Diagnosis of extrapulmonary tuberculosis by Gen-Probe amplified Mycobacterium tuberculosis direct test

Diagnostic value of nucleic acid amplification tests for tuberculous pleural effusion

Diagnosing tuberculous pleural effusion (TPE) is challenging for pulmonologists and laboratory scientists. The gold standards for TPE diagnosis are pleural fluid Ziehl-Neelsen staining, Mycobacterium tuberculosis (Mtb) culture and pleural biopsy. These tools have limitations, including low sensitivity, long turnaround time and invasiveness. The nucleic acid amplification test (NAAT) is a rapid and minimally invasive tool for diagnosing TPE. This review summarizes the diagnostic accuracy of available NAATs for TPE, with a focus on the evidence from systematic reviews and meta-analyses. The NAATs summarized in this review include in-house NAATs, GeneXpert-MTB/RIF, GeneXpert-MTB/RIF Ultra, simultaneous amplification and testing-tuberculosis, FluoroType MTB and loop-mediated isothermal amplification.

Methods for rapid diagnosis of meningitis etiology in adults

Infectious meningitis can be caused by viral, bacterial or fungal pathogens. Despite widely available treatments, many types of infectious meningitis are still associated with significant morbidity and mortality. Delay in diagnosis contributes to poor outcomes. Cerebrospinal fluid cultures have been used traditionally but are time intensive and sensitivity is decreased by empiric treatment prior to culture. More rapid techniques such as the cryptococcal lateral flow assay (IMMY), GeneXpert MTB/Rif Ultra (Cepheid) and FilmArray multiplex-PCR (Biofire) are three examples that have drastically changed meningitis diagnostics. This review will discuss a holistic approach to diagnosing bacterial, mycobacterial, viral and fungal meningitis.

Comparison of amplicor and GeneXpert MTB/RIF tests for diagnosis of tuberculous meningitis

There are no data about the comparative accuracy of commercially available nucleic acid amplification tests (GeneXpert MTB/RIF and Roche Amplicor) for the diagnosis of tuberculous meningitis (TBM). A total of 148 patients with suspected TBM were evaluated, and cultures served as the reference standard. The sensitivities and specificities (95% confidence interval [CI]) for the Amplicor and Xpert MTB/RIF tests were similar: 46 (31-60) versus 50 (33-67) and 99 (93-100) and 94 (84-99), respectively.

Detection of 123 bp fragment of insertion element IS6110 Mycobacterium tuberculosis for diagnosis of extrapulmonary tuberculosis

PURPOSE

Extrapulmonary tuberculosis (EPTB) is emerging problem in developing and developed countries. The diagnosis of EPTB in its different clinical presentations remains a true challenge. IS6110-based polymerase chain reaction (PCR) is used for rapid identification and positivity rate of the Mycobacterium tuberculosis complex in clinical isolates of different sites of EPTB. The present study was carried out to study the prevalence of M. tuberculosis complex in clinical isolates of EPTB at tertiary care centres in Lucknow.

MATERIALS AND METHODS

Seven hundred fifty-six specimens were collected from the suspected cases of EPTB which were processed for Mycobacteria by Ziehl Neelson (ZN) staining and BACTEC culture. All the specimens were also processed for IS6110-based PCR amplification with primers targeting 123 bp fragment of insertion element IS6110 of the M. tuberculosis complex.

RESULTS

Of these 756 specimens, 71(9.3%) were positive for acid fast bacilli (AFB) by ZN staining, 227(30.1%) were positive for mycobacteria by BACTEC culture and IS6110 PCR were positive for M. tuberculosis complex in 165 (20.7%) isolates. We found a significant difference in sensitivities of different tests (P<0.05).

CONCLUSIONS

This study reveals the positivity of M. tuberculosis complex in clinical isolates of EPTB case in tertiary care hospitals in Northern India. 72.7% of M. tuberculosis complex was confirmed by IS6110-PCR in culture isolates from different sites of EPTB. The high prevalence of the M. tuberculosis complex was seen in lymph node aspirate and synovial fluid. However, utility of PCR may play a potentially significant role in strengthening the diagnosis of EPTB especially targeting IS6110.

Use of amplified Mycobacterium tuberculosis direct test (Gen-probe Inc., San Diego, CA, USA) in the diagnosis of tubercular synovitis and early arthritis of knee joint

BACKGROUND

The diagnosis of knee joint tuberculosis, especially in early stages of synovial disease, has more often been based on clinicoradiological suspicion, with no single test claiming to be a dependable rapid diagnostic test with high sensitivity and specificity. Nuclear amplification tests in vogue like the polymerase chain reaction have shown variable sensitivity and false positivity rates in various studies. We evaluated the role of Amplified Mycobacterium tuberculosis Direct Test (AMTDT) or Genprobe in the diagnosis of knee joint tuberculosis in early, especially, early synovitis and arthritis cases.

PATIENTS AND METHODS

Thirty two patients of suspected knee joint tuberculosis were subjected to diagnostic arthroscopy during the study period. The synovial fluid and tissue were subjected to mycobacterial culture, histopathology, and AMTDT. A comparative analysis of the sensitivity and specificity of this new test with culture and histopathology was done and the time taken for reporting was calculated for each test.

RESULTS

Out of 32 tissue samples, 8 were found to be positive with mycobacterial culture [Lowenstein Jensen (LJ)/Bactec], 11 were positive with histopathology, and 5 were found to positive with AMTDT. The sensitivity of AMTDT was found to be 62.5% and specificity was 100% with a P value of 0.083. The results were obtained earliest with AMTDT with a mean reporting time of 1.2 days, while the results of histopathology were obtained in a mean time of 6.8 days, BacT alert in 22.5 days, and conventional LJ medium culture results in 48.6 days.

CONCLUSION

AMTDT or Genprobe is a rapid diagnostic test for early diagnosis of tubercular arthritis, but has low sensitivity in knee joint tuberculosis. Nuclear amplification tests are still far from being a single promising alternative to conventional tests in cases of joint tuberculosis. Routine use of arthroscopic biopsies in all suspected cases is helpful in the early diagnosis of knee joint tuberculosis.

Comparison of two molecular methods for rapid diagnosis of extrapulmonary tuberculosis

Application of real-time PCR for the detection of Mycobacterium tuberculosis enables results to be obtained in about 2 h. A total of 340 nonrespiratory samples were processed using two real-time PCR assay kits: Xpert MTB/RIF and Cobas TaqMan MTB. The sensitivity and specificity of the Xpert assay were 95% and 100%, respectively, compared to 78% and 98% for the Cobas assay.

Clinical evaluation of Gen-Probe's amplified mycobacterium tuberculosis direct test for rapid diagnosis of Mycobacterium tuberculosis in Egyptian children at risk for infection

CONTEXT

Diagnostic detection of tuberculosis (TB) has improved considerably. Available, standardized, nucleic acid-based amplification techniques have been shown to yield reliable results within 4 to 7 hours of sample processing.

OBJECTIVE

To study the diagnostic performance of Gen-Probe's technique for direct detection of Mycobacterium tuberculosis in comparison with BACTEC 460 TB culture for both positive and negative Ziehl-Neelsen smears in Egyptian children at risk for TB infection.

DESIGN

We prospectively evaluated 50 children from families with a positive history of TB. All patients were referred from outpatient clinics of the Mansoura University Children's Hospital, Egypt. The children had a positive tuberculin skin test with an induration diameter of more than 10 mm and had scars from a bacille Calmette-Guérin vaccination within the past 2 years. Three consecutive sputum samples were taken from each patient. The samples were examined to detect M. tuberculosis by means of the Gen-Probe technique, direct smear microscopy, and bacterial culture by BACTEC 460 TB.

RESULTS

Of the 50 cases, 30 (60%) had sputum samples that were positive for TB by BACTEC 460 TB culture, and 29 cases (58%) were positive by the Gen-Probe technique. Sensitivity and specificity of Ziehl-Neelsen smears was 83.3% and 100%, respectively, with overall accuracy of 90%. Sensitivity and specificity of the Gen-Probe technique were 96.7% and 100%, respectively, with overall accuracy of 98%.

CONCLUSIONS

The results of this study suggest that the Gen-Probe technique is an accurate method for rapid detection of M. tuberculosis complexes in respiratory samples from children at risk for TB. It can be used for diagnosis of smear-negative cases that are suspect for TB.

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.

Clinical utility of polymerase chain reaction for diagnosis of smear-negative pleural tuberculosis

BACKGROUND

Polymerase chain reaction (PCR) is a molecular biology technique which can detect Mycobacterium tuberculosis (TB) genome in pleural fluid; however, the results are variable.

METHODS

Two hundred and twelve pleural fluid specimens suspected to be possibly associated with tuberculosis with negative acid-fast smears were sent to our laboratory to test for the presence of M. tuberculosis DNA using nested PCR, the target for the amplification being a segment of IS6110 in the genome of M. tuberculosis. The final diagnosis of TB pleurisy was based on combining clinical judgment with radiologic findings, microbiologic tests, and the histopathologic findings. Forty-nine patients were excluded due to incomplete or inconsistent clinical information.

RESULTS

Of 163 patients enrolled, PCR was positive in 23 (43.4%) of 53 patients with TB pleurisy and 5 (4.5%) of 110 patients with non-TB pleurisy, with a sensitivity and specificity of 43.4% and 95.5%, respectively. Positive culture of pleural fluid was found in 15 (28.3%) of the TB pleurisy group and none in the non-TB group. Fifteen (55.6%) of 27 with pleural biopsy demonstrated chronic granulomatous inflammation with or without caseous necrosis. Of these 27 patients, PCR was positive in 12 (44.4%). A higher proportion (70.4%) of patients with TB pleurisy was diagnosed when PCR was combined with biopsy results.

CONCLUSION

These data indicate that PCR alone has limited value in diagnosis of TB pleurisy with negative smear. However, when used in combination with pleural biopsy, it can be used to increase early detection of TB pleurisy in such patients.

The Clinical Utility of Polymerase Chain Reaction for the Diagnosis of Pleural Tuberculosis

BACKGROUND

There is no exact consensus about the usefulness of the Mycobacterium tuberculosis polymerase chain reaction (PCR) testing for the diagnosis of tuberculous pleural effusion because of the diverse PCR methods and the different diagnostic criteria that are described in other studies.

METHODS

We analyzed pleural effusion specimens obtained from 111 patients for whom the exclusion of the possibility of tuberculous pleural effusion was necessary. We performed M. tuberculosis PCR testing using the Cobas Amplicor MTB test (Roche Diagnostic Systems), which is fully automated and commercially available.

RESULTS

Results of the M. tuberculosis PCR test of pleural effusion specimens were positive for 7 (17.1%) of the 41 patients with confirmed pleural tuberculosis and for 3 (18.8%) of the 16 patients with probable pleural tuberculosis. The overall sensitivity and specificity of M. tuberculosis PCR testing of pleural effusion were 17.5% and 98.1%, respectively. The sensitivity of M. tuberculosis PCR testing for each group of patients with tuberculous pleural effusion detected by smear-positive results, smear-negative and culture-positive results, and culture-negative and pleural biopsy-positive results, was 100.0%, 33.3%, and 3.7%, respectively. Of the 57 patients with pleural tuberculosis, only 3 (5.3%) had positive results of M. tuberculosis PCR testing along with negative results of smearing, negative results of pleural pathological analysis, and a low level of adenosine deaminase.

CONCLUSION

For specimens such as pleural effusion, in which the bacillary load is very low, the clinical utility of PCR testing seems highly limited.

Clinical evaluation of the gen-probe amplified mycobacterium tuberculosis direct test for rapid diagnosis of tuberculosis lymphadenitis

This prospective study evaluated the performance of the Amplified Mycobacterium Tuberculosis Direct Test (MTD) for the diagnosis of lymph node tuberculosis in Djibouti, Republic of Djibouti. Of 197 specimens sampled from 153 patients, 123 were from 95 tuberculous patients. The sensitivity and specificity of MTD were 93 and 100%, respectively. The sensitivity of culture was 89%.

Apport de la PCR dans le diagnostic des tuberculoses extrapulmonaires

Extrapulmonary tuberculosis is usually more difficult to diagnose than pulmonary tuberculosis. It often involves inaccessible sites and it is paucibacillary.

OBJECTIVE AND METHOD

In this study, we tried to analyze the performance of various bacteriological methods used to diagnose 51 cases of extrapulmonary tuberculosis in an infectious diseases ward.

RESULTS AND COMMENTS

The culture was positive for 55% of patients. The new amplification methods used were very disappointing for the testing of nonrespiratory samples. The sensitivity of PCR was 32% compared to that of diagnostic culture which remains the most sensitive reference method. Liquid media allow for rapid growth and limit the contaminations. The combined inoculation of liquid and solid medium increases the sensitivity and helps to identify the pathogen.

Tuberculous orchiepididymitis diagnosed by nucleic acid amplification test: a case report

Symptoms of tuberculous orchiepididymitis in a 39-year-old male started with swelling of left scrotum, followed by fistula formation with suppurative discharge. There was no any improvement produced by antibiotics. Surgical extirpation of inflammatory destroyed testicle and epidydimis was performed. Presence of tubercle bacilli was not shown by bacteriological analysis of testicle tissue. Tuberculous etiology was suggested after histopathological examination of testis and epididymis. Exudate from surgical wound was examined on presence of Mycobacterium tuberculosis DNA. Etiology of orchiepididymitis was proved by positive assay and inflammatory process was completely cured by antituberculotics therapy. By this report it was clearly shown that sometimes only molecular methods could confirm etiology of inflammatory process.

Improved sensitivity of nucleic acid amplification for rapid diagnosis of tuberculous meningitis

Early diagnosis of tuberculous meningitis (TBM) is essential for a positive outcome; but present microbiological diagnostic techniques are insensitive, slow, or laborious. We evaluated the standard BDProbeTec ET strand displacement amplification method (the standard ProbeTec method) for the detection of Mycobacterium tuberculosis complex organisms in parallel with the ProbeTec method with a modified pretreatment procedure with 101 prospectively collected cerebrospinal fluid specimens from 94 patients with suspected TBM. By the modified method, the sample-washing step was omitted. A definitive diagnosis was attained by culture. Thirteen specimens from 12 patients were culture positive for M. tuberculosis complex organisms; three specimens (23%) were microscopy positive for acid-fast bacilli. Among the culture-positive specimens, the standard ProbeTec method was positive for 8 (61.5%) and the modified assay was positive for 10 (76.9%). The overall specificity by both procedures was 98.8% compared to the results of culture. After discrepancy analysis, conducted by reviewing the patients' previous laboratory data, the specificity increased to 100%. If the cutoff value for respiratory specimens was adjusted from the recommended value of 3,400 to 1,000, the sensitivity of the modified procedure increased to 84.7%, with unchanged specificity. Results were obtained in 3 to 4 h. The new pretreatment procedure with the ProbeTec assay described here provides a rapid, simple, and sensitive tool for the diagnosis of TBM.

Possible role of Mycobacterium tuberculosis complex in Melkersson-Rosenthal syndrome demonstrated with Gen-Probe amplified Mycobacterium tuberculosis direct test

Melkersson-Rosenthal (MRS) syndrome is characterized by a classical triad of recurrent or persistent orofacial swelling, peripheral facial nerve paralysis and lingua plicata. Granulomatous cheilitis (GC) is regarded as a monosymptomatic form of MRS. The exact aetiologies of MRS and GC are unknown. In this study we investigated the possible role of mycobacteria in these two conditions. A ribosomal RNA amplification-based Gen-Probe amplified Mycobacterium tuberculosis direct test was used to investigate the presence of M. tuberculosis complex in paraffin-embedded skin biopsy specimens from five patients with MRS and one patient with GC. Three of the six specimens were shown to be positive using this system; one of the positive specimens also showed positive Ziehl-Neelsen staining. These results suggest a possible mycobacterial aetiology for MRS and GC.

Comparison of conventional bacteriology with nucleic acid amplification (amplified mycobacterium direct test) for diagnosis of tuberculous meningitis before and after inception of antituberculosis chemotherapy

The role of nucleic acid amplification techniques in the rapid diagnosis of tuberculous meningitis remains uncertain. We compared the performance of Ziehl-Neelsen (ZN) staining, the Gen-Probe amplified Mycobacterium tuberculosis direct test (MTD), and culture with 341 cerebrospinal fluid specimens from 152 adults (73 with and 79 without tuberculous meningitis) before and after inception of antituberculosis chemotherapy. The sensitivity, specificity, and positive and negative predictive values of ZN staining before treatment were 34/66 (52%), 79/79 (100%), 34/34 (100%), and 79/111 (71%), compared with 25/66 (38%), 78/79 (99%), 25/26 (96%), and 79/120 (66%) for MTD. The sensitivity of combined ZN staining and MTD (either positive) was 45/66 (68%). The sensitivity of staining and culture fell more rapidly than that of MTD after the start of treatment: after 5 to 15 days of treatment, MTD was more sensitive than ZN staining (12/43 [28%] versus 2/43 [2%]; P = 0.013). Slower bacterial clearance was observed if M. tuberculosis was resistant to isoniazid and/or streptomycin: resistant organisms were more likely to be cultured from cerebrospinal fluid after 2 to 5 days of treatment than fully sensitive organisms (P < 0.001). The sensitivities of ZN staining, MTD, and the two tests combined were improved by repeated sampling to 38/59 (64%), 35/59 (59%), and 49/59 (83%), respectively. In conclusion, ZN staining of the cerebrospinal fluid is at least as good as MTD for the rapid diagnosis of tuberculosis and is much faster and less expensive. However, the combination of these methods on serial samples detects more cases. Alternative tests are still urgently required.

Diagnostic value of gastric aspirate smear and polymerase chain reaction in smear-negative pulmonary tuberculosis

OBJECTIVE

The aim of this study was to determine the validity of acid-fast bacilli (AFB) smear and polymerase chain reaction (PCR) from gastric aspirates for the diagnosis of smear-negative pulmonary tuberculosis.

METHODOLOGY

A cross-sectional study was conducted in a university hospital. One hundred and nine patients with suspected pulmonary tuberculosis in whom either sputum smears were negative or who were not producing sputum were recruited to the study. All patients underwent gastric aspiration after an overnight fast followed by standard fibreoptic bronchoscopy. Specimens were subjected to AFB smear, culture, and pathological examination. PCR was performed on culture filtrate after 1 week of incubation.

RESULTS

Eight patients did not complete the follow-up schedule. Of the 101 patients with final outcomes, a diagnosis of pulmonary tuberculosis from microbiological evidence was established in 54 patients. The gastric aspirate smear, PCR, or either one of them was positive in 34, 30, and 39 tuberculosis patients, respectively. There were 13 false positive smears from 47 non-tuberculosis patients, with five resulting from non-tuberculous mycobacteria (NTM). The PCR was falsely positive in eight patients, five of whom had previous histories of tuberculosis. The overall sensitivity, specificity, positive predictive value, and negative predictive value of gastric aspirate examination by combined smear and PCR were 72, 58, 66, and 64%, respectively.

CONCLUSIONS

Gastric aspiration is a useful tool for the diagnosis of smear-negative pulmonary tuberculosis warranting institution of antituberculosis treatment. Interpretation of the results should be cautious in those who have had tuberculosis in the past or who have been at risk for acquisition of NTM.

Nucleic acid amplification tests in the diagnosis of tuberculous pleuritis: a systematic review and meta-analysis

Background

Conventional tests for tuberculous pleuritis have several limitations. A variety of new, rapid tests such as nucleic acid amplification tests – including polymerase chain reaction – have been evaluated in recent times. We conducted a systematic review to determine the accuracy of nucleic acid amplification (NAA) tests in the diagnosis of tuberculous pleuritis.

Methods

A systematic review and meta-analysis of 38 English and Spanish articles (with 40 studies), identified via searches of six electronic databases, hand searching of selected journals, and contact with authors, experts, and test manufacturers. Sensitivity, specificity, and other measures of accuracy were pooled using random effects models. Summary receiver operating characteristic curves were used to summarize overall test performance. Heterogeneity in study results was formally explored using subgroup analyses.

Results

Of the 40 studies included, 26 used in-house ("home-brew") tests, and 14 used commercial tests. Commercial tests had a low overall sensitivity (0.62; 95% confidence interval [CI] 0.43, 0.77), and high specificity (0.98; 95% CI 0.96, 0.98). The positive and negative likelihood ratios for commercial tests were 25.4 (95% CI 16.2, 40.0) and 0.40 (95% CI 0.24, 0.67), respectively. All commercial tests had consistently high specificity estimates; the sensitivity estimates, however, were heterogeneous across studies. With the in-house tests, both sensitivity and specificity estimates were significantly heterogeneous. Clinically meaningful summary estimates could not be determined for in-house tests.

Conclusions

Our results suggest that commercial NAA tests may have a potential role in confirming (ruling in) tuberculous pleuritis. However, these tests have low and variable sensitivity and, therefore, may not be useful in excluding (ruling out) the disease. NAA test results, therefore, cannot replace conventional tests; they need to be interpreted in parallel with clinical findings and results of conventional tests. The accuracy of in-house nucleic acid amplification tests is poorly defined because of heterogeneity in study results. The clinical applicability of in-house NAA tests remains unclear.

Diagnostic accuracy of nucleic acid amplification tests for tuberculous meningitis: a systematic review and meta-analysis

Conventional tests are not always helpful in making a diagnosis of tuberculous meningitis. We did a systematic review and meta-analysis to establish the summary accuracy of nucleic acid amplification (NAA) tests for tuberculous meningitis. We searched six electronic databases and contacted authors, experts, and manufacturers. Measures of diagnostic accuracy were pooled using a random effects model. 49 studies met our inclusion criteria. The summary estimates in 14 studies with commercial NAA tests were: sensitivity 0.56 (95% CI 0.46, 0.66), specificity 0.98 (0.97, 0.99), positive likelihood ratio 35.1 (19.0, 64.6), negative likelihood ratio 0.44 (0.33, 0.60), and diagnostic odds ratio 96.4 (42.8, 217.3). In the 35 studies with in-house ("home-brew") tests, the summary accuracy could not be established with confidence because of wide variability in test accuracy. On current evidence, commercial NAA tests show a potential role in confirming tuberculous meningitis diagnosis, although their overall low sensitivity precludes the use of these tests to rule out tuberculous meningitis with certainty.

Rapid diagnosis of extrapulmonary tuberculosis by PCR: impact of sample preparation and DNA extraction

In cases of suspected extrapulmonary tuberculosis, rapid and accurate laboratory diagnosis is of prime importance, since traditional techniques of detecting acid-fast bacilli have limitations. The major difficulty with mycobacteria is achieving optimal cell lysis. Buffers used in commercial kits do not allow this complete lysis in a number of clinical specimens. A comparison of two sample preparation methods, pretreatment with proteinase K (PK-Roche) and complete DNA purification (cetyltrimethylammonium bromide [CTAB]-Roche), was conducted on 144 extrapulmonary specimens collected from 120 patients to evaluate the impact on the Cobas-Amplicor method. Thirty patients were diagnosed with tuberculosis, with 15 patients culture positive for Mycobacterium tuberculosis. Amplification and detection of the amplicons were impaired by a high number of inhibitory specimens (39 to 52%). CTAB-Roche allowed the detection of more culture-positive specimens by PCR than PK-Roche. Comparison with the final diagnoses of tuberculosis confirmed that CTAB-Roche produced the best sensitivity (53.8%) compared to culture (43.3%), PK-Roche (16%), and smear (13%). However, the specificity of the PCR assay with CTAB-Roche-extracted material was always lower (78.8%) than those with culture (100%) and PK-Roche (96.5%). False-positive specimens were lung biopsy material, lymph node biopsy material and aspirate, or bone marrow aspirate, mainly from immunocompromised patients. Despite the efficiency of complete DNA extraction for the rapid diagnosis by PCR of extrapulmonary tuberculosis, the false-positive results challenge our understanding of PCR results.

[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.

Detection of mycobacterium tuberculosis in paraffin-embedded pleural biopsy specimens by commercial ribosomal RNA and DNA amplification kits

STUDY OBJECTIVES

To evaluate the utility of two gene amplification systems in historical paraffin-embedded pleural biopsy (PEB) tissues from patients with pleural tuberculosis, and to compare the results to those obtained with conventional histologic and microbiological methods.

DESIGN

A retrospective study.

PATIENTS AND METHODS

Seventy-four formalin-fixed PEB tissues collected and stored over 12 years (1984 through 1995) were retrieved. Gene amplifications were performed in 57 tissues from patients with diagnoses of pleural tuberculosis and in 17 from patients with carcinoma as controls, using the first version of the Amplified Mycobacterium tuberculosis Direct Test (AMTDT; Gen-Probe; San Diego, CA) and the LCx Mycobacterium tuberculosis Assay (LCxMTB; Abbott Laboratories; Abbott Park, IL).

RESULTS

The sensitivities of the AMTDT and LCxMTB were 52.6% and 63.2%, respectively (p = not statistically significant). The specificity of both tests was 100%. Twenty tissue samples (35.1%) were positive by both systems, and 10 tissues (17.5%) were positive only by the AMTDT, while 16 tissues (28.1%) were positive only by the LCxMTB. Both tests gave negative results for 11 specimens (19.3%). When both tests were used, a positive diagnosis was achieved in 80.7% of the samples. Diagnosis of 73.7% of patient conditions had previously been made by smear examination of pleural biopsy and sputum, pleural liquid, or biopsy culture. The overall diagnostic yield with both culture and amplification techniques was 96.5% (55 of 57 patients) for pleural tuberculosis, with amplification techniques adding 22.8% of the diagnoses.

CONCLUSIONS

Amplification techniques are useful in archival PEB tissues, providing additional diagnoses beyond culturing, although the sensitivity should be improved, possibly by standardizing protocols.

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

The new version of the Amplified Mycobacterium Tuberculosis Direct Test, MTD2 (Gen-Probe Inc., San Diego, CA) has been implemented as part of the regular testing algorithm for detecting Mycobacterium tuberculosis (MTB) in selected respiratory and non-respiratory specimens in our laboratory. At the Central Public Health Laboratory, Etobicoke, Ontario, we receive specimens for the detection of mycobacteria from all areas of the Province of Ontario. The laboratory processes approximately 25,000 specimens per year, and receives approximately 2000 reference cultures for identification. There are 600 to 700 new cases of tuberculosis detected yearly. Over the 1-year period (1997-98), 823 specimens were tested by MTD2 and the results were compared with radiometric culture (Bactec, Becton Dickinson, Sparks, MD) and clinical diagnosis, giving an overall sensitivity, specificity, positive predictive value and negative predictive values of 100%, 99.6%, 97.4% and 100%, respectively. Two hundred and two cases of respiratory TB and 56 cases of extrapulmonary TB were detected by MTD2 within 0-4 days of specimen arrival in the laboratory. By appropriate selection of specimens for testing, the MTD2 can provide a fast, accurate, and cost-effective method for the detection of MTB in clinical specimens.

Molecular methods in the detection and identification of mycobacterial infections

Nucleic acid amplification (NAA) tests for direct detection of Mycobacterium tuberculosis complex in respiratory specimens have the potential to provide a more rapid diagnosis of pulmonary tuberculosis (TB) than is currently possible by conventional stain, culture, and identification tests. Currently, 2 NAA tests-enhanced Amplified Mycobacterium Tuberculosis Direct (MTD) Test (Gen-Probe, Inc) and Amplicor Mycobacterium tuberculosis Test (Roche Molecular Systems, Inc)-have been approved by the Food and Drug Administration for testing respiratory specimens that are smear positive for acid-fast bacilli (AFB). This restriction to AFB smear-positive specimens was based on data from the initial clinical trials conducted to evaluate these products that showed low sensitivity (ie, 48%-53%) and less-than-optimal specificity (ie, 96%-99%) in AFB smear-negative specimens. Data from the clinical trial for the enhanced MTD test and from 2 subsequent studies, however, suggest that this version of the MTD test is a reliable tool for rapid diagnosis of pulmonary TB, regardless of the AFB smear result. Both NAA tests have been evaluated for diagnosis of extrapulmonary TB, and results were comparable to the results of tests performed with respiratory specimens. The NAA tests also appear to be reliable for rapid identification 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 AFB smear result. With smear-positive results, public health and hospital infection control resources are predominantly affected. With smear-negative results, however, the potential for affecting patient outcome is much greater. In patients with smear-negative results, the NAA test can result in earlier diagnosis of TB and subsequent initiation of therapy. Use of these tests also may eliminate the need for invasive diagnostic procedures, which are costly and pose an added risk to the patient, and they may allow earlier discharge of hospitalized patients.

Diagnosis of pediatric tuberculosis in the modern era

BACKGROUND

Correctly diagnosing tuberculosis (TB) in children is critical to provide appropriate treatment and to detect undiagnosed source cases. However, diagnosing TB in children may be difficult.

OBJECTIVE

We sought to determine whether Amplicor, a Food and Drug Administration-approved polymerase chain reaction (PCR) assay used to detect Mycobacterium tuberculosis in sputum and computerized tomography (CT) would facilitate the diagnosis of TB in children. We also examined the applicability of the Centers for Disease Control and Prevention clinical case definition for TB.

SETTING

A university-affiliated pediatric hospital in New York City.

SUBJECTS

From March, 1995, to November, 1997, 27 children < 15 years of age (mean age, 3.9 years) were evaluated for suspected TB.

RESULTS

M. tuberculosis was cultured from 5 of 76 (6.6%) gastric aspirate specimens, and PCR detected M. tuberculosis DNA in 3 (4.1%) of these specimens. There was poor correlation between culture and PCR because 6 specimens were discordant. CT scans were diagnostic of mediastinal or hilar adenopathy in 6 children with equivocal or negative chest radiographs and confirmed adenopathy in 8 others. Six children received alternative diagnoses.

CONCLUSIONS

We conclude that the commercially available PCR technology had very limited utility in detecting M. tuberculosis from gastric aspirates, but CT scans were useful in assessing pediatric patients with suspected TB.

Comparison of culture and acid-fast bacilli stain to PCR for detection of Mycobacterium tuberculosis in clinical samples

The major drawback in effective use of polymerase chain reaction (PCR) for detecting Mycobacterium tuberculosis (MTB) in clinical samples is the presence of PCR inhibitors and unique cell components of the organism that complicate DNA extraction and subsequent PCR amplification. A PCR assay with a unique multistep DNA extraction method that minimizes these problems was compared in a prospective study to acid-fast bacilli stain (AFBS) and culture for detecting MTB in clinical samples. A total of 254 clinical specimens in two separate studies were processed for MTB by these techniques. While PCR and culture were 100% sensitive and specific, culture required up to 8 weeks of incubation and additional time to perform biochemical testing to identify the isolated micro-organism. Acid-fast bacilli stain had a specificity of about 87% and did not differentiate among Mycobacterial species. In contrast, the results from PCR were available within 48 h and did not require additional testing to attain a final result. Polymerase chain reaction was highly reliable for detection and confirmation and interpretation of positive AFBS results. The assay was easy to perform with a turn around time of about 2 days.

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.

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.

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.

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).

Rapid identification of Mycobacterium tuberculosis complex on urine samples by Gen-Probe amplification test

The aim of the study was to evaluate the applicability to urine samples of the Amplified Mycobacterium tuberculosis Direct Detection Test (AMTD), which is currently used to identify this organism in respiratory specimens within a few hours. The study was performed on 95 patients, comprising 35 subjects with a high index of suspicion for active tuberculosis of the urinary tract and 60 subjects with evidence of non-mycobacterial disease. One urine specimen from each subject was examined by microscopy, culture and AMTD. AMTD was positive in 38 specimens and negative in 57. Assuming culture as the reference standard, the sensitivity, specificity, positive predictive value and negative predictive value of AMTD were 100%, 91.93%, 86.84% and 100%, respectively. Reassessing the discrepancies between AMTD and culture by review of patients' charts, the sensitivity, specificity, positive predictive value and negative predictive value of AMTD were 100%, 93.44%, 89.47% and 100%. The results of the study as well as the characteristics of AMTD encourage its use for the rapid recognition of urinary tract tuberculosis, although its findings should be interpreted cautiously when the clinical picture is not consistent with an active tuberculosis.

Comparison of PCR, culture, and histopathology for diagnosis of tuberculous pericarditis

Nucleic acid amplification techniques for the diagnosis of tuberculosis (TB) are rapidly being developed. Scant work, however, has focused on pericardial TB. Using cryopreserved specimens from a prior study of pericarditis, we compared PCR to culture and histopathology for the diagnosis of tuberculous pericarditis in 36 specimens of pericardial fluid and 19 specimens of pericardial tissue from 20 patients. Fluid and tissue were cultured on Lowenstein-Jensen and Middlebrook solid media and in BACTEC radiometric broth. Tissue specimens were stained with hematoxylin-eosin, Ziehl-Neelsen, auramine O, and Kinyoun stains and were examined for granuloma formation and acid-fast bacilli. PCR was performed with both fluid and tissue with IS6110-based primers specific for the Mycobacterium tuberculosis complex by published methods. Sixteen of the 20 patients had tuberculous pericarditis and 4 patients had other diagnoses. TB was correctly diagnosed by culture in 15 (93%) patients, by PCR in 13 (81%) patients, and by histology in 13 of 15 (87%) patients. PCR gave one false-positive result for a patient with Staphylococcus aureus pericarditis. Considering the individual specimens as the unit of analysis, M. tuberculosis was identified by culture in 30 of 43 specimens (70%) from patients with tuberculous pericarditis and by PCR in 14 of 28 specimens (50%) from patients with tuberculous pericarditis (P > 0.15). The sensitivity of PCR was higher with tissue specimens (12 of 15; 80%) than with fluid specimens (2 of 13; 15%; P = 0.002). In conclusion, the overall accuracy of PCR approached the results of conventional methods, although PCR was much faster. Therefore, PCR merits further development in this regard. The sensitivity of PCR with pericardial fluid was poor, and false-positive results with PCR remain a concern.

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.