Nested polymerase chain reaction for diagnosis and monitoring treatment response in AIDS patients with tuberculous meningitis

Tuberculosis of the Central Nervous System

PURPOSE OF REVIEW

This article details the epidemiology and clinical manifestations of central nervous system (CNS) tuberculosis (TB), provides guidance for diagnostic imaging and CSF testing, and recommends treatment strategies for tuberculous meningitis and other forms of CNS TB, illustrating key aspects of diagnosis and management with case presentations.

RECENT FINDINGS

Although improvements in our understanding of the pathogenesis and management of CNS TB have occurred over the past 50 years, the emergence of multidrug-resistant and extensively drug-resistant TB, the advent of acquired immunodeficiency syndrome (AIDS), and the subsequent availability of highly active antiretroviral therapy that can produce the immune reconstitution inflammatory syndrome have complicated the diagnosis and treatment of CNS TB. Advances in diagnostic assays promise to increase the speed of diagnosis as well as the percentage of people with a confirmed rather than a presumptive diagnosis. Advances in precision medicine have identified polymorphisms in the LTA4H gene that influence the risk for inflammation in patients with tuberculous meningitis.

SUMMARY

CNS TB continues to be a major cause of morbidity and mortality, with the majority of people affected living in low-income and middle-income countries. Newer diagnostic assays promise to increase the speed of diagnosis and improve appropriate selection of antituberculous therapy and anti-inflammatory medications. Despite these advances, CNS TB remains difficult to diagnose, and clinicians should have a low threshold for initiating empiric therapy in patients with presumptive infection.

Immunological diagnosis as an adjunctive tool for an early diagnosis of tuberculous meningitis of an immune competent child in a low tuberculosis endemic country: a case report

BACKGROUND

Pediatric tuberculous meningitis is a highly morbid, often fatal disease. Its prompt diagnosis and treatment saves lives, in fact delays in the initiation of therapy have been associated with high mortality rates.

CASE PRESENTATION

This is a case of an Italian child who was diagnosed with tuberculous meningitis after a history of a month of headache, fatigue and weight loss. Cerebrospinal fluid analysis revealed a lymphocytic pleocytosis with predominance and decreased glucose concentration. Microscopy and conventional diagnostic tests to identify Mycobacterium tuberculosis were negative, while a non classical method based on intracellular cytokine flow cytometry response of CD4 cells in cerebral spinal fluid helped us to address the diagnosis, that was subsequently confirmed by a nested polymerase chain reaction amplifying a 123 base pair fragment of the M. tuberculosis DNA.

CONCLUSIONS

We diagnosed tuberculous meningitis at an early stage through an innovative immunological approach, supported by a nested polymerase chain reaction for detection of M. tuberculosis DNA. An early diagnosis is required in order to promptly initiate a therapy and to increase the patient's survival.

[Current advancement of the PCR-based molecular diagnosis for tuberculous meningitis]

Central nervous system (CNS) tuberculosis, particularly tuberculous meningitis (TBM), is one of the severest forms of tuberculosis. At present, the diagnosis of CNS tuberculosis remains a complex issue because the most widely used conventional "gold standard" based on bacteriological detection methods, such as direct smear and culture identification, cannot rapidly detect Mycobacterium tuberculosis (M.Tb) bacilli in CSF specimens with sufficient sensitivity in the acute phase of TBM. Recently, instead of the conventional "gold standard", the various molecular-based methods, such as polymerase chain reaction (PCR) assay, has emerged as a promising new method for the diagnosis of TBM. Moreover, nested PCR assay has been reported as a key method that drastically increases the sensitivity and specificity of DNA amplification compared with conventional single-step PCR. Currently, a novel assay technique, which is internally controlled and combines the high sensitivity of nested PCR with the accurate quantification of real-time PCR, namely, Wide Range Quantitative Nested Real-time PCR (WR-QNRT-PCR) assay, has been developed. This novel assay technique is useful for the rapid diagnosis and the assessment of anti-tuberculosis treatment during clinical course of TBM. Therefore, in actual clinical practice, its wider use for diagnosis of TBM is expected in the future.

Diagnostic efficacy of adenosine deaminase levels in cerebrospinal fluid in patients of tubercular meningitis: A comparison with PCR for Mycobacterium Tuberculosis

Background

The rapid diagnosis of Tubercular meningitis (TBM) is fundamental to clinical outcome. The key to diagnosis lies in Cerebrospinal fluid (CSF) analysis and radiological investigations. There are numerous lacunae in the confirmation of diagnosis of TBM from CSF.

Purpose

The aim of present study was to compare the efficacy of CSF adenosine deaminase (ADA) level assays and Polymerase chain reaction (PCR) for Mycobacterium tuberculosis (M. tuberculosis) in the diagnosis of TBM.

Methods

Fifty four adult patients with suspected TBM and 37 controls were included in the study and CSF analyzed for ADA and PCR for M. tuberculosis. The cases were subdivided into definite (5), highly probable (22), probable (22) and possible TBM (5) as per previously validated criteria. The first two were grouped as "most likely" TBM (27) and last two as "unconfirmed" TBM (27).

Results

The mean ADA of the "most likely" TBM was 29±24, "unconfirmed" TBM was 21 ± 15 and controls were 4.8±2.2 U/L. The ADA levels correlated with CSF proteins, absolute lymphocyte count and the staging of the disease. Using a cut off level of >L10 U/L, CSF ADA had a sensitivity of 92.5% and specificity of 97%. PCR for M. tuberculosis was positive in 12 out of 27 "most likely" TBM cases, 5 out of 27 "unconfirmed" TBM cases and 3 out of 37 controls. PCR for M. tuberculosis had a sensitivity of 44.5% and specificity of 92% in the "most likely" TBM cases. Conclusions: ADA is a rapid, inexpensive and sensitive test in the diagnosis of TBM. It is more sensitive than AFB smear and culture. PCR is another rapid test in the diagnosis of TBM with a good specificity, even in those patients already on presumptive anti-tuberculous treatment. However, despite the sensitivity and specificity of CSF ADA, it should be corroborated with AFB smear and CSF PCR.

Diagnostic value of a "wide-range" quantitative nested real-time PCR assay for varicella zoster virus myelitis

Myelitis is one of the rarest neurological complications of varicella zoster virus (VZV) infection. In this study, the authors remodeled the "wide-range" quantitative nested real-time (QNRT) polymerase chain reaction (PCR) assay to quantitatively detect a small amount of VZV-DNA in cerebrospinal fluid (CSF). For use as a specific internal control "calibrator," an original mutation-VZV (MZ) plasmid was developed. The initial copy number of VZV-DNA in CSF specimens was measured by the amplification rate of the MZ-plasmid. For 17 consecutive CSF specimens collected from three elderly patients with VZV myelitis, the diagnostic value of the wide-range QNRT-PCR assay was evaluated and compared with other conventional PCR assays and enzyme immunoassay (EIA). The MZ-plasmid demonstrated statistically uniform amplifications (F=1.016) against a wide range (1-100,000) of copy numbers of mimic VZV-DNA. The wide-range QNRT-PCR assay quantitatively and rapidly (within 48 hr) detected 5,863, 3,052, 958, and 6,721 copies/ml of VZV-DNA in the CSF specimens collected from all patients in the acute phase. Additionally, there was a significant difference (*P=0.023) in the copy number of VZV-DNA between before and after acyclovir treatment. Other conventional single PCR assays all revealed negative results, but were nevertheless time-consuming (7 days). The IgG EIA-value for VZV was continually elevated throughout the clinical course of all patients. The MZ-plasmid was thus regarded as an appropriate "calibrator" in the wide-range QNRT-PCR assay. This assay is a novel, rapid, accurate, quantitative, and highly sensitive technique, and will contribute as a reliable and useful clinical examination for the rapid diagnosis of VZV infection to central nervous system.

Laboratory diagnosis of CNS infections by molecular amplification techniques

The initial presentation of symptoms and clinical manifestations of CNS infectious diseases often makes a specific diagnosis difficult and uncertain, and the emergence of polymerase chain reaction-led molecular techniques have been used in improving organism-specific diagnosis. These techniques have not only provided rapid, non-invasive detection of microorganisms causing CNS infections, but also demonstrated several neurologic disorders linked to infectious pathogens. Molecular methods performed on cerebrospinal fluid are recognized as the new 'gold standard' for some of these infections caused by microorganisms that are difficult to detect and identify. Although molecular techniques are predicted to be widely used in diagnosing and monitoring CNS infections, the limitations as well as strengths of these techniques must be clearly understood by both clinicians and laboratory personnel.

Comparison of real time IS6110-PCR, microscopy, and culture for diagnosis of tuberculous meningitis in a cohort of adult patients in Indonesia

BACKGROUND

Bacteriological confirmation of tuberculous (TB) meningitis is difficult. Culture is slow and microscopy has insufficient sensitivity. We evaluated real time PCR targeting insertion sequence IS6110 among 230 consecutive adult patients with subacute meningitis in a referral hospital in Indonesia.

METHODS

Cerebrospinal fluid (CSF) samples were examined using microscopy, solid and liquid culture, and real time IS6110-PCR with a fluorescence-labeled probe using DNA extracted from CSF. CSF samples from 40 non-infectious neurology patients were used as negative controls. IS6110-PCR results were linked with clinical and CSF characteristics.

RESULTS

Most patients presented with subacute meningitis, after a median of 14 days of symptoms (range 7-30). After exclusion of cryptococcal and bacterial meningitis, 207 patients were classified as definite or probable TB meningitis; 17.9% with HIV infection. Among this group IS6110-PCR gave the highest positivity rate (68%, 95% CI 62-74%) compared with microscopy of ZN-stained slides (11%, 95% CI 7-15%), and mycobacterial culture using solid (36%, 95% CI 29-42%) and liquid (44%, 95% CI 37-51%) media. IS6110-PCR was positive in 92% of patients with culture-positive and 42% of patients with culture-negative probable TB meningitis. Among culture-negative patients, a positive PCR was associated with a history of TB treatment, a longer duration of illness, a higher CSF cell count and protein, and a lower CSF glucose. IS6110-PCR was negative in all CSF samples from non-meningitis control patients.

CONCLUSIONS

Real time IS6110-PCR is a quick, sensitive, and specific test for diagnosing of TB meningitis in this setting. Its performance in other (less-developed) settings needs further study.

The PCR-Based Diagnosis of Central Nervous System Tuberculosis: Up to Date

Central nervous system (CNS) tuberculosis, particularly tuberculous meningitis (TBM), is the severest form of Mycobacterium tuberculosis (M.Tb) infection, causing death or severe neurological defects in more than half of those affected, in spite of recent advancements in available anti-tuberculosis treatment. The definitive diagnosis of CNS tuberculosis depends upon the detection of M.Tb bacilli in the cerebrospinal fluid (CSF). At present, the diagnosis of CNS tuberculosis remains a complex issue because the most widely used conventional “gold standard” based on bacteriological detection methods, such as direct smear and culture identification, cannot rapidly detect M.Tb in CSF specimens with sufficient sensitivity in the acute phase of TBM. Recently, instead of the conventional “gold standard”, the various molecular-based methods including nucleic acid amplification (NAA) assay technique, particularly polymerase chain reaction (PCR) assay, has emerged as a promising new method for the diagnosis of CNS tuberculosis because of its rapidity, sensitivity and specificity. In addition, the innovation of nested PCR assay technique is worthy of note given its contribution to improve the diagnosis of CNS tuberculosis. In this review, an overview of recent progress of the NAA methods, mainly highlighting the PCR assay technique, was presented.

Evaluation of sensitivity of multiplex PCR for Detection of Mycobacterium tuberculosis and Pneumocystis jirovecii in clinical samples

A multiplex PCR assay for the simultaneous detection of Mycobacterium tuberculosis and Pneumocystis jirovecii was developed using IS6110-based detection for M. tuberculosis and mitochondrial large-subunit (mtLSU) rRNA gene detection for P. jirovecii. Ninety-five pulmonary blinded samples were examined using the developed multiplex PCR assay, and the results were compared with those obtained by the single nested PCRs targeting IS6110 for M. tuberculosis and mtLSU rRNA for P. jirovecii. Of the 95 pulmonary samples tested, the multiplex nested PCR developed here could detect 36 cases of M. tuberculosis infection, 35 cases of P. jirovecii infection, and 17 cases of M. tuberculosis and P. jirovecii coinfections. The sensitivities of the multiplex nested PCR in detecting M. tuberculosis and P. jirovecii were 92.1% and 81.4%, respectively, whereas the specificities in detecting M. tuberculosis and P. jirovecii were 98.2% and 100%, respectively.

To compare CSF adenosine deaminase levels and CSF-PCR for tuberculous meningitis

This study was planned to compare the adenosine deaminase (ADA) levels and polymerase chain reaction (PCR) in cerebrospinal fluid (CSF) as a rapid method to diagnose tuberculosis meningitis (TBM). Fifty-four adult patients with suspected TBM and 37 controls were included in this study. The median ADA level was 21U/L of most likely TBM, 14U/L of unconfirmed TBM and 5U/L of controls. PCR for Mycobacterium tuberculosis was positive in 12 out of 27 most likely TBM cases, 5 out of 27 unconfirmed TBM cases and 3 out of 37 controls. Using a cut off level of >10U/L, CSF-ADA had a sensitivity of 92.5% and specificity of 97% for the diagnosis of TBM. PCR for M. tuberculosis had a sensitivity of 44.5% and specificity 92% in the most likely TBM cases. This study shows that CSF-ADA is a more sensitive indicator than PCR for the diagnosis of M. tuberculosis.

Evaluation of different primer sets for the rapid diagnosis of tuberculosis

Pleural fluid samples from patients with exudative effusion who were diagnosed with tuberculous pleuritis are examined using a new designed primer set based on IS1081 gene (IS1081-PCR) and rpoB-PCR. The PCR results are compared with the results of the sample cultures, using Loewenstein-Jensen (LJ) medium and Ziehl-Neelsen (ZN) staining. Of 78 cases that were confirmed as tuberculous pleuritis by histopathology, supported by sputum culture, biochemical markers (adenosine deaminase, gamma interferon and tumor necrosis factor), radiographic and clinical data, 61 (78.2%) were positive by IS1081-PCR, 43 (55.1%) by rpoB-PCR, 17 (21.7%) by culture and 3 (3.8%) by ZN stain. When IS1081-PCR test results were compared with the confirmed culture, the sensitivity, specificity, positive predictive value and negative predictive value for the IS1081-PCR were 94.1, 55.7, 37.2 and 97.1%, respectively. The corresponding values for the rpoB-PCR were 94.1, 26.2, 26.2 and 94.1%, respectively. When tests results were compare with the confirmed radiographic, histopathology, biochemical markers and clinical diagnosis of tuberculous pleuritis, the IS1081-PCR assay is more sensitive, specific and reliable than both rpoB-PCR assay and culture.

Central nervous system tuberculosis: pathogenesis and clinical aspects

Tuberculosis of the central nervous system (CNS) is a highly devastating form of tuberculosis, which, even in the setting of appropriate antitubercular therapy, leads to unacceptable levels of morbidity and mortality. Despite the development of promising molecular diagnostic techniques, diagnosis of CNS tuberculosis relies largely on microbiological methods that are insensitive, and as such, CNS tuberculosis remains a formidable diagnostic challenge. Insights into the basic neuropathogenesis of Mycobacterium tuberculosis and the development of an appropriate animal model are desperately needed. The optimal regimen and length of treatment are largely unknown, and with the rising incidence of multidrug-resistant strains of M. tuberculosis, the development of well-tolerated and effective antibiotics remains a continued need. While the most widely used vaccine in the world largely targets this manifestation of tuberculosis, the BCG vaccine has not fulfilled the promise of eliminating CNS tuberculosis. We put forth this review to highlight the current understanding of the neuropathogenesis of M. tuberculosis, to discuss certain epidemiological, clinical, diagnostic, and therapeutic aspects of CNS tuberculosis, and also to underscore the many unmet needs in this important field.

Improved diagnosis of central nervous system tuberculosis by MPB64-Target PCR

Central nervous system (CNS) tuberculosis is a serious clinical problem, the treatment of which is sometimes hampered by delayed diagnosis. Clearly, prompt laboratory diagnosis is of vital importance as the spectrum of disease is wide and abnormalities of the cerebrospinal fluid (CSF) are incredibly variable. Since delayed hypersensitivity is the underlying immune response, bacterial load is very low. The conventional bacteriological methods rarely detect Mycobacterium tuberculosis in CSF and are of limited use in diagnosis of tuberculous meningitis (TBM). This double blind study was, therefore, directed to the molecular analysis of CNS tuberculosis by an in-house-developed PCR targeted for amplification of a 240bp nucleotide sequence coding for MPB64 protein specific for Mycobacterium tuberculosis. Based on the clinical criteria, 47 patients with CNS tuberculosis and a control group of 10 patients having non-tubercular lesions of the CNS were included in the study. Analyses were done in three groups; one group consisting of 27 patients of TBM, a second group of 20 patients with intracranial tuberculomas and a third group of 10 patients having nontubercular lesions of the CNS acted as control. There were no false positive results by PCR and the specificity worked out to be 100%. In the three study groups, routine CSF analysis (cells and chemistry), CSF for AFB smear and culture were negative in all cases. PCR was positive for 21/27 patients (77.7% sensitivity) of the first group of TBM patients, 6/20 patients (30% sensitivity) of the second group with intracranial tuberculomas were positive by PCR and none was PCR-positive (100% specificity) in the third group. Thus, PCR was found to be more sensitive than any other conventional method in the diagnosis of clinically suspected tubercular meningitis.

Novel wide-range quantitative nested real-time PCR assay for Mycobacterium tuberculosis DNA: development and methodology

Previously, we designed an internally controlled quantitative nested real-time (QNRT) PCR assay for Mycobacterium tuberculosis DNA in order to rapidly diagnose tuberculous meningitis. This technique combined the high sensitivity of nested PCR with the accurate quantification of real-time PCR. In this study, we attempted to improve the original QNRT-PCR assay and newly developed the wide-range QNRT-PCR (WR-QNRT-PCR) assay, which is more accurate and has a wider detection range. For use as an internal-control "calibrator" to measure the copy number of M. tuberculosis DNA, an original new-mutation plasmid (NM-plasmid) was developed. It had artificial random nucleotides in five regions annealing specific primers and probes. The NM-plasmid demonstrated statistically uniform amplifications (F = 1.086, P = 0.774) against a range (1 to 10(5)) of copy numbers of mimic M. tuberculosis DNA and was regarded as appropriate for use as a new internal control in the WR-QNRT-PSR assay. In addition, by the optimization of assay conditions in WR-QNRT-PCR, two-step amplification of target DNA was completely consistent with the standard curve of this assay. Due to the development of the NM-plasmid as the new internal control, significantly improved quantitative accuracy and a wider detection range were realized with the WR-QNRT-PCR assay. In the next study, we will try to use this novel assay method with actual clinical samples and examine its clinical usefulness.

Novel wide-range quantitative nested real-time PCR assay for Mycobacterium tuberculosis DNA: clinical application for diagnosis of tuberculous meningitis

Although the "gold standard" for diagnosis of tuberculous meningitis (TBM) is bacterial isolation of Mycobacterium tuberculosis, there are still several complex issues. Recently, we developed an internally controlled novel wide-range quantitative nested real-time PCR (WR-QNRT-PCR) assay for M. tuberculosis DNA in order to rapidly diagnose TBM. For use as an internal control calibrator to measure the copy number of M. tuberculosis DNA, an original new-mutation plasmid (NM-plasmid) was developed. Due to the development of the NM-plasmid, the WR-QNRT-PCR assay demonstrated statistically significant accuracy over a wide detection range (1 to 10(5) copies). In clinical applications, the WR-QNRT-PCR assay revealed sufficiently high sensitivity (95.8%) and specificity (100%) for 24 clinically suspected TBM patients. In conditional logistic regression analysis, a copy number of M. tuberculosis DNA (per 1 ml of cerebrospinal fluid) of >8,000 was an independent risk factor for poor prognosis for TBM (i.e., death) (odds ratio, 16.142; 95% confidence interval, 1.191 to 218.79; P value, 0.0365). In addition, the copy numbers demonstrated by analysis of variance statistically significant alterations (P < 0.01) during the clinical treatment course for 10 suspected TBM patients. In simple regression analysis, the significant correlation (R(2) = 0.597; P < 0.0001) was demonstrated between copy number and clinical stage of TBM. We consider the WR-QNRT-PCR assay to be a useful and advanced assay technique for assessing the clinical treatment course of TBM.

Clinicopathologic characteristics of Rosai-Dorfman disease in a medical center in northern taiwan

BACKGROUND/PURPOSE

Rosai-Dorfman disease (RDD) is a rare histiocytic proliferative disorder that usually presents as cervical lymphadenopathy. Extranodal involvement occurs in up to 40% of patients. The disease is most prevalent in blacks and rare in Asians. This study analyzed the characteristics of RDD in patients from Taiwan.

METHODS

Fourteen patients with a diagnosis of RDD were identified by review of records from 1995 to 2004 at National Taiwan University Hospital. Tissue sections from each patient were reviewed and immunohistochemical staining was performed. Data on clinical presentations, associated diseases, treatment and outcome were analyzed. In situ hybridization for Epstein-Barr virus (EBV)-encoded small RNAs (EBER-1) was also performed. Sets of primers specific for the conservative region of bacterial 16S-rDNA, IS6110 of Mycobacterium tuberculosis complex and consensus region of human herpes virus (HHV) DNA polymerase genome were used to detect the presence of these infectious agents in the specimens.

RESULTS

There were six men and eight women with a mean age of onset of 44 years. Nine patients presented with skin lesions, four with lymph node involvement and one with nasal tumor. All lesions followed a chronic and indolent course. Most of the lesions regressed spontaneously, and no patients died as a result of this disease during follow-up. Three patients had associated immune-mediated disease, i.e. hemolytic anemia, ankylosing spondylitis and asthma. Two patients had a history of tuberculosis. Histologically, all lesions were characterized by a mixed infiltrate of large pale histiocytes, abundant plasma cells and lymphocytes regardless of the site of involvement. The strong immunoreactivities of these histiocytes to S-100 protein, CD68 and CD14 with occasional lymphophagocytosis were helpful in confirming the diagnosis, polymerase chain reaction analysis of 16S-rDNA, IS6110 and HHV gene and in situ hybridization for EBV were all negative.

CONCLUSION

RDD in Taiwan is characterized by older age of onset compared to Western countries (44 years vs. 20 years) and more frequent extranodal involvement. The skin was the most common site of extranodal involvement, with about two-thirds of patients presenting with cutaneous lesions. There was no evidence of bacterial, mycobacterial or HHV infection in this series.

Evaluation of the IS6110 PCR assay for the rapid diagnosis of tuberculous meningitis

Background

Tuberculous meningitis (TBM) is one of the common clinical manifestations of extra-pulmonary tuberculosis. It is difficult to diagnose due to a lack of rapid, sensitive, and specific tests. Newer methods, which are easy and reliable, are required to diagnose TBM at an early stage. Thus our aim was to evaluate the polymerase chain reaction (PCR) technique, using primers directed against the IS6110 gene, for the detection of Mycobacterium tuberculosis in the CSF, for the diagnosis of TBM patients.

Methods

An in-house IS6110 PCR method using a specific pair of primers designed to amplify the insertion sequence, IS6110, in the M. tuberculosis genome was used to analyze CSF. A total of 80 CSF samples from different groups of patients were studied (confirmed TBM n = 35, clinically suspected TBM n = 16, non-TBM infectious meningitis n = 12, non infectious neurological diseases n = 17).

Results

PCR gave a sensitivity of 91.4% and specificity of 75.9% for the diagnosis of TBM in patients with TBM confirmed by culture. In 16 clinically diagnosed, but unconfirmed, TBM cases PCR was positive in 10 (62.5%) cases. There were seven (24.1%) PCR-positive cases among the 29 patients with non-TBM and non-infectious neurological disease.

Conclusion

We conclude that the performance of an in-house IS6110 PCR assay is valuable in the rapid diagnosis of tuberculous meningitis.

Diagnosis of tuberculous meningitis: clinical and laboratory parameters

BACKGROUND

Confirming the clinical suspicion of tuberculous meningitis (TBM) has always been problematic. Whilst smear and culture positivity are diagnostic, these tests have low sensitivity. The polymerase chain reaction (PCR) assay has given variable results.

AIM

This study attempted to improve the diagnostic yield by: (a) increasing the cerebrospinal fluid (CSF) volumes; (b) testing the yield from three specimens of CSF assumed to represent lumbar, cervico-thoracic cord, and base of brain CSF samples; (c) undertaking PCR assays using multiple primer sets; and (d) using real-time PCR.

METHOD

Patients suspected of having cranial or spinal meningeal tuberculosis were entered into the study. Three aliquots of CSF were subjected to smear, culture, and conventional and real-time PCR. Three sets of primers - IS6110, MPB64, and PT8/9 - were used. Patients were retrospectively classified into four categories: 'definite TB' (culture positive), 'probable TB' (clinical and other tests suggestive of TB), 'not TB', and 'uncertain diagnosis'.

RESULTS

A total of 68 patients were studied. There were 20 patients classified as definite TB, 24 probable TB, 17 not TB, and seven uncertain diagnosis. Forty-eight of 57 (84.2%) patients tested were HIV seropositive. The IS6110 PCR was positive in 27 patients which included 18/20 culture positive cases, six in the probable TB group, and three in the not TB group. The MPB64 and PT8/9 primers did not increase the yield. Real-time PCR was positive in seven additional patients. Combining the definite and probable TB, the sensitivity of all PCR assays was 70.5% (31/44) and specificity 87.5% (21/24).

CONCLUSION

Targeting multiple sites of the TB genome using conventional PCR did not increase the number of positive cases. Real-time PCR was more sensitive. However, all the current techniques are still too insensitive to confidently exclude the diagnosis on laboratory grounds.

Quantitative nested real-time PCR assay for assessing the clinical course of tuberculous meningitis

Although the "gold standard" for diagnosis of tuberculous meningitis (TBM) is bacterial isolation of Mycobacterium tuberculosis (M. Tb), there are still several complex issues. Recently, in the diagnosis of TBM, the detection of M. Tb DNA in cerebrospinal fluid (CSF) samples using PCR has been widely performed as more rapid, sensitive, and specific diagnostic method. Based on Taq Man(R) PCR, the authors developed a novel technique of internally controlled quantitative nested real-time (QNRT) PCR assay that provided a prominent improvement in detection sensitivity and quantification. Total 43 CSF samples from 8 serial patients with suspected TBM were analyzed. The CSF samples were collected before and during standard anti-tuberculosis treatments (ATT). The QNRT-PCR assay revealed positive results for 24 out of 43 serial CSF samples (55.8%) collected during the treatment course of ATT. Moreover, the bacterial cell (BC) numbers of M. Tb analyzed by the QNRT-PCR assay decreased gradually, correlating with the improvements of the patient's clinical conditions. Since the QNRT-PCR assay provides the ability to calculate a numerical value for the initial BC numbers of M. Tb in CSF samples, this method is an extremely useful and advanced technique for use in assessing the clinical course of TBM.

Biopsy-proven tuberculous meningitis mimicking CNS sarcoidosis

We report a 31-year-old man with tuberculous meningitis (TM) mimicking CNS sarcoidosis. Although Mycobacterium tuberculosis (MTB) was not detected in CSF, the level of adenosine deaminase (ADA) in CSF was significantly raised. Brain biopsy showed caseous granuloma and a diagnosis of TM was made. The diagnosis of TM is often difficult and brain biopsy should be considered if MTB is not detected in the CSF. Evaluation of CSF ADA level could also strongly contribute to distinguishing TM from other meningitis. In addition to antituberculosis drugs, corticosteroid therapy was effective in our patient but careful reduction of its dosage was required.

Interferon γ quantification in cerebrospinal fluid compared with PCR for the diagnosis of tuberculous meningitis

PURPOSE

To assess the utility of interferon gamma (INF-gamma) levels in cerebrospinal fluid (CSF), for the diagnosis of tuberculous meningitis (TBM), and compare these results with aPCR technique.

METHODS

We studied CSF samples from patients with proven or probable TBM and a control group, composed by patients with other causes of meningitis and without meningitis. INFgamma levels were measured by radioimmunoassay. A PCR technique was performed using IS6110 primers.

RESULTS

Of the 127 patients studied, 20 (15.6%) had TBM, 59 (46%) had meningitis of another aetiology and 49 (38.4%) had were HIV and non-HIV patients with normal CSF. The area below the ROC curve for interferon gamma levels in the diagnosis of TBM was 0.94. A cut-off of 6.4 IU/mL yielded a sensitivity of 70% and a specificity of 94%. False positive results were observed in 7 of the 59 patients (11.8%) with non-TB meningitis, (patients with herpetic meningoencephalitis and meningitis due to intracellular microorganisms). INF-gamma sensitivity was higher than PCR (70% vs. 65%). Both tests performed together showed higher sensitivity (80%) and specificity (92.6%).

CONCLUSION

CSF INF-gamma levels (> 6.4 IU/mL) are very valuable in TBM diagnosis. PCR and INF-gamma could be simultaneously used to increase the diagnostic yield.

Novel technique of quantitative nested real-time PCR assay for Mycobacterium tuberculosis DNA

The diagnosis of tuberculous meningitis (TBM) remains a complex issue because the most widely used conventional diagnostic tools, such as culture and PCR assay for cerebrospinal fluid (CSF) samples, are unable to rapidly detect Mycobacterium tuberculosis with sufficient sensitivity in the acute phase of TBM. Based on TaqMan PCR, we designed a novel technique consisting of an internally controlled quantitative nested real-time (QNRT) PCR assay that provided a marked improvement in detection sensitivity and quantification. We applied this novel technique to quantitatively detect M. tuberculosis DNA in CSF samples from patients with suspected TBM. For use as the internal control in the measurement of the M. tuberculosis DNA copy numbers in the QNRT-PCR assay, the original mutation (M) plasmid, which included an artificial random 22-nucleotide sequence within an inserted DNA fragment of the MPB64 gene of M. tuberculosis, was prepared. The QNRT-PCR assay showed high sensitivity and specificity that were approximately equivalent to those of the conventional nested PCR assay. Moreover, the QNRT-PCR assay made it possible to precisely and quantitatively detect the initial copy number of M. tuberculosis DNA in CSF samples. Therefore, compared to the conventional PCR assay, the QNRT-PCR assay can be considered a more useful and advanced technique for the rapid and accurate diagnosis of TBM. To establish the superiority of this novel technique in TBM diagnosis, it will be necessary to accumulate data from a larger number of patients with suspected TBM.

Sudden Death from Tubercular Myocarditis

Tuberculous myocarditis is a rare finding. We present the case of a 33-year-old woman who was in good health and who died suddenly at home. Autopsy and histopathologic examinations revealed granulamatous lesions in the myocardium, lungs, lymph nodes, liver, and spleen. No fast acid bacilli were demonstrated on histological examination. The presence of a Mycobacterium tuberculosis DNA complex was identified using a polymerase chain reaction (PCR) on formalin-fixed paraffin-embedded histological samples. An HIV test carried out on the blood obtained during the autopsy was negative according to the DNA amplification technique (PCR) and enzyme-linked immunosorbent assay serological test. We hypothesize that the mechanism of death was severe ventricular arrhythmia due to granulomatous proliferation in the structures of the interventricular septum.

[Location of the lesion and the cerebrospinal fluid findings in tuberculous meningitis: differences in the lumbar, cisternal and ventricular compartments]

Tuberculosis remains one of the most prevalent infectious diseases worldwide. In the present study, we describe a case of tuberculous meningitis that caused cerebrospinal fluid (CSF) flow block, leading to difficulties in the diagnosis. The importance of the lesion site and its influence on CSF analysis as a support for the diagnosis of tuberculous meningitis is discussed. In this case, the search for acid-fast bacilii was positive in the cisternal CSF, but not in the ventricular and lumbar CSF, demonstrating the relationship between the accuracy of the test and the location of the inflamatory lesion disease.

Rapid diagnosis of mycobacterial infections and quantitation of Mycobacterium tuberculosis load by two real-time calibrated PCR assays

Sensitive and specific techniques to detect and identify Mycobacterium tuberculosis directly in clinical specimens are important for the diagnosis and management of patients with tuberculosis (TB). We developed two real-time PCR assays, based on the IS6110 multicopy element and on the senX3-regX3 intergenic region, which provide a rapid method for the diagnosis of mycobacterial infections. The sensitivity and specificity of both assays were established by using purified DNA from 71 clinical isolates and 121 clinical samples collected from 83 patients, 20 of whom were affected by TB. Both assays are accurate, sensitive, and specific, showing a complementary pattern of Mycobacterium recognition: broader for the IS6110-based assay and restricted to the M. tuberculosis complex for the senX3-regX3-based assay. Moreover, the addition of a synthetic DNA calibrator prior to DNA extraction allowed us to measure the efficiency of DNA recovery and to control for the presence of PCR inhibitors. The mycobacterial burden of the clinical samples, as assessed by direct microscopy, correlates with the M. tuberculosis DNA load measured by the senX3-regX3-based assay. In addition, reduced levels of M. tuberculosis DNA load are present in those patients subjected to successful therapy, suggesting a potential use of this assay for monitoring treatment efficacy. Therefore, these assays represent a fully controlled high-throughput system for the evaluation of mycobacterial burden in clinical specimens.

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.

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.

Presumed tubercular serpiginouslike choroiditis: clinical presentations and management

PURPOSE

Choroiditis, choroidal tubercles, and tuberculomas are well known ocular manifestations of systemic tuberculosis. The present series aimed to report the occurrence of serpiginouslike choroiditis of presumed tubercular origin.

DESIGN

Retrospective, noncomparative, interventional case series.

PARTICIPANTS

Eleven eyes in seven consecutive patients with a diagnosis of choroidal tuberculosis simulating serpiginous choroiditis were studied between 1997 and 2000. TESTING AND INTERVENTION: All patients had their fundus photographs taken at the time of initial presentation as well as during follow-up. All patients underwent a Mantoux skin test and chest radiography. In addition, five patients had their aqueous or vitreous humor subjected to polymerase chain reaction (PCR) for Mycobacterium tuberculosis. Sputum examination, biopsy, or both were carried out whenever recommended by the pulmonologist. Systemic antituberculosis chemotherapy was instituted in combination with treatment for ocular inflammation.

MAIN OUTCOME MEASURE

Therapeutic response and visual improvement.

RESULTS

There were five men and two women ranging in age from 17 to 32 years. Clinical presentations included three morphologic variants; multifocal progressive choroiditis showing wavelike progression to confluent, diffuse lesions resembling serpiginous choroiditis (three eyes); diffuse choroiditis characterized by diffuse plaquelike choroiditis with an amoeboid pattern suggestive of serpiginous choroiditis at initial presentation (four eyes); and mixed variety where opposite eyes had mixed features (four eyes). All patients had strongly positive Mantoux skin test results and positive chest radiograph results. The PCR results from aqueous and vitreous humor in four samples was positive for Mycobacterium tuberculosis; one had sputum positive for acid-fast bacilli, whereas two had histopathologic evidence of tuberculosis from cervical or parahilar lymph nodes. Treatment was associated with resolution of choroidal lesions and visual improvement. Final visual acuity of 20/30 or better was achieved in five eyes.

CONCLUSIONS

Choroidal tuberculosis may present as multifocal progressive or diffuse choroiditis resembling serpiginous choroiditis. It is important to recognize these presentations because these eyes show good response to systemic antituberculosis chemotherapy.

Comparison of polymerase chain reaction with histopathologic features for diagnosis of tuberculosis in formalin-fixed, paraffin-embedded histologic specimens

Objective.-To investigate the relationship between various histopathologic features and the results of the tuberculosis (TB)-polymerase chain reaction (PCR) method in routinely submitted histologic specimens for the histopathologic diagnosis of TB. Design.-We used 95 formalin-fixed, paraffin-embedded tissue blocks from 81 patients who were clinically suspected of having TB. We assessed the presence of histopathologic features including well-formed granuloma, poorly formed granuloma, caseous necrosis, and Langhans-type giant cells. We performed nested PCR for IS6110 and Ziehl-Neelsen staining for acid-fast bacilli (AFB). Results.-Of the 81 patients studied, 53 patients had chronic granulomatous inflammation, whereas 28 patients had only chronic inflammation without definite granulomatous inflammation. Of the 53 cases with chronic granulomatous inflammation, 17 (32%) were AFB positive and 36 (68%) were TB-PCR positive. Among cases with chronic granulomatous inflammation, the percentage that were positive and negative by TB-PCR differed significantly with the presence of various histopathologic features. All of the 13 cases with well-formed granuloma, caseous necrosis, and Langhans-type giant cells were TB-PCR positive; however, 10 (36%) of the 28 cases with chronic inflammation without granulomatous lesions were also TB-PCR positive. Conclusions.-TB-PCR is a rapid, sensitive method for the diagnosis of TB in routinely processed formalin-fixed, paraffin-embedded histologic specimens and is readily available in histopathology laboratories. We recommend use of TB-PCR when TB is suspected clinically, especially in cases of chronic inflammation without definite evidence of granulomatous inflammation.

Nested polymerase chain reaction for Mycobacterium tuberculosis DNA detection in aqueous and vitreous of patients with uveitis

BACKGROUND

Tuberculosis may be a lethal disease. Its ocular manifestations are commonly associated with severe difficulties in diagnosis and therapy; furthermore, it may cause blindness. DNA amplification methods may allow early detection of small amounts of Mycobacterium tuberculosis DNA to afford the possibility of prompt diagnosis. We evaluated a nested polymerase chain reaction (nPCR) assay for detection of Mycobacterium tuberculosis DNA in aqueous and vitreous.

METHODS

In a case-control study, 22 cases of diagnosed TB uveitis (three HIV-infected patients) and 38 controls (18 HIV-infected patients) with other types of uveitis (syphilis, nine; cytomegalovirus, seven; toxoplasmosis, five; herpes simplex, one; autoimmune vasculitis, eight; Vogt-Koyanagi-Harada, four; pars planitis, one; serpinginous choroiditis, one; Wegener granulomatosis, one; and Fuchs iridocyclitis, one studied). Samples from aqueous or vitreous were cultured and analyzed by nPCR for presence of M. tuberculosis nucleic acids. We used two sets of primers corresponding to IS6110 region coding for 219 bp and 123 bp DNA sequences.

RESULTS

Results were confirmed by Southern blot. All samples were tested by PCR simultaneously for Herpes simplex I, Herpes zoster, cytomegalovirus (CMV) and Toxoplasma gondii. nPCR was positive in 17 cases (77.2%) and only in three controls (8.8%) p = 0.022. All cultures were negative. Southern blot confirmed all positive nPCR tests. According to our definition of cases, there were five false negative results: two in patients with pulmonary tuberculosis; two in patients with tuberculous lymphadenitis, and one with positive skin test and hematuria. There were three cases considered false positives for nPCR: one with autoimmune vasculitis, and two with toxoplasmic uveitis.

CONCLUSIONS

nPCR for TB in ocular fluids was positive in the majority of cases of ocular TB. This method is useful in early confirmation of ocular tuberculosis.

Molecular Techniques in the Diagnosis of Central Nervous System Infections

Development of polymerase chain reaction (PCR)-based molecular techniques has initiated a revolution in the field of diagnostic microbiology. These techniques have not only provided rapid, noninvasive detection of microorganisms that cause central nervous system (CNS) infections, but have also demonstrated that several neurologic disorders are linked to infectious agents. While PCR-based techniques are predicted to be widely used in diagnosing and monitoring CNS infections, the limitations, as well as strengths, of these techniques must be clearly understood by both clinicians and laboratory personnel to ensure proper utilization.

Central nervous system infection during immunosuppression

Suppression of the immune system by human immunodeficiency virus (HIV) infection or immunosuppressive therapy following transplantation increases susceptibility to CNS infection. Examination of the level and type of immunosuppression, in addition to the clinical and radiologic findings at the time of diagnosis can aid the clinician in determining the most likely etiology of infection. This article discusses how suppression of the host immune status modifies the presentation and diagnosis of selected CNS infections and the recommended treatment for these infections.

Tuberculous meningoencephalitis in HIV-seronegative patients: variety of clinical presentation and impact on diagnostics and treatment

Tuberculous meningoencephalitis (TBM), an infrequent disease in Western European countries, shows a wide heterogeneity of clinical symptoms.

MATERIAL AND METHODS

We present 4 patients (age range 42-72 years) with the definite diagnosis of isolated TBM. All patients were HIV-seronegative, only 1 patient was known to be immunoincompetent on admission due to acute myelocytic leukemia; other reasons for immune suppression were detected in 2 other patients (leukemia and idiopathic CD4+ T-lymphocytopenia, respectively).

RESULTS

The diagnosis of TBM was confirmed in 3 cases by culture from CSF, in 1 case Mycobacterium tuberculosis was proven only in tracheal aspirate. In 1 patient M. bovis was found, which is an extremely rare cause of TBM in Germany. We report the contributions of different diagnostic tools (CSF analysis, neuroimaging) in reaching the presumptive diagnosis and in monitoring the further course. All patients developed neurological complications despite prompt tuberculostatic treatment. Three of the patients presented a chronic severe loss of consciousness of unclear origin.

CONCLUSION

The possible causative relationships of these complications and their impact on the prognosis are discussed.

Monitoring treatment of patients with pulmonary tuberculosis: can PCR be applied?

To assess whether PCR is applicable for monitoring the efficacy of antituberculous treatment, respiratory specimens obtained during treatment and follow-up from sputum smear-positive tuberculosis (TB) patients were examined. First, results of smear, culture, and PCR for Mycobacterium tuberculosis complex (MTB) and an internal inhibition control (MCC) were correlated retrospectively on 1,601 respiratory specimens from patients with no previous cultures of MTB. MTB optical density (OD) values increased to a maximum level of 3.5 to 4.0, with both increasing numbers of acid-fast bacilli and CFU. MTB/MCC OD ratios also increased with both smear and culture grading and correlated significantly better with both than the MTB OD value. Second, changes in MTB OD values and MTB/MCC OD ratios were compared with microscopy and culture for MTB in monthly sputa obtained during treatment and follow-up in 22 smear-positive pulmonary TB patients. Declines in MTB/MCC OD ratios during antituberculous treatment and follow-up were observed. Patients with moderate disease reached the baseline after 6 to 8 months of standard antituberculous treatment regimen, whereas patients with extensive disease were predicted to reach the baseline 1 year or more after the initiation of treatment. Although PCR detects both dead and live bacteria, we believe that PCR can be used to assess the efficacy of antituberculous treatment since increases or slow reductions in MTB/MCC OD ratios would indicate nonoptimal treatment, noncompliance, reduced bioavailability of drugs, or resistant strains of MTB and thereby would identify patients at risk for treatment failure or reactivation.

Cerebrospinal fluid testing for the diagnosis of central nervous system infection

The central nervous system (CNS) is susceptible to bacterial, viral, and fungal infections, and prion diseases. Examination of the cerebrospinal fluid (CSF) is crucial in diagnosing these infections. Cerebrospinal tests may directly identify an organism and its nucleic acid and surface constituents by culture, polymerase chain reaction (PCR), or antigen detection. Alternatively, antibody to an organism may be identified in CSF by enzyme-linked immunosorbent assay (ELISA), Western blot, or complement fixation assay. This article discusses how these CSF tests are performed and addresses the sensitivity and specificity of such tests for the diagnosis of selected CNS infections.

Central nervous system tuberculosis

Involvement of the central nervous system (CNS) by Mycobacterium tuberculosis, particularly meningitis, is the most severe form of tuberculous infection. Parenchymal CNS involvement can occur in the form of tuberculoma or, more rarely, abscess. Although surgery was initially advocated as the mainstay of therapy, more recent evidence suggests that parenchymal forms of CNS tuberculosis can be cured with medical treatment alone. Also, damage of the spinal cord, roots, and spine can occur in the form of spinal meningitis, radiculomyelitis, spondylitis, or spinal cord infarction.

Detection of rifampin resistance in Mycobacterium tuberculosis by double gradient-denaturing gradient gel electrophoresis

We applied double gradient-denaturing gradient gel electrophoresis (DG-DGGE) for the rapid detection of rifampin (RMP) resistance from rpoB PCR products of Mycobacterium tuberculosis isolates and clinical samples. The results of this method were fully concordant with those of DNA sequencing and susceptibility testing analyses. DG-DGGE is a valid alternative to the other methods of detecting mutations for predicting RMP resistance.

A simple method for PCR based analyses of immunohistochemically stained, microdissected, formalin fixed, paraffin wax embedded material

Microdissection was performed on sections cut from formalin fixed, paraffin wax embedded archival material, which had been subjected to conventional immunohistochemistry. Crude DNA extracts, which were obtained from these microdissected samples by a simple microwave step, were then added directly to amplification reactions. Analyses using a range of polymerase chain reaction (PCR) based techniques, including microsatellite repeat polymorphism analysis at the NM23-H1 locus and sequencing of exons 5, 7, and 8 of the p53 gene, were performed successfully. Universal PCR amplification was also carried out on the microdissected material and probes suitable for use in comparative genomic hybridisation (CGH) were obtained in all cases. This technique will enable a range of effective genetic analyses to be carried out on specific subsets of cells that have been characterised previously by immunohistochemistry.

Use of magnetic beads for tissue DNA extraction and IS6110 Mycobacterium tuberculosis PCR

Polymerase chain reaction (PCR) techniques are used increasingly for the diagnosis of Mycobacterium tuberculosis infection and can be used on the DNA obtained from both frozen and formalin fixed, paraffin wax embedded tissues. However, the extraction of DNA by means of the conventional phenol/chloroform method is time consuming and requires the use of potentially dangerous chemical reagents. This paper describes a method based upon the use of magnetic beads for the extraction of M tuberculosis DNA from both routinely formalin fixed, paraffin wax embedded tissues and frozen tissues. Magnetic bead extracted DNA from brain, lymph node, and lung tissues collected from patients with human immunodeficiency virus and tuberculosis was compared with that extracted using the phenol/chloroform method. The magnetic bead extraction procedure requires less than two hours, including the time necessary to dewax the tissue sections. In all cases, the DNA extracted with both methods was amplified successfully by PCR for the M tuberculosis IS6110 sequence. Magnetic bead DNA extraction can be used on both frozen and archival tissues: the method is reliable, simple, sensitive, and rapid; in addition, it does not use hazardous procedures or specialised laboratory equipment and can be used for routine DNA isolation from various human tissues.

Evaluation of PCR in detection of Mycobacterium tuberculosis from formalin-fixed, paraffin-embedded tissues: comparison of four amplification assays

We compared the sensitivities and specificities of four nested PCR assays for the detection of Mycobacterium tuberculosis from formalin-fixed, paraffin-embedded tissues. Thirty-seven autopsy samples from human immunodeficiency virus-positive patients were analyzed: 15 were M. tuberculosis positive, 11 served as negative controls, and 11 were Ziehl-Neelsen positive without cultural confirmation of M. tuberculosis. Three genomic sequences (mtp40, 65-kDa antigen gene, and IS6110) with different molecular masses and numbers of repetitions within the M. tuberculosis genome were targeted. On the IS6110 sequence, two fragments of different sizes (106 and 123 bp, respectively) were amplified with two separate pairs of primers. The highest sensitivity rates were obtained by amplifying the highly repetitive IS6110 insertion sequence, and the different primers tested showed a sensitivity ranging from 80 to 87%. Amplification of the large 223-bp fragment of the mtp40 sequence present in a single copy in the M. tuberculosis genome yielded a high rate of false-negative results, ranging from 66 to 80%. A poor sensitivity (from 47 to 60%) was also shown by PCR amplification of the 142-bp 65-kDa antigen gene. All the PCRs except that for the 65-kDa antigen gene showed a specificity of 100%. Moreover, different results were obtained with different dilutions of DNA, and DNA concentrations of 1 and 3 microg yielded the highest sensitivities depending upon which protocol was used. Application of the PCRs to the Ziehl-Neelsen-positive, culture-negative samples confirmed the sensitivities of the PCRs obtained with the control samples. In conclusion, PCR can successfully be used to detect M. tuberculosis from paraffin-embedded tissues and can be particularly useful in the validation of a diagnosis of tuberculosis in clinical settings in which the diagnosis is uncertain. However, the efficacy of PCR strictly depends on several amplification parameters such as DNA concentration, target DNA size, and the repetitiveness of the amplified sequence.

The application of the polymerase chain reaction of cerebrospinal fluid in the clinical management of AIDS-related CNS disorders

In AIDS patients central nervous system (CNS) illness may be caused by HIV disease itself or by opportunistic agents, resulting in serious morbidity such as behavioral and motor disturbances, meningitis or encephalitis, among other disorders. Early diagnosis can allow specific treatment (e.g., antimicrobial treatment) that may prevent, ameliorate, or slow the catastrophic sequelae of infection, as well as reduce the need for expensive diagnostic procedures. Conventional microbiology techniques have proven inadequate for the diagnosis of most AIDS-related CNS diseases. However, the development in the past decade of the application of polymerase chain reaction (PCR) to clinical specimens has facilitated the early diagnosis of a number of infectious diseases in these patients. The technique permits the amplification of target nucleic acids such that common laboratory methods may then be used for diagnosis. The application of PCR to cerebrospinal fluid for early diagnosis of AIDS-related neurologic complications has been an impressive example of the application of PCR and may form the basis of new algorithms for diagnosis and possibly the evaluation of treatment protocols.

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.

Detection of rifampin resistance by single-strand conformation polymorphism analysis of cerebrospinal fluid of patients with tuberculosis of the central nervous system

Mutations in a 69-bp region of the rpoB gene of Mycobacterium tuberculosis are associated with rifampin resistance (Rif[r]). These have been detected with mycobacterial DNA extracted from bacterial suspensions or respiratory specimens that were acid-fast smear positive. We experimented with a strategy for the rapid detection of Rif(r) in cerebrospinal fluid (CSF) samples. The strategy involves the amplification of the 69-bp region of rpoB by means of PCR and the identification of nucleotide mutations by single-strand conformation polymorphism (SSCP) analysis of the amplification products. Sixty-five CSF specimens collected from 29 patients (19 patients were coinfected with human immunodeficiency virus) with culture or autopsy-confirmed (22 patients) or highly probable (7 patients) tuberculosis of the central nervous system (CNS-TB) were processed. Amplified products suitable for evaluation by SSCP analysis were obtained from 37 CSF specimens from 25 subjects (86.2%). PCR-SSCP of CSF correctly identified the rifampin susceptibility phenotype of isolates from all 17 patients for whom the results of susceptibility tests carried out with strains cultured from CSF or respiratory samples were available. Moreover, this assay revealed the rifampin susceptibility genotype of isolates from the eight patients (three patients with culture-confirmed CNS-TB and five patients in whom CNS-TB was highly probable) for whom no susceptibility test results were available; the PCR-SSCP data obtained for these patients were concordant with the outcome after a standard antituberculosis treatment. The evolution of a mutation in the rpoB gene was documented in a patient during the course of treatment. PCR-SSCP analysis of CSF seems to be an efficacious method of predicting Rif(r) and would reduce the time required for susceptibility testing from approximately 4 to 8 weeks to a few days.

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

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

Detection of Mycobacterium tuberculosis by PCR analysis of urine and other clinical samples from AIDS and non-HIV-infected patients

A number of different clinical specimens, such as sputum, cerebrospinal fluid and blood, have been reported to be good substrates for the detection of Mycobacterium tuberculosis by PCR assay. We wanted to search for the presence of mycobacteria in other body fluids, such as urine. Urine samples and other samples obtained from AIDS patients and non HIV-infected patients were analysed by PCR. The results were compared with those obtained using conventional methods (Bactec 460 TB and AFB (acid fast bacilli strain)). We analysed 412 urine samples and 210 different other samples (sputum and cerebrospinal fluid) obtained from AIDS patients by PCR; almost identical levels of PCR-positive (14-17%) results were observed in all samples analysed. The results were then compared with those obtained with the Bactec 460 TB and AFB. PCR, Bactec 460 TB and acid fast stain were also used to analyse 190 urine samples and 230 other samples from non-HIV infected patients in the consumption ward of Sassari Hospital. The number of urine samples positive by PCR (6.3%) and Bactec 460 TB (2.1%) was half that obtained from samples taken from the AIDS patients. As expected, an increase in the number of positive sputum samples was observed with all methods. The results indicate that PCR analysis of urine samples represents a valid alternative for fast and sensitive detection of M. tuberculosis. This method can be routinely used in the clinical laboratory, especially in HIV-infected patients.