Monitoring the therapy of pulmonary tuberculosis by nested polymerase chain reaction assay

HIV-1 Tat Induces Unfolded Protein Response and Endoplasmic Reticulum Stress in Astrocytes and Causes Neurotoxicity through Glial Fibrillary Acidic Protein (GFAP) Activation and Aggregation

HIV-1 Tat is a major culprit for HIV/neuroAIDS. One of the consistent hallmarks of HIV/neuroAIDS is reactive astrocytes or astrocytosis, characterized by increased cytoplasmic accumulation of the intermediate filament glial fibrillary acidic protein (GFAP). We have shown that that Tat induces GFAP expression in astrocytes and that GFAP activation is indispensable for astrocyte-mediated Tat neurotoxicity. However, the underlying molecular mechanisms are not known. In this study, we showed that Tat expression or GFAP expression led to formation of GFAP aggregates and induction of unfolded protein response (UPR) and endoplasmic reticulum (ER) stress in astrocytes. In addition, we demonstrated that GFAP up-regulation and aggregation in astrocytes were necessary but also sufficient for UPR/ER stress induction in Tat-expressing astrocytes and for astrocyte-mediated Tat neurotoxicity. Importantly, we demonstrated that inhibition of Tat- or GFAP-induced UPR/ER stress by the chemical chaperone 4-phenylbutyrate significantly alleviated astrocyte-mediated Tat neurotoxicity in vitro and in the brain of Tat-expressing mice. Taken together, these results show that HIV-1 Tat expression leads to UPR/ER stress in astrocytes, which in turn contributes to astrocyte-mediated Tat neurotoxicity, and raise the possibility of developing HIV/neuroAIDS therapeutics targeted at UPR/ER stress.

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.

Dynamics of the laboratory results in patients with pulmonary tuberculosis

The process of infection and disease development is difficult to follow-up before tuberculosis (TB) confirmation. The laboratory analysis mirrors the infection with the possible subsequent breakdown to clinical TB. To better define the dynamics of the laboratory results in suspected and already confirmed patients with pulmonary TB, we studied the analysis of 1467 pathologic samples collected during the hospitalization of 841 patients. The samples were analyzed by 3 laboratory methods--direct microscopy, culture, and polymerase chain reaction (PCR). It was found that compared to cultures, the PCR method is more sensitive. For few cases, we demonstrate that the PCR result is positive about 2 weeks before the first positive culture. During the treatment follow-up, the PCR result remains positive for a long time, up to 4 to 5 months after the last positive culture. For better definition of the period during which microscopy and culture results remain positive, we studied the laboratory results of 100 casually selected patients with pulmonary TB positive on culture. The median periods during which these patients were found to be microscopy and culture positive were 10 and 25 days, respectively. Second to the dynamics of the laboratory results, we demonstrate that TB development is very rapid, whereas the period of recovery is long. The PCR results have to be reproducibly negative to accept that the process of active therapy is completed and the patient can remain under surveillance. On the basis of the laboratory data obtained, we propose empiric models for the dynamics of the laboratory results for patients with pulmonary tuberculosis.

Biologie moléculaire et microbiologie clinique en 2007

La biologie moléculaire est omniprésente en biologie médicale et plus particulièrement en microbiologie. De nombreux articles démontrent son importance tant dans le domaine du diagnostic que du pronostic, de l'évaluation thérapeutique, de l'épidémiologie ou des risques biologiques naturels ou non. La quantité considérable d'articles sur ce sujet n'apporte pas toujours une réponse évidente sur le rôle de la biologie moléculaire dans un laboratoire de microbiologie qu'il soit hospitalier ou non. Cette revue constitue une synthèse des apports de cette discipline en microbiologie. À partir de cet état des lieux, certaines questions se posent, par exemple : la biologie moléculaire constitue-t-elle un réel apport en microbiologie ? Dans quelles indications prescrire un examen de biologie moléculaire ? Les réponses ne sont pas toujours simples. Elles sont évidentes dans certains cas (l'hépatite C par exemple) et le sont moins dans d'autres, la tuberculose par exemple. Dans la première partie de l'article, nous avons parlé des généralités appliquées à la microbiologie. Dans cette deuxième partie, nous abordons certaines applications, reflets de l'importance prise par la biologie moléculaire en microbiologie.

Molecular diagnostics in tuberculosis

Molecular diagnostics in tuberculosis has enabled rapid detection of Mycobacterium tuberculosis complex in clinical specimens, identification of mycobacterial species, detection of drug resistance, and typing for epidemiological investigation. In the laboratory diagnosis of tuberculosis, the nucleic acid amplification (NAA) test is rapid and specific but not as sensitive as culture of mycobacteria. The primary determinant of successful NAA testing for tuberculosis depends on the shedding of mycobacterial DNA in secretions from caseating granulomas and its dissemination into sterile body fluids or tissue biopsies. In multibacillary diseases with a high mycobacterial load, a positive Ziehl-Neelsen smear with a positive NAA test is diagnostic of active tuberculosis, whereas a positive Ziehl-Neelsen smear with a negative NAA test in the absence of inhibitors would indicate nontuberculous mycobacterial disease. The role of the NAA test is more important in paucibacillary diseases with low mycobacterial loads. The presence of polymerase chain reaction (PCR) inhibitors, however, especially in extrapulmonary specimens, may produce false-negative results. Although this problem can be overcome to some extent by extra extraction steps, the additional processing invariably leads to the loss of mycobacterial DNA. To circumvent this problem, a brief culture augmentation step is carried out before the NAA test is performed, which can enhance the mycobacterial load while concomitantly diluting inhibitors, thereby maintaining the sensitivity of the test without excessively increasing turnaround time.

Direct detection of Mycobacterium tuberculosis in clinical specimens using single-tube biotinylated nested polymerase chain reaction-enzyme linked immunoassay (PCR-ELISA)

A biotinylated single-tube nested polymerase chain reaction (PCR) assay with microwell hybridization assay (bPCR-ELISA) was developed for detection of Mycobacterium tuberculosis in clinical specimens. A total of 659 specimens (601 respiratory specimens and 58 nonrespiratory specimens) were collected for evaluation using three DNA amplification techniques: newly designed bPCR-ELISA, in-house single-tube nested PCR for IS6110 gene sequence (nPCR), and commercial automated assays, the Cobas Amplicor System from Roche Diagnostic Systems (aPCR). Sixty-four (9.7%) specimens were culture-positive for M. tuberculosis. Eleven (1.7%) specimens culture-positive for nontuberculosis mycobacteria were negative by all three PCR assays. The resolved performance of bPCR-ELISA, nPCR, and aPCR was found at sensitivities of 97%, 94%, and 97%, respectively. All three PCR assays exhibited a 100% specificity. In evaluation of bPCR-ELISA, a clear distinction between PCR-positive and PCR-negative specimens when an OD405 value of 0.6 was chosen as cut-off. With serial dilutions of M. tuberculosis H37Rv DNA, the detection limit of bPCR-ELISA was found to be 0.75 cfu per reaction at OD405 value of 0.6. Our developed bPCR-ELISA provides a highly sensitive and low-costing molecular diagnosis suitable for developing countries with high prevalence of tuberculosis.

Clinical evaluation of the polymerase chain reaction for the rapid diagnosis of tuberculosis

AIMS

Use of the polymerase chain reaction for the detection of Mycobacterium tuberculosis (TB PCR) as a basis for making clinical decisions on the initiation of antituberculosis treatment was studied.

METHODS

A retrospective study involving a cohort of 155 patients being investigated for tuberculosis in an infectious disease consultation service was undertaken. TB PCR was performed on pulmonary and extrapulmonary specimens from these patients. The sensitivity of TB PCR was analysed.

RESULTS

Of the 155 patients, 144 fitted the clinical diagnosis of tuberculosis, and 112 of them were culture positive for M tuberculosis. Sixty (58.3%) patients with clinical features suggestive of tuberculosis received antituberculosis treatment based on positive TB PCR alone. Of 224 clinical specimens (138 pulmonary and 86 extrapulmonary) sent for TB PCR, 148 (99 pulmonary and 49 extrapulmonary) were positive in 117 patients. Of the 690 clinical specimens sent for culture, 279 were positive for M tuberculosis in 112 patients. The diagnostic sensitivity of TB PCR was 75.9% (85 of 112) and 81.3% (117 of 144) in patients with culture confirmed and clinically diagnosed tuberculosis, respectively. Using culture as the gold standard, the overall sensitivity of TB PCR was 78.3%, and for pulmonary and extrapulmonary specimens it was 82.3% and 72.0%, respectively.

CONCLUSIONS

TB PCR is a rapid and reliable test in the diagnosis and management of tuberculosis.

Can serial qualitative polymerase chain reaction monitoring predict outcome of pulmonary tuberculosis treatment?

BACKGROUND

The aim of this study was to assess the use of qualitative one-tube nested polymerase chain reaction (PCR) for monitoring the treatment response in smear-positive pulmonary tuberculosis, and the factors determining the negative conversion of sputum smear, culture, and PCR during treatment.

METHODOLOGY

A total of 53 patients receiving a standard short course of chemotherapy with 24 months follow-up period after treatment cessation were included in the study. Sputum specimens were collected serially for smear, culture, and PCR until the treatment was complete.

RESULTS

The conversion rate for sputum culture, smear, and PCR at 8 weeks after treatment were 84.9, 58.5, and 47.1%, and at 16 weeks of treatment were 100, 88.7, and 79.2%, respectively. At the end of the treatment period, there were four PCR persisters, one of whom had disease relapse. Only cavitary disease had an influence over the negative conversion of the smear and PCR at 8 weeks (RR 3.5, 95% CI 1.04-11.95, P=0.04 for smear; RR 5.06, 95% CI 1.196-21.42, P=0.03 for PCR).

CONCLUSION

Qualitative PCR was not useful for monitoring therapy in smear-positive pulmonary tuberculosis. Mycobacterium DNA was cleared slowly in cavitary disease. The PCR may be performed at the time of treatment cessation to identify those with potential for disease relapse.

Comparison of the ABI 7700 system (TaqMan) and competitive PCR for quantification of IS6110 DNA in sputum during treatment of tuberculosis

Mycobacterium tuberculosis can persist in sputum for long periods of time after the initiation of antituberculosis chemotherapy. The purpose of this study was to determine whether quantitative estimates of M. tuberculosis DNA in sputum correlate with the numbers of viable bacilli and thus measure the therapeutic response of patients during treatment. Two methods of M. tuberculosis DNA quantification were examined by using DNA isolated from sputum specimens serially collected during the course of chemotherapy. A competitive PCR assay was compared to an automated system of real-time quantification with the ABI Prism 7700 Sequence Detection System (TaqMan). The ABI 7700 system uses standard PCR in conjunction with a fluorogenic probe in which the intensity of fluorescence is proportional to the amount of target DNA present. The results showed that both PCR systems are reproducible and accurate. The amounts of M. tuberculosis DNA quantified in sputum corresponded well with the numbers of acid-fast bacilli (AFB) counted by microscopy. Before initiation of antituberculosis therapy, measures of AFB, M. tuberculosis DNA, and cultivable bacilli were similar, suggesting that quantification of DNA is a good method for measuring the initial bacillary load. However, the rate of disappearance of both AFB and M. tuberculosis DNA did not correlate with the decline in cultivable bacilli in the specimen; therefore, these tests are not appropriate for monitoring treatment efficacy.

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.

IS6110 homologs are present in multiple copies in mycobacteria other than tuberculosis-causing mycobacteria

We have previously demonstrated homology between a 181-bp fragment of IS6110 and DNA from mycobacteria other than tuberculosis-causing mycobacteria (MOTT). Genomic DNA from 14 strains of MOTT was digested with PvuII and was hybridized with a probe derived from the 181-bp fragment and the INS1/INS2 international standard probe at high stringency. Multiple banding patterns were obtained from isolates of M. avium-M. intracellulare, M. fortuitum, M. kansasii, and M. malmoense. Differences in the banding patterns between and within species were obtained. This suggests that mycobacteria possess a family of IS3-like elements. The species of isolates suspected of being M. tuberculosis must be carefully determined before IS6110 restriction fragment length polymorphism analysis, and caution must be used in designing and evaluating diagnostic PCR tests based on this element.