method with the C18-carboxypropylbetaine specimen processing method using the MB/BacT liquid culture system

The ability of physicians to diagnose tuberculosis is impacted by the use of smear and culture techniques combined with specimen processing methods. The objective of this study was to evaluate the effects of specimen processing on smear and culture sensitivity by comparing the specimen processing method that uses C(18)-carboxypropylbetaine with the method that combines sodium dodecyl sulfate and sodium hydroxide. A total of 1,201 specimens were entered into this study. Specimens were split approximately equally such that one-half of each specimen was processed with sodium dodecyl sulfate-sodium hydroxide, while the other half was processed with C(18)-carboxypropylbetaine. All sediments were subjected to acid-fast staining and then analyzed using the MB/BacT liquid culture system (bioMérieux, France) and solid media. The sensitivity of smear following processing with sodium dodecyl sulfate-sodium hydroxide and C(18)-carboxypropylbetaine was 61.2% and 58.6% (P>0.05), respectively, while the specificities were identical (99.7%). The sensitivity of culture was 84.2% and 96.1% (P<0.05), respectively. The time to detection in the MB/BacT liquid culture system was 13.2+/-5.6 and 15.0+/-8.8 days (P>0.05), respectively, and 20.0+/-7.6 and 15.7+/-8.9 days (P<0.05), respectively, on solid media. The contamination rates in the MB/BacT system were 0.8% and 8.7%, respectively, whereas the contamination rates on solid media were 2.6% and 4.3%, respectively. C(18)-carboxypropylbetaine specimen processing was less labor-intensive than sodium dodecyl sulfate-sodium hydroxide processing and improved the ability of laboratory staff to detect the presence of mycobacteria by culture.

Rapid detection of several mycobacterial species using a polymerase chain reaction reverse hybridisation assay

The ability of a polymerase-chain-reaction-based technique combined with a reverse hybridisation line-probe assay to detect and identify eight of the most clinically significant mycobacterial species directly from cultures in liquid medium was evaluated. The line-probe assay allows simultaneous identification of eight different mycobacterial species. Ninety-seven mycobacterial strains belonging to 22 different species were evaluated. All strains were previously inoculated into MB/BacT bottles (Organon Teknika, USA). The sensitivity and specificity of the test when applied on positive MB/BacT liquid cultures containing isolates from mycobacterial species included as specific probes on the line-probe assay strip was 100% and 100%, respectively. These results further support the potential clinical usefulness of this technique in the diagnosis of mycobacterial infections.

Evaluation of a fluorescence hybridisation assay using peptide nucleic acid probes for identification and differentiation of tuberculous and non-tuberculous mycobacteria in liquid cultures

The performance was evaluated of a fluorescence in situ hybridisation assay using peptide nucleic acid probes (Dako Probe MTB Culture Confirmation Test; Dako, Denmark) for identification of Mycobacterium tuberculosis complex (MTC) organisms and differentiation between tuberculous and non-tuberculous mycobacteria (NTM) in material taken directly from Bactec 12B (Becton Dickinson, USA) and MB/BacT (Organon Teknika, USA) bottles. The test was applied to 129 smear-positive (Ziehl-Neelsen stain) clinical specimens, 48 previously identified clinical strains of mycobacteria (12 MTC and 36 NTM), and 51 reference strains (7 MTC and 44 NTM) which were all previously inoculated into Bactec 12B and MB/BacT bottles. The sensitivity and specificity of the assay for MTC-positive cultures was 87.6% and 100%, respectively, for Bactec 12B, and 100%, respectively, for MB/BacT. The sensitivity and specificity of the assay for NTM-positive cultures was 100% for both media.

Comparison of a nonradiometric system with Bactec 12B and culture on egg-based media for recovery of mycobacteria from clinical specimens

The MB/BacT (Organon-Teknika, USA) is a fully automated, rapid, nonradiometric system for the culture of mycobacteria from clinical samples. The rate of recovery of mycobacteria and the time to detection obtained with the MB/ BacT were compared with those obtained with Löwenstein-Jensen and Coletsos solid media and Bactec 7H12 (12B) (Becton-Dickinson, USA) broth when 600 processed specimens were inoculated into all media in parallel. Specimens included 383 respiratory samples, 20 urine samples, 23 purulent exudates, 13 stool samples, 103 blood samples, 14 bone marrow aspirates, and 44 body fluid samples or aspirates. Overall, 106 mycobacterial isolates comprising six species were recovered, of which 100 (94.3%) were detected with MB/BacT, 98 (92.5%) with egg-based media, and 96 (90.2%) with Bactec 12B. The recovery rates of Mycobacterium tuberculosis complex with MB/BacT, egg-based media, and Bactec 12B were 98.7%, 93.7, and 89.9%, respectively. The average number of days to detection of single mycobacterial isolates was 14.2 days for MB/BacT, 26.1 days for egg-based media, and 11.7 days for Bactec 12B. The contamination rates were higher in MB/BacT (5%) than in Bactec 12B (1.8%) or egg-based media (1.5%). MB/BacT is a reliable, nonradiometric, less labor-intensive alternative to Bactec 12B for recovery of mycobacteria, but, as with other liquid culture methods, MB/BacT should be used in combination with a solid medium, not on its own.

Rapid diagnosis of extrapulmonary tuberculosis by ligase chain reaction amplification

A rapid amplification-based test for the diagnosis of extrapulmonary tuberculosis, the LCx Mycobacterium tuberculosis Assay from Abbott Laboratories, was evaluated. Results from the LCx M. tuberculosis Assay were compared with those from culture and the final clinical diagnosis for each patient. A total of 526 nonrespiratory specimens from 492 patients were tested. The specimens included urine; feces; lymph node exudates; pleural, cerebrospinal, articular, and ascitic fluids; tissue biopsies; gastric aspirates; purulent exudates; blood; and bone marrow aspirates. After combination of the culture results and the patient's clinical data, a total of 135 specimens were collected from 122 patients with a diagnosis of extrapulmonary tuberculosis. The sensitivity, specificity, and positive and negative predictive values for the LCx M. tuberculosis Assay were 77.7, 98.7, 95.2, and 93.1%, respectively; these values rose in resolved cases of TB to 78.5, 100, 100, and 93.1%, respectively. For 37 (27.4%) specimens from patients smear positive for the disease and 98 (72.6%) specimens from patients smear negative for the disease, the sensitivities of the LCx M. tuberculosis Assay were 100 and 71.1%, respectively. Statistically significant differences (P < 0.01) in sensitivities were found between culture and the LCx M. tuberculosis Assay. These differences were even greater among smear-negative specimens. The results demonstrate that the LCx M. tuberculosis Assay will provide rapid and valuable information for the diagnosis of extrapulmonary tuberculosis.

Evaluation of a commercial probe assay for detection of rifampin resistance in Mycobacterium tuberculosis directly from respiratory and nonrespiratory clinical samples

A commercial assay (Inno-Line Probe Assay; Innogenetics, Belgium) was evaluated to determine its ability to detect rifampin resistance in Mycobacterium tuberculosis directly from clinical specimens. Fifty-nine selected specimens (42 respiratory and 17 nonrespiratory) culture positive for Mycobacterium tuberculosis were tested along with their corresponding isolates in culture. The results were compared with those obtained by in vitro susceptibility testing. The results of the line probe assay to detect rifampin resistance in Mycobacterium tuberculosis present in clinical specimens and in cultured isolates were concordant for 58 of 59 (98.3%) isolates (95% confidence limits = 90.9-99.9%). The line probe assay failed only once, when a fecal specimen was tested; no amplification was observed due to the presence of inhibitory compounds. The most frequently observed mutation was His526-->Asp (58.7%), followed by the His526-->Tyr (23.9%); together, they represented 82.6% of rifampin-resistant samples. In conclusion, the Inno-Line Probe Assay is a rapid, useful method for detecting the presence of Mycobacterium tuberculosis complex and its resistance to rifampin directly from clinical specimens and culture. Moreover, since rifampin resistance is a potential marker for multidrug resistance in Mycobacterium tuberculosis, this assay may constitute an important tool for the control of tuberculosis.

Comparative evaluation of initial and new versions of the Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test for direct detection of Mycobacterium tuberculosis in respiratory and nonrespiratory specimens

We evaluated the initial version of the Amplified Mycobacterium Tuberculosis Direct Test (Gen-Probe) (AMTDT 1) and the new version of AMTDT (AMTDT 2) for the detection of Mycobacterium tuberculosis directly from respiratory and nonrespiratory samples and compared the results with those of culture and staining methods. The assays were applied to 410 respiratory and 272 nonrespiratory samples collected from 515 patients. The combination of the culture results and clinical diagnosis was considered to be the "gold standard." Ninety-five respiratory specimens were collected from 67 patients with a diagnosis of pulmonary tuberculosis (TB) and 68 nonrespiratory specimens were collected from 61 patients with a diagnosis of extrapulmonary TB. With respiratory specimens, the sensitivity, specificity, and positive and negative predictive values were 83, 100, 100, and 96%, respectively, for AMTDT 1 and 94.7, 100, 100, and 98.4%, respectively, for AMTDT 2. With nonrespiratory specimens, the sensitivity, specificity, and positive and negative predictive values were 83, 100, 100, and 94%, respectively, for AMTDT 1 and 86.8, 100, 100, and 98.4%, respectively, for AMTDT 2. The overall results of AMTDT 1 and AMTDT 2 were concordant for 97% (661 of 682) of the samples. Statistically significant differences in sensitivities were found between AMTDT 1 and AMTDT 2 with respiratory specimens. It was concluded that although both nucleic acid amplification methods are rapid, sensitive, and specific for the detection of M. tuberculosis complex in all types of clinical samples, AMTDT 2 appeared to be more sensitive than AMTDT 1 when applied to smear-negative specimens. In contrast AMTDT 2 is more susceptible than AMTDT 1 to inhibitory substances in the amplification reaction. The turnaround time of AMTDT 2 is shorter (3.5 h) than that for AMTDT 1 (5 h).

Comparative evaluation of two commercial assays for direct detection of Mycobacterium tuberculosis in respiratory specimens

Two commercial systems for the amplification and detection of Mycobacterium tuberculosis directly from respiratory samples were compared. The Roche Cobas Amplicor MTB Test and the Roche manual Amplicor MTB Test (Roche Diagnostic Systems, USA) were applied to 755 decontaminated respiratory specimens collected from 470 patients. Results were compared with those of acid-fast staining and culture. A total of 251 specimens were collected from 156 patients diagnosed with pulmonary tuberculosis, including 28 specimens corresponding to 13 patients that were receiving antituberculous treatment. Given the overall positivity rate of 33.2% (251/755), the sensitivity, specificity, and positive and negative predictive values were 92.4, 100, 100, and 96.5%, respectively, for the Cobas Amplicor MTB Test and 90.8, 100, 100, and 95.8%, respectively, for the Amplicor MTB Test. For 204 (81.3%) smear positive specimens and 47 (19.7%) smear negative specimens, the sensitivity values were 100 and 59.6%, respectively, for the Cobas Amplicor MTB Test and 100 and 51%, respectively, for the Amplicor MTB Test. There were no statistically significant differences in sensitivity or specificity between the two assays and culture (p>0.05). The overall results of both assays were concordant for 99.5% of the samples. It is concluded that although both nucleic acid amplification methods are rapid and specific for the detection of Mycobacterium tuberculosis complex in respiratory specimens, the Cobas Amplicor MTB Test appears to be slightly more sensitive than the Amplicor MTB Test when smear negative specimens are investigated.

Rapid detection of Mycobacterium tuberculosis in respiratory specimens, blood and other non-respiratory specimens by amplification of rRNA

SETTING

Diagnostic methods employing gene technology based on amplification of DNA or RNA are expected to improve the speed, sensitivity, and specificity of Mycobacterium tuberculosis detection. The Amplified Mycobacterium Tuberculosis Direct Test (AMTDT) enables the amplification and detection of M. tuberculosis rRNA directly from respiratory specimens.

OBJECTIVE

To evaluate the performance of the AMTDT in direct detection of M. tuberculosis in respiratory specimens, blood and other clinical samples, and to compare this method with conventional culture and staining techniques.

DESIGN

A total of 554 samples from 450 patients were examined in this study. All clinical specimens (with the exception of bone marrow aspirates and blood samples) were digested and decontaminated with sodium dodecyl (lauryl) sulfate (SDS)-NaOH. Bone marrow aspirates and blood samples were treated with 10% SDS. All processed samples were stained by auramine-rhodamine fluorochrome and inoculated onto Löwenstein-Jensen and Coletsos solid media, and into BACTEC-12B medium. In addition, the blood samples were inoculated into BACTEC 13A medium. The AMTDT was performed according to manufacturer's instructions. In those cases where discrepant results were obtained for AMTDT and cultures, patients' clinical data and other microbiological results were evaluated.

RESULTS

The sensitivity, specificity, and positive and negative predictive values for AMTDT were 87.5, 100, 100, and 96.7%, respectively, in respiratory specimens and 86.8, 100, 100, and 92.8%, respectively, in non-respiratory specimens. The differences in sensitivity of these two groups of specimens were not highly statistically significant (P > 0.005).

CONCLUSION

The sensitivity and specificity of the AMTDT were satisfactory for detection of M. tuberculosis in all types of clinical samples. Some minor changes in assay format and laboratory protocols may increase the sensitivity of the AMTDT without adversely affecting its specificity.

Detection and identification of mycobacteria by amplification of RNA and DNA in pretreated blood and bone marrow aspirates by a simple lysis method

A sodium dodecyl (lauryl) sulfate method was evaluated for the preparation of blood specimens and bone marrow aspirates for use in two amplification procedures (Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test [AMTDT] and Roche Amplicor M. avium/M. intracellulare [MAI] Test) for the detection and identification of Mycobacterium tuberculosis and M. avium and M. intracellulare, respectively. The AMTDT is based on amplification of rRNA, whereas the Amplicor MAI Test amplifies a specific DNA region of the 16S rRNA gene. The results of amplification techniques were compared with those of standard culture and culture in BACTEC 13A and BACTEC 12B liquid media. A total of 121 blood specimens and 15 bone marrow aspirates were collected from 136 AIDS patients. Mycobacterial growth was recovered for 103 specimens; 35 yielded M. tuberculosis, 62 yielded M. avium, 5 yielded M. genavense, and 1 yielded M. kansasii. The values of sensitivity and specificity in pretreated specimens for detection of M. tuberculosis by the AMTDT were 94.3 and 100%, respectively, and those for detection of M. avium by the Amplicor MAI Test were 91.9 and 100%, respectively. The simple lysis method described in the present work allows the recovery of mycobacteria from blood specimens and bone marrow aspirates and may be used in combination with the AMTDT and the Amplicor MAI Test to detect and identify different members of the genus Mycobacterium. This method might also be applicable for the identification of mycobacteria from blood culture fluids with acridinium-ester-labeled DNA probes.

Evaluation of the semiautomated Abbott LCx Mycobacterium tuberculosis assay for direct detection of Mycobacterium tuberculosis in respiratory specimens

Five hundred twenty processed respiratory specimens from 326 patients received for the diagnosis of tuberculosis or other mycobacterial infections were tested by means of the LCx Mycobacterium tuberculosis Assay from Abbott Laboratories, which uses ligase chain reaction technology for the direct detection of M. tuberculosis complex in respiratory specimens. The results of the LCx M. tuberculosis Assay were compared with the results of culture and staining techniques. After a combination of culture results and the patient's clinical data, a total of 195 specimens were collected from 110 patients who were positively diagnosed as having pulmonary tuberculosis. Twenty-three of these 195 specimens which corresponded to 10 patients with a history of pulmonary tuberculosis (TB) and anti-TB treatment ranging from 1 to 6 months were culture negative. The other 172 specimens were culture positive for M. tuberculosis. With an overall positivity rate of 37.5% (195 of 520 specimens), the sensitivity, specificity, and positive and negative predictive values were 90.8, 100, 100, and 94.7%, respectively, for the LCx M. tuberculosis Assay; 88.2, 100, 100, and 93.4%, respectively, for culture; and 82.6, 92, 72.9, and 97.6%, respectively, for acid-fast staining. For 161 specimens (82.6%) from patients smear positive for the disease and 34 specimens (17.4%) from patients smear negative for the disease, the sensitivity values for the LCx M. tuberculosis Assay were 98.8 and 53%, respectively. There were no statistically significant differences in the sensitivities and specificities between the LCx M. tuberculosis Assay and culture (P > 0.05). Conclusively, the LCx M. tuberculosis Assay has proved to have an acceptable sensitivity and a high specificity in detecting M. tuberculosis and has the potential of reducing the diagnosis time to an 8-h working day.

Direct detection of Mycobacterium tuberculosis complex in nonrespiratory specimens by Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test

The Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test (AMTDT) was adapted for the detection of Mycobacterium tuberculosis complex in 224 nonrespiratory specimens from 188 patients. The sensitivity and specificity of the AMTDT for such specimens, after resolution of discrepant results, were 85.7 and 100%, respectively. Pretreatment of nonrespiratory specimens with sodium dodecyl (lauryl) sulfate is mandatory to obtain consistent and reproducible AMTDT results. The use of 500 microliters of decontaminated specimen improves the sensitivity of the test. Because the AMTDT detects stable rRNA from noncultivable bacilli, it is not useful for monitoring patients receiving treatment.

Inhibitory effect of sodium dodecyl sulfate in detection of Mycobacterium tuberculosis by amplification of rRNA

The concentrations of sodium dodecyl (lauryl) sulfate (SDS) found in the sediments of the respiratory samples pretreated with SDS-NaOH varied between 3.36 and 12.42 mg/ml. These concentrations of SDS were higher than the level considered critical (> or = 0.16 mg/ml) to obtain negative results with the Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test. Extensive washing, after neutralization of sediment, is sufficient to remove all traces of detergent which interfere with the enzymes used by the Mycobacterium Tuberculosis Direct Test assay.