Nested-PCR using MPB64 fragment improves the diagnosis of pleural and meningeal tuberculosis

Evaluation of real time polymerase chain reaction targeting mpb64 gene for diagnosis of extrapulmonary tuberculosis

BACKGROUND

Paucibacillary nature of extrapulmonary tuberculosis (EPTB) has paved way for molecular methods increasingly being used for diagnosis. We undertook a study for evaluation of sensitivity and specificity of real-time polymerase chain reaction (RT-PCR) targeting mpb64 gene for diagnosis of EPTB.

METHODS

A total of 152 clinical samples from suspected cases of EPTB were included in this study. All samples were extracted using spin column based commercial DNA extraction kit and were subjected to RT-PCR targeting mpb64 and IS6110. Smear and culture was also done for samples whenever quantity was sufficient. Cytology report was noted from hospital information system. Receiver operating characteristic (ROC) curve analysis was done for determining cut-off Ct value for mpb64 RT-PCR. Melt curve analysis was done for samples whose cycle threshold (Ct) value was more than 37. The sensitivity and specificity of the mpb64 RT-PCR was calculated using a composite gold standard i.e., positive for one or more of the following: microscopy (including fine needle aspiration cytology (FNAC), acid-fast bacilli positivity), culture and IS6110 RT-PCR.

RESULTS

Out of the 152 samples, 72 (47.4%) were positive for tuberculosis by composite gold standard. Samples consisted of ascitic fluid (12), CSF (35), pus (23), lymph node aspirate (35), pleural fluid (37), synovial fluid (4), urine (1), pericardial fluid (1) and tissue bits (4). Microscopy (AFB smear including lymph node aspirate) was done for 124 samples of which 43 (34.7%) were positive. Culture results were available for 79 samples, 25 (31.6%) of which were positive and 42 (27.6%) of the 152 samples were positive by IS6110 PCR. Based on ROC and melt curve analysis, mpb64 RT-PCR was able to detect 38 (52.8%) of the 72 positive samples. In comparison to IS6110 RT PCR, 4 additional cases were detected by mpb64 RT-PCR. Compared to composite gold standard mpb64 showed overall sensitivity of 52.8%.

CONCLUSION

The mpb64 RT-PCR is highly specific or MTB and can be used as a supplemental test for diagnosis of EPTB along with other diagnostic tests. However the overall sensitivity of mpb64 RT-PCR is too low to be used as an independent test for diagnosis of EPTB. Combining the results of IS6110 RT PCR and mpb64 RT PCR improved the overall sensitivity and hence mpb64 can be used as an additional target for diagnosis of EPTB.

Bleb-related tuberculous endophthalmitis following combined phacoemulsification and trabeculectomy with mitomycin C

A one-eyed 67-year-old man with 20/400 vision, dense cataract, previously failed trabeculectomy and medically uncontrolled advanced glaucoma underwent a single-site phacoemulsification with repeat trabeculectomy and mitomycin C. One-week postoperatively, vision in the right eye improved to 20/120, good bleb and intraocular pressure (IOP) of 14 mm Hg. By third postoperative week, patient presented to the emergency with diminished vision, pain and redness in right eye of 2 days duration and was diagnosed to have bleb-related endophthalmitis (BRE). Vitreous biopsy, smear from the bleb were taken and underwent pars plana vitrectomy with intraocular antibiotic injection. Smears and cultures were negative however, aqueous DNA-PCR was positive for Mycobacterium tuberculosis Revisited history revealed treated pulmonary tuberculosis 3 years ago with a positive Mantoux test (17 mm) and hilar prominence on chest X-ray. One month after starting anti-tubercular therapy (ATT), the BRE resolved and vision improved to 20/60 with IOP of 14 mm Hg and the ATT was continued.

Modified genome comparison method: a new approach for identification of specific targets in molecular diagnostic tests using Mycobacterium tuberculosis complex as an example

BACKGROUND

The first step of designing any genome-based molecular diagnostic test is to find a specific target sequence. The modified genome comparison method is one of the easiest and most comprehensive ways to achieve this goal. In this study, we aimed to explain this method with the example of Mycobacterium tuberculosis complex and investigate its efficacy in a diagnostic test.

METHODS

A specific target was identified using modified genome comparison method and an in-house PCR test was designed. To determine the analytical sensitivity and specificity, 10 standard specimens were used. Also, 230 specimens were used to determine the clinical sensitivity and specificity.

RESULTS

The identity and query cover of our new diagnostic target (5KST) were ≥ 90% with M. tuberculosis complex. The 5KST-PCR sensitivity was 100% for smear-positive, culture-positive and 85.7% for smear-negative, culture-positive specimens. All of 100 smear-negative, culture-negative specimens were negative in 5KST-PCR (100% clinical specificity). Analytical sensitivity of 5KST-PCR was approximately 1 copy of genomic DNA per microliter.

CONCLUSIONS

Modified genome comparison method is a confident way to find specific targets for use in diagnostic tests. Accordingly, the 5KST-PCR designed in this study has high sensitivity and specificity and can be replaced for conventional TB PCR tests.

Challenges in pleural tuberculosis diagnosis: existing reference standards and nucleic acid tests

Pleural tuberculosis (pTB) is a grave form of extrapulmonary tuberculosis. Microbiological tests are usually found to be inadequate for pTB diagnosis. The absence of a uniform 'composite reference standard' is challenging; therefore, diagnosis is usually performed using a combination of diversified criteria. Nucleic acid tests vary in diagnostic accuracy and have not yet been integrated into clinical decision making. This review assesses the varied criteria used for pTB classification and the challenges afflicting pleural fluid-based DNA diagnostic tests, namely, PCR and Xpert^® MTB/RIF. In the 58 studies (PCR: n = 33; Xpert: n = 25) analyzed, reference standards were heterogeneous and PCR/Xpert pooled sensitivity values (range: 0-100%) were inadequate. However, the consistent high specificity of Xpert (range: 90-100%) indicated its utility as a 'rule-in' test. There is an urgent need to evaluate existing and new molecular tests in well-designed studies  to accurately assess their utility for pTB diagnosis. To conclude, rapid and accurate tests are warranted for pTB diagnosis.

Performance of an in-house real-time polymerase chain reaction for identification of Mycobacterium tuberculosis isolates in laboratory routine diagnosis from a high burden setting

Brazil is one of the high burden countries for tuberculosis, and a rapid diagnosis is essential for effective control of the disease. In the present study, an in-house real-time polymerase chain reaction (PCR) assay targeting the mpt64 gene for identification of Mycobacterium tuberculosis complex isolates was evaluated under routine diagnosis conditions in a reference laboratory. From May 2011 to July 2012, 1,520 isolates of mycobacteria were prospectively submitted for phenotypic and/or PRA-hsp65 identification and to real-time PCR. The mpt64 real-time PCR showed 99.7% sensitivity and 96% specificity and detected 79.4% of the cases missed by phenotypic and PRA-hsp65 identification. The in-house real-time PCR assay showed high sensitivity and specificity and was successfully implemented in the routine diagnosis of tuberculosis in a reference laboratory from a high burden setting.

Evaluation of multiplex PCR using MPB64 and IS6110 primers for rapid diagnosis of tuberculous meningitis

Tuberculous meningitis (TBM) is one of those most serious manifestations of extra-pulmonary tuberculosis and prompt diagnosis and treatment is required for better clinical outcome. It is difficult to diagnose due to 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 Multiplex polymerase chain reaction (PCR) technique, using primers directed against the insertion sequence IS6110 and MPB64 gene for the detection of Mycobacterium tuberculosis in Cerebrospinal fluid (CSF), for rapid diagnosis of TBM patients. 102 CSF samples were analyzed from patients suspected with TBM along with a control group of 10 patients having other neurological disorders. CSF sediments were analyzed individually for M. tuberculosis DNA by Multiplex PCR using two set of primers targeting insertion sequence IS6110 and gene MBp64, which is very specific for MTBC. Out of 37 patients diagnosed with TBM clinically, MPB64 PCR was positive in 22, IS6110 PCR was positive in 28, both PCR using Multiplex were positive in 34 and Microscopy was positive in one. Thus Sensitivity of MPB64 PCR, IS6110 PCR, Multiplex PCR and Microscopy were found to be 62.3%, 75.4%, 91.8% and 2.7% respectively. In non TBM group PCR was negative in all cases hence, the specificity was 100%. Multiplex PCR system using primers targeting IS6110 and MPB64, for the detection of M. tuberculosis DNA in CSF samples, has high sensitivity than any one of them alone, and could be used for the early detection of TBM in CSF samples.

Diagnosis of extrapulmonary tuberculosis by PCR

During the last two decades, the resurgence of tuberculosis (TB) has been documented in both developed and developing nations, and much of this increase in TB burden coincided with human immunodeficiency virus (HIV) epidemics. Since then, the disease pattern has changed with a higher incidence of extrapulmonary tuberculosis (EPTB) as well as disseminated TB. EPTB cases include TB lymphadenitis, pleural TB, TB meningitis, osteoarticular TB, genitourinary TB, abdominal TB, cutaneous TB, ocular TB, TB pericarditis and breast TB, although any organ can be involved. Diagnosis of EPTB can be baffling, compelling a high index of suspicion owing to paucibacillary load in the biological specimens. A negative smear for acid-fast bacilli, lack of granulomas on histopathology and failure to culture Mycobacterium tuberculosis do not exclude the diagnosis of EPTB. Novel diagnostic modalities such as nucleic acid amplification (NAA) can be useful in varied forms of EPTB. This review is primarily focused on the diagnosis of several clinical forms of EPTB by polymerase chain reaction (PCR) using different gene targets.

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.

Histopathology and TB-PCR kit analysis in differentiating the diagnosis of intestinal tuberculosis and Crohn’s disease

AIM: To compare the histopathologic features of intestinal tuberculosis (ITB) and Crohn’s disease (CD) and to identify whether polymerase chain reaction for Mycobacterium tuberculosis (TB-PCR) would be helpful for differential diagnosis between ITB and CD.

METHODS: We selected 97 patients with established diagnoses (55 cases of ITB and 42 cases of CD) who underwent colonoscopic biopsies. Microscopic features of ITB and CD were reviewed, and eight pathologic parameters were evaluated. Nine cases of acid fast bacilli culture-positive specimens and 10 normal colonic tissue specimens were evaluated as the positive and negative control of the TB-PCR test, respectively. PCR assays were done using two commercial kits: kit <A> detected IS6110 and MPB64, and kit <B> detected IS6110 only; a manual in-house PCR method was also performed on formalin-fixed, paraffin-embedded colonoscopic biopsy specimens.

RESULTS: Statistically significant differences were noted between ITB and CD with regard histopathologic criteria: size of granulomas (P = 0.000), giant cells (P = 0.015), caseation necrosis (P = 0.003), confluent granulomas (P = 0.001), discrete granulomas (P = 0.000), and granulomas with lymphoid cuffs (P = 0.037). However, 29 cases (52.7%) of ITB showed less than five kinds of pathologic parameters, resulting in confusion with CD. The sensitivities and specificities of the TB-PCR test by kit <A>, kit <B>, and the in-house PCR method were 88.9% and 100%, 88.9% and 100%, and 66.7% and 100% in positive and negative controls, respectively. The PCR test done on endoscopic biopsy specimens of ITB and CD were significantly different with kit <A> (P = 0.000) and kit <B> (P = 0.000). The sensitivities and specificities of TB-PCR were 45.5% and 88.1%, 36.4% and 100%, and 5.8% and 100%, for kit <A> and kit <B> and in-house PCR method on endoscopic biopsy specimens. Among the 29 cases of histopathologically confusing CD, 10 cases assayed using kit <A> and 6 cases assayed using kit <B> were TB-PCR positive. A combination of histologic findings and TB-PCR testing led to an increase of diagnostic sensitivity and the increase (from 47.3% to 58.2) was statistically significant with kit <B> (P = 0.000).

CONCLUSION: The TB-PCR test combined with histopathologic factors appears to be a helpful technique in formulating the differential diagnosis of ITB and CD in endoscopic biopsy samples.

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.

[Nested-PCR for gene that encodes the antigen b applied to the diagnosis of pulmonary tuberculosis]

The polymerase chain reaction used for amplifying an internal sequence of a previously amplified fragment (nested-PCR) was investigated as a complementary alternative for searching for alcohol-acid resistant bacilli and Mycobacterium tuberculosis cultures in Lowenstein-Jensen medium. 144 sputum samples were investigated from patients with suspected tuberculosis that were sent to the Tuberculosis Laboratory of the Evandro Chagas Institute in Belém, between June 2002 and December 2003. From the 144 samples, 121 were characterized as tuberculosis: 119 were positive in cultures, 95 under bacilloscopy and 128 using nested-PCR. The sensibility of the nested-PCR was 96% (116/121), while the specificity was 48% (11/23). Nested-PCR may be a complementary tool for diagnosing tuberculosis, since it presents sensitivity equivalent to that of cultures. However, further evaluations are needed with the aim of minimizing the number of false-positive results.

Diagnosis and treatment of tuberculous pleural effusion in 2006

Tuberculous (TB) pleural effusion occurs in approximately 5% of patients with Mycobacterium tuberculosis infection. The HIV pandemic has been associated with a doubling of the incidence of extrapulmonary TB, which has resulted in increased recognition of TB pleural effusions even in developed nations. Recent studies have provided insights into the immunopathogenesis of pleural TB, including memory T-cell homing and chemokine activation. The definitive diagnosis of TB pleural effusions depends on the demonstration of acid-fast bacilli in the sputum, pleural fluid, or pleural biopsy specimens. The diagnosis can be established in a majority of patients from the clinical features, pleural fluid examination, including cytology, biochemistry, and bacteriology, and pleural biopsy. Measurement of adenosine deaminase and interferon-gamma in the pleural fluid and polymerase chain reaction for M tuberculosis has gained wide acceptance in the diagnosis of TB pleural effusions. Although promising, these tests require further evaluation before their routine use can be recommended. The treatment of TB pleural effusions in patients with HIV/AIDS is essentially similar to that in HIV-negative patients. At present, evidence regarding the use of corticosteroids in the treatment of TB pleural effusion is not clear-cut.

Modified immunohistological staining allows detection of Ziehl-Neelsen-negative Mycobacterium tuberculosis organisms and their precise localization in human tissue

The diagnosis of mycobacterial infection depends on the Ziehl-Neelsen (ZN) stain, which detects mycobacteria because of their characteristic acid-fast cell wall composition and structure. The histological diagnosis of tuberculosis (TB) comprises various aspects: (1) sensitive detection of mycobacteria; (2) precise localization of mycobacteria in the context of granulomatous lesions; (3) 'staging' of disease according to mycobacterial spread and granulomatous tissue integrity. Thus, detection of minute numbers of acid-fast bacteria in tissue specimens is critical. The conventional ZN stain fails to identify mycobacteria in numbers less than 10(4) per ml. Hence many infections evade diagnosis. PCR is highly sensitive, but allows neither localization within tissues nor staging of mycobacterial disease, and positive findings frequently do not correlate with disease. In this study, an anti-Mycobacterium bovis bacille Calmette-Guérin polyclonal antiserum (pAbBCG) was used to improve immunostaining, which was compared to the ZN stain in histological samples. Screening of tissue samples including lungs, pleural lesions, lymph nodes, bone marrow, and skin for mycobacterial infection revealed that pAbBCG staining detects infected macrophages harbouring intracellular mycobacteria or mycobacterial material as well as free mycobacteria that are present at low abundance and not detected by the ZN stain. The positive pAbBCG staining results were confirmed either by PCR analysis of microdissected stained tissue or by culture from tissue. This immunostaining approach allows precise localization of the pathogen in infected tissue.

Molecular genetic methods for diagnosis and antibiotic resistance detection of mycobacteria from clinical specimens

Mycobacteria comprise a diverse group of bacteria that are widespread in nature, some of which cause significant disease in humans. Members of the Mycobacterium tuberculosis complex (MTBC) are the most important human pathogens of the genus Mycobacterium. Traditional methods for detection and identification of mycobacteria include microscopy, culture and phenotypic tests. These methods either lack sensitivity, specificity, or are time consuming. Advances in the field of molecular biology have provided rapid diagnostic tools that have reduced the turnaround times for detecting MTBC and drug resistance in cultures and directly in clinical specimens from weeks to days. This review discusses the molecular genetic techniques for detecting and identifying MTBC as well as drug resistance of mycobacteria in clinical specimens.

Análise de diferentes primers utilizados na PCR visando ao diagnóstico da tuberculose no Estado do Amazonas

INTRODUÇÃO: Há diferentes primers sendo testados para a detecção do DNA do Mycobacterium tuberculosis. A acuidade da reação em cadeia da polimerase (PCR) depende da existência da seqüência alvo no bacilo e de os testes serem realizados em cepas isoladas ou em amostras clínicas. OBJETIVO: Verificar a presença das seqüências de DNA alvo mais relatadas na literatura para o diagnóstico da tuberculose em amostras clínicas usando como controle positivo as respectivas cepas de M. tuberculosis isoladas. MÉTODO: Oitenta e uma amostras clínicas de pacientes com suspeita de tuberculose foram submetidas à baciloscopia e cultivo. A técnica de PCR foi realizada nas amostras clínicas e cepas isoladas com primers específicos para os seguintes alvos: IS6110, 65 kDa, 38 kDa e MPB64. RESULTADOS: Em 24 amostras com baciloscopia e cultivo negativos, a PCR também foi negativa com todos os primers testados. Em 19 amostras com baciloscopia positiva e nas cepas isoladas obteve-se 100% de resultados positivos nas PCR, exceto nas PCR em amostras clínicas com os primers para a seqüência MPB64 (89,4%). Em 38 amostras com baciloscopia negativa e cultivo positivo, as PCR tiveram resultados variáveis, sendo que os primers específicos que amplificam o fragmento de 123 pb da seqüência IS6110 foram os que forneceram os maiores percentuais de positividade (92,1%), concordância diagnóstica (0,9143), co-positividade (94,7%) e co-negatividade (100%). CONCLUSÃO: As seqüências IS6110, 38 kDa, MPB64 e 65 kDa foram encontradas no genoma de todas as cepas de M. tuberculosis isoladas desses pacientes do Estado do Amazonas. O protocolo utilizado no processamento das amostras clínicas e os primers específicos utilizados para amplificação do fragmento de 123 pb da seqüência IS6110 demonstraram maior eficiência no diagnóstico da tuberculose pulmonar (paucibacilar) em comparação com a literatura.

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

Background

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

Methods

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

Results

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

Conclusions

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

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

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

Modern laboratory diagnosis of tuberculosis

One-third of the global population is believed to be infected with bacteria of the Mycobacterium tuberculosis complex, the causative agent of tuberculosis. More than 8 million new cases of tuberculosis occur annually leading to 2 million deaths. Mortality is particularly high in those coinfected with HIV and where the bacteria are multiple-drug-resistant strains--ie, strains resistant to at least isoniazid and rifampicin. Early diagnosis of tuberculosis and drug resistance improves survival and by identifying infectious cases promotes contact tracing, implementation of institutional cross-infection procedures, and other public-health actions. This review addresses significant advances made in the diagnosis of infection, clinical disease, and drug resistance over the past decade. It proposes operational criteria for a modern diagnostic service in the UK (as a model of a low-incidence country) and explores some of the economic issues surrounding the use of these techniques.