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

Rapid detection of Mycobacterium tuberculosis using a novel ultrafast chip-type real-time polymerase chain reaction system

BACKGROUND

NBS LabChip G2-3 is a novel, ultrafast, chip-type portable real-time polymerase chain reaction (PCR) system. We evaluated the clinical usefulness of this system in detecting pulmonary TB and assessed its diagnostic performance compared with a conventional tube-type PCR system.

METHODS

A total of 247 sputum samples were collected from patients suspected of having pulmonary TB. After the decontamination process, these samples were examined by fluorescence staining for acid-fast bacilli, cultures with both solid and liquid media, and real-time PCR with the NBS LabChip and a conventional tube-type system. The diagnostic accuracy of the NBS LabChip system and the agreement between the two assays were evaluated.

RESULTS

Considering mycobacterial culture results as a gold standard, the overall sensitivity and specificity of the NBS LabChip was 83.8% (95% CI, 73.8%-91.1%) and 94.0% (95% CI, 89.3%-97.1%), respectively. For the detection of TB from the smear-positive samples, the sensitivity and specificity of the NBS LabChip was 96.0% (95% CI, 86.3%-99.5%) and 83.3% (95% CI, 72.3%-95.7%), respectively. For the smear-negative samples, the sensitivity and specificity of the NBS LabChip was 63.3% (95% CI, 43.9%-80.1%) and 95.0% (95% CI, 90.4%-97.8%), respectively. There were no significant differences in the sensitivity and specificity between the NBS LabChip and a conventional tube-type system, although the NBS LabChip shortened the PCR time (27 min for 45 cycles).

CONCLUSIONS

The NBS LabChip G2-3 system has potential as an ultrafast, cost-effective diagnostic tool for pulmonary TB with high sensitivity and specificity.

The predictive value of Gen-Probe's amplified Mycobacterium tuberculosis direct test compared with culturing in paraffin-embedded lymph node tissue exhibiting granulomatous inflammation and negative acid fast stain

BACKGROUND AND OBJECTIVES

The diagnosis of granulomatous inflammation with possible tuberculosis (TB) infection in histopathology is often difficult. There is a need for a rapid and reliable diagnostic test. Thus, we evaluated the performance of the Mycobacterium tuberculosis direct (MTD) test in specimens with granulomatous lymphadenitis and negative acid fast stains.

METHODS

The M. tuberculosis direct (MTD) test by Gen-Probe was performed on 45 formalin-fixed paraffin-embedded tissue samples including 34 lymph nodes. We measured the predictive values of the MTD test in specimens with granulomatous lymphadenitis and negative acid fast stains.

RESULTS

The overall test sensitivity was 73.9%, and specificity was 95.4%. The MTD test sensitivity and specificity for lymph node tissue were 72.7% and 91.67%, respectively. In the presence of granulomatous inflammation, the MTD test sensitivity and specificity were higher than those for all tissue samples, at 75% and 100%, respectively.

CONCLUSION

Based on this study, the MTD test should be used as a supportive test in addition to conventional histochemical or immunological staining methods when evaluating lymph node tissue with a granulomatous inflammation to deliver stronger evidence to support clinical decisions at a much earlier time than a culture would allow.

Amplified Mycobacterium tuberculosis direct test for diagnosing tuberculous pleurisy--a diagnostic accuracy study

BACKGROUND

The study was designed to investigate the clinical usefulness of Amplified Mycobacterium Tuberculosis Direct (AMTD) tests for diagnosing TB pleurisy.

METHODS

One hundred and fifty-two patients for whom the exclusion of tuberculous pleural effusion was necessary were retrospectively analyzed.

RESULTS

The sensitivity of AMTD in diagnosing pleural TB was 36.4% (20 of 55). Combining sputum and pleural effusion AFB smear, pleural biopsy, and AMTD test of pleural effusion increased sensitivity to 82.5% (33/40). There were significantly higher percentages of neutrophils in the pleural effusion in the positive than in the negative AMTD group (38.0 ± 6.7% vs. 11.1 ± 3.7%, p<0.001). Patients with symptom duration <18 days prior to pleural effusion studies had more positive AMTD tests than those with symptom >18 days (70% vs. 31.4%; OR 5.09; 95% CI 1.54-16.79; p = 0.011).

CONCLUSIONS

Combining AMTD tests with conventional diagnostic methods offer good sensitivity for pleural TB diagnosis. Patients in the early course of the disease are better candidates for AMTD tests.

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

[Consensus document on the diagnosis, treatment and prevention of tuberculosis]

Pulmonary TB should be suspected in patients with respiratory symptoms longer than 2-3 weeks. Immunosuppression may modify clinical and radiological presentation. Chest X-ray shows very suggestive, albeit sometimes atypical, signs of TB. Complex radiological tests (CT scan, MR) are more useful in extrapulmonary TB. At least 3 serial representative samples of the clinical location are used for diagnosis whenever possible. Bacilloscopy and liquid medium cultures are indicated in all cases. Genetic amplification techniques are coadjuvant in moderate or high TB suspicion. Administration of isoniazid, rifampicin, ethambutol and pyrazinamide (HREZ) for 2 months and HR for 4 additional months is recommended in new cases of TB, except in cases of meningitis in which treatment should continue for up to 12 months and up to 9 months in spinal TB with neurological involvement, and in silicosis. Appropriate adjustments with antiretroviral treatment should be made in HIV patients. Combined therapy is recommended to avoid development of resistance. An antibiogram to first line drugs should be performed in all the initial isolations of new patients. Treatment control is one of the most important activities in TB management. The Tuberculin Skin Test (TST) is positive in TB infection when >or=5mm, and Interferon-Gamma Release Assays (IGRA) are recommended in combination with TT. The standard treatment schedule for infection is 6 months with isoniazid. In pulmonary TB, respiratory isolation is applied for 3 weeks or until 3 negative bacilloscopy samples are obtained.

[Consensus document on the diagnosis, treatment and prevention of tuberculosis]

Pulmonary TB should be suspected in patients with respiratory symptoms longer than 2-3 weeks. Immunosuppression may modify clinical and radiological presentation. Chest x-ray shows very suggestive, albeit sometimes atypical, signs of TB. Complex radiological tests (CT scan, MR) are more useful in extrapulmonary TB. At least 3 serial representative samples of the clinical location are used for diagnosis whenever possible. Bacilloscopy and liquid medium cultures are indicated in all cases. Genetic amplification techniques are coadjuvant in moderate or high TB suspicion. Administration of isoniazid, rifampicin, ethambutol and pyrazinamide (HREZ) for 2 months and HR for 4 additional months is recommended in new cases of TB, except in cases of meningitis in which treatment should continue for up to 12 months and up to 9 months in spinal TB with neurological involvement, and in silicosis. Appropriate adjustments with antiretroviral treatment should be made in HIV patients. Combined therapy is recommended to avoid development of resistance. An antibiogram to first line drugs should be performed in all the initial isolations of new patients. Treatment control is one of the most important activities in TB management. The Tuberculin Skin Test (TST) is positive in TB infection when >or=5mm, and Interferon-Gamma Release Assays (IGRA) are recommended in combination with TT. The standard treatment schedule for infection is 6 months with isoniazid. In pulmonary TB, respiratory isolation is applied for 3 weeks or until 3 negative bacilloscopy samples are obtained.

Detection and identification of aquatic mycobacteria in formalin-fixed, paraffin-embedded fish tissues

The isolation of mycobacteria from field samples is problematic, and isolation of the bacterium is sometimes not even attempted. The detection of mycobacteria through traditional histology using formalin-fixed, paraffin-embedded (FFPE) tissues is neither sensitive nor specific. However, detection of mycobacterial DNA from FFPE specimens, suspected of being infected with mammalian mycobacteriosis, is a routine clinical procedure. In the present study, a polymerase chain reaction (PCR)-based method was used to detect and identify mycobacteria in FFPE specimens sampled from fish suspected of being infected with fish mycobacteriosis. A total of 45 fish tissue samples, comprising of 12 tissue samples obtained from experimentally infected fish and the remainder from fish naturally infected with mycobacteria, were analysed using a PCR protocol which amplifies a fragment of the mycobacterial 65 kDa heat-shock protein (hsp65) gene. PCR-restriction enzyme analysis and/or sequencing were employed to further analyse the PCR amplicons. The PCR results were compared with those obtained by histology and culture. Mycobacterial DNA was detected in 34 of the 45 samples examined, of which 16 samples (47%) showed granulomatous reactions on histological examination. Using histology as the gold standard, no false-negative PCR results were obtained. Also, considering the presence or absence of granulomas as a diagnostic criterion, the sensitivity and specificity of PCR in 42 of the FFPE tissues were 16/16 (100%) and 8/26 (approximately 30.8%), respectively. Corresponding microbiological cultures were available for 15 cases, of which 13 were pure Mycobacterium cultures. Of these, 13 were PCR positive (100% sensitivity and 50% specificity). The PCR-based methods used here proved sensitive, specific and rapid for the detection of mycobacteria in routinely processed paraffin wax-embedded and formalin-fixed histological samples, and the results of the study suggest that this method has potential use in retrospective epidemiological studies.

Constrictive pericarditis: Detection of mycobacterium tuberculosis in paraffin-embedded pericardial tissues by polymerase chain reaction

BACKGROUND

Although the utility of polymerase chain reaction (PCR) for diagnosis of acute pleuro-pericardial tuberculosis has been well established, its use for chronic constrictive pericarditis is yet to be reported.

AIMS

To define the sensitivity and specificity of PCR for diagnosis of tuberculosis (TB) in patients with constrictive pericarditis.

METHODS

The medical records of 30 consecutive patients with constrictive pericarditis were reviewed. In addition their historical paraffin-embedded pericardial tissues were used for new histopathologic examination and PCR amplification for Mycobacterium tuberculosis genome.

RESULTS

There were 23 males and 7 females with a mean age of 35+/-19.5 years. The anticipated causes of constriction included idiopathic (n=21), tuberculosis (n=5), cardiac surgery (n=2) and post traumatic (n=2). PCR became positive in nine patients. Four out of 5 patients with tuberculous granuloma had a positive test result. In addition all 4 patients with non-tuberculous constrictive pericarditis had a negative test result. Therefore considering the presence or absence of granuloma as a diagnostic criteria, the sensitivity and specificity of PCR were 4/5 (80%) and 20/25 (80%), respectively.

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.

Detection of Mycobacterium tuberculosis complex in formalin-fixed, paraffin-embedded tissue specimens with necrotizing granulomatous inflammation by strand displacement amplification

Rapid, reliable diagnosis of tuberculosis is essential to initiate correct treatment, avoid severe complications, and prevent transmission. Conventional microbiological methods may not be an option if samples are formalin-fixed and paraffin-embedded (FFPE) for histopathological examination. With the demonstration of necrotizing granulomatous inflammation, tuberculosis becomes an important differential diagnosis, although it was not initially suspected. Following paraffin extraction, BDProbeTec ET strand displacement amplification for detection of Mycobacterium tuberculosis complex (MTC) was applied to 47 prospectively and 19 retrospectively collected FFPE samples from various sources with granulomatous inflammation and results were compared to tuberculosis notification. Of the prospective samples, 20 were from patients who were notified as having tuberculosis and the assay was positive in 18 (90%). Specificity was 100%. For 27 of the patients with prospectively collected FFPE specimens, culture was performed on a specimen collected at a later date from the same location. Culture revealed MTC in 14 and nontuberculous mycobacteria in four. BDProbeTec ET was positive in 13 (92.8%) of the patients with positive MTC culture and negative in the remaining. The sensitivity and specificity in 19 archival samples was 40% and 100%, respectively, compared to notification data. The assay provided rapid, correct diagnosis on different sources of FFPE samples collected prospectively and therefore offers an important supplementary method for patients where tuberculosis was not initially suspected.

Polymerase Chain Reaction of Pleural Biopsy Is a Rapid and Sensitive Method for the Diagnosis of Tuberculous Pleural Effusion

BACKGROUND

Tuberculous pleural effusion occurs in 30% of patients with tuberculosis (TB). Rapid diagnosis of a tuberculous pleural effusion would greatly facilitate the management of many patients. Polymerase chain reaction (PCR) has been used to detect Mycobacterium tuberculosis in pleural fluid with highly variable sensitivity.

OBJECTIVE

To improve our laboratory diagnosis of tuberculous pleural effusion.

METHODS

We applied PCR to detect DNA specific for M tuberculosis in 33 of the studied pleural biopsy specimens using an IS986-based primer that was specific for mycobacterium complex, and compared it to the results of pleural fluid and biopsy cultures performed on either Lowenstein-Jensen (LJ) medium or BACTEC 12B liquid medium (Becton Dickinson Microbiology Systems; Cockeysville, MD), Ziehl-Neelsen (ZN) staining, and histopathology in 45 patients with pleural effusion.

RESULTS

Of the 45 patients with pleural effusion who were studied, 26 patients received diagnoses of tuberculous pleural effusion that had been confirmed by either culture and or histopathology, 10 patients received diagnoses of exudative effusion due to causes other than TB, and 9 patients received diagnoses of transudative effusion. Histopathology of the pleural biopsy specimen had a sensitivity of 53.8%. The sensitivity of the ZN staining of pleural fluid and biopsy specimens was 0.0% and 3.8%, respectively. The sensitivity of the culture on both BACTEC 12B liquid medium and LJ medium was higher in pleural biopsy specimens (92.3%) than in pleural fluid specimens (15.4%; p > 0.001). The improvements of the BACTEC culture system improved and shortened the detection time of M tuberculosis in pleural biopsy specimens. PCR of pleural biopsy specimens had 90% sensitivity and 100% specificity. The positive predictive value and the negative predictive value for pleural biopsy specimen cultures were 100% and 90.5% vs 100% and 86.7% for pleural biopsy specimen PCRs.

CONCLUSION

The overall accuracy of PCR of pleural biopsy was similar to the results of pleural biopsy culture, however, PCR of the pleural biopsy was much faster in reaching diagnosis. PCR of pleural biopsy is a useful method when used in combination with the BACTEC culture system and histopathologic examination of pleural biopsy to reach a rapid diagnosis of tuberculous pleural effusion.

DNA genotyping of unbuffered formalin fixed paraffin embedded tissues

Formalin-induced DNA degradation was studied at different fixation times (3, 7, 16 and 32 days) each on 10 formalin fixed paraffin embedded tissues (FFPET) stored for 15 years at room temperature. The four different extraction protocols used in this study showed that Chelex100 extracts performed the best at 3 and 7 days of formalin fixation (DFF) (with regard to the quantity and the quality of the DNA). However, Qiamp extracts showed better results for long sized alleles, as well for single polymerase chain reaction (PCR) amplifications after 16 and 32 DFF, as for multiplex PCR at shorter fixation times. DNA degradation is expressed by the size of the amplified alleles, only 100 bp templates surviving after 32 DFF (AMG locus). Single locus amplifications (CD4 and FES/FPS alleles) performed better than multiplex PCR (ProfilerPlus), with nearly 100% positive results at 7 DFF. In both types of amplifications, the success rate decreased proportionally with the time of formalin fixation and, consequently, with the size of the required DNA template.