Multiplex polymerase chain reaction using insertion sequence 6110 (IS6110) and mycobacterial protein fraction from BCG of Rm 0.64 in electrophoresis target genes for diagnosis of tuberculous lymphadenitis

Determining the diagnostic potential of Truenat MTB Plus for Tubercular lymphadenitis and detection of drug resistance and a comparison with GeneXpert Ultra

SETTING

Tubercular lymphadenitis (TBLA), the most common form of extrapulmonary tuberculosis, is a diagnostic challenge.

OBJECTIVE

Truenat MTB Plus (TruPlus) along with Truenat Rif assay (TruRif) was evaluated for detection of TBLA and rifampicin resistance and compared with GeneXpert Ultra (Xpert Ultra).

DESIGN

100 fine-needle aspirated specimens [50 confirmed by culture/smear/cytology, 20 clinically suspected, and 30 controls], processed in the mycobacteriology division of department of microbiology were subjected to TruPlus and TruRif, Xpert Ultra and multiplex PCR. The results of TBLA detection were compared against composite reference standard (CRS) and those of rifampicin resistance were compared against phenotypic drug susceptibility testing and rpoB gene sequencing.

RESULTS

In comparison to CRS, the diagnostic yield of TruPlus, Xpert Ultra and MPCR was 77.14%, 59.18% and 84.28%, respectively; with substantial agreement for TruPlus (k = 0.66) and MPCR (k = 0.76) and moderate for Xpert Ultra (k = 0.60). TruRif reported four cases as RifR and Xpert Ultra reported two. On comparing with phenotypic DST and gene sequencing, only two cases of RifR were confirmed, hence TruRif reported false-RifR in two cases.

CONCLUSION

TruPlus could be used as a reliable tool for diagnosing TBLA. The reporting of RifR by TruRif should be confirmed by phenotypic DST or gene sequencing.

Comparative evaluation of loop-mediated isothermal amplification (LAMP) assay, GeneXpert MTB/Rif and multiplex PCR for the diagnosis of tubercular lymphadenitis in HIV-infected patients of North India

BACKGROUND

Tubercular lymphadenitis (TBLA) is one of the most common extrapulmonary manifestations of tuberculosis in patients with HIV. With several other pathological conditions presenting as lymphadenitis and lack of consensus regarding a gold standard test, the diagnosis of TBLA remains a challenge for the clinician.

OBJECTIVES

and design: In this study, we have assessed the potential of loop-mediated isothermal amplification (LAMP) test for the diagnosis of TBLA in HIV-infected patients. The study group included samples collected by fine needle aspiration (FNAC) of lymph nodes from 24 HIV-infected patients with TBLA. A composite reference standard was used to identify cases of TBLA based on clinical suspicion, results of cytology, AFB smear, MGIT culture, GeneXpert MTB/RIF, multiplex polymerase chain reaction (MPCR) and subsequently clinical response to antitubercular therapy. These tests were also carried out in 26 control samples of lymph node FNAC from HIV-infected patients with non-tubercular lymphadenitis.

RESULTS

LAMP assay was positive in 19/24 TBLA cases and yielded a sensitivity of 79.17% with 100% specificity. Cytology was suggestive in 18/24 (75%) TBLA cases. GeneXpert MTB/RIF assay correctly identified 16/24 TBLA cases, but the test did show one false positive result reducing its specificity. MPCR had the highest sensitivity of 91.67% as it correctly identified 22/24 cases and showed no false positive result.

CONCLUSION

The current study highlights the potential of LAMP test for the specific diagnosis of tubercular lymphadenitis in FNAC samples from HIV-infected patients, especially when cytology is either non-conclusive or non-available. Though MPCR had a higher sensitivity than LAMP assay, the added advantages of low cost, minimal technical expertise and simplicity of procedure make LAMP assay a suitable diagnostic test in resource-limited settings.

Multiplex Polymerase Chain Reaction for diagnosis of gastrointestinal tuberculosis

Background and Aim

To evaluate the role of multiplex polymerase chain reaction (PCR) for diagnosis of gastrointestinal tuberculosis (GITB).

Methods

This was a prospective observational study conducted from July 2015 to November 2016 at a tertiary care teaching institution in north India. Fifty individuals with clinically suspected GITB and older than 18 years of age were recruited. Patients underwent radiological investigations, esophagogastroduodenoscopy, or colonoscopy as clinically indicated. Multiple biopsies for tissue diagnosis and PCR were taken. All specimens were subjected to Ziehl Neelsen staining, histopathology, and multiplex PCR using specific primers for genes IS6110, MPB64, and Protein b. The performance of the assay was assessed using a composite reference standard for diagnosis of tuberculosis. It comprised a combination of clinical characteristics and microbiological methods, including smear, Bactenecin (BACTEC) culture, histopathology, and response to antitubercular therapy.

Results

A final diagnosis of tuberculosis was made in 32 cases (Duodenal‐4, Ileo‐colonic‐28). The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of histopathology for the diagnosis of tuberculosis was 28.12, 100, 100, and 43.9%, respectively. The sensitivity, specificity, PPV and NPV of BACTEC Mycobacteria Growth Indicator Tube (MGIT) culture for the diagnosis of tuberculosis was 9.3, 100, 100, and 38.29%, respectively. The sensitivity, specificity, PPV, and NPV of multiplex PCR for the diagnosis of tuberculosis was 87.5, 100, 100, and 86.2%, respectively.

Conclusion

Multiplex PCR using specific primers for genes IS6110, MPB64, and Protein b had a higher sensitivity compared to conventional techniques for the diagnosis of GITB.

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.

Comparative Study of GeneXpert MTB/RIF Assay and Multiplex PCR Assay for Direct Detection of Mycobacterium tuberculosis in Suspected Pulmonary Tuberculosis Patients

Pulmonary tuberculosis (PTB) is one of the major infectious diseases in developing countries. The objective of this study was to compare rapid diagnostics technique, GeneXpert MTB/RIF (GeneXpert) and Multiplex PCR assay (MPCR) targeting IS6110 segment and mpb64 gene for direct detection of Mycobacterium tuberculosis (MTB) in suspected PTB patients. A cross sectional study was carried among 105 sputum samples from suspected PTB patients to evaluate GeneXpert and Multiplex PCR who visited National Tuberculosis Center, Nepal. The patient's sputum samples were used directly for the GeneXpert whereas DNA extraction by CTAB method was followed to process the sample for MPCR. The sensitivity and specificity of GeneXpert and MPCR in smear positive cases was 78.6, 33.3, and 100.0%, 66.7%, respectively (P = 0.125). However, in smear negative cases sensitivity and specificity of both methods exhibited 90.9, 95.2, and 100.0%, 100.0% respectively (P = 0.625). Finally, the sensitivity and specificity of GeneXpert and MPCR were 82.9, 95.3 and 100.0%, 98.5% respectively, (P = 0.549) in pulmonary cases. Comparatively, we observed higher sensitivity and specificity for MPCR than GeneXpert for both smear positive and negative samples. Thus, we recommend MPCR alongside GeneXpert for the better diagnostic accuracy of PTB in a resource-limited country where tuberculosis is endemic.

Performance of nested multiplex PCR assay targeting MTP40 and IS6110 gene sequences for the diagnosis of tubercular lymphadenitis

The conventional methods for diagnosis of tubercular lymphadenitis (TBLN) such as - fine needle aspiration cytology, Ziehl-Neelsen staining and culture have limitations of low sensitivity and/or specificity. So, it becomes essential to develop a rapid, sensitive, and specific method for an early diagnosis of TBLN. Therefore, the present study was conducted to evaluate nested multiplex polymerase chain reaction (nMPCR) targeting MTP40 and IS6110 gene sequences of Mycobacterium tuberculosis and Mycobacterium tuberculosis complex, respectively in 48 successive patients of TBLN and 20 random patients with non-tubercular lymph node lesions. Out of the 48 cases of TBLN, 14 (29.2%) were found to be positive by Ziehl-Neelsen staining, 15 (31.2%) were positive by culture and 43 (89.6%) cases were positive after first round of PCR while 48 (100%) cases were positive by nMPCR assay. The sensitivity and specificity of nMPCR was found to be 100% for the diagnosis of TBLN. The results thus obtained indicate that nMPCR assay is a highly sensitive and specific tool for the diagnosis of TBLN.

Utility of multiplex real-time PCR in the diagnosis of extrapulmonary tuberculosis

Objective

The diagnosis of extrapulmonary tuberculosis is still a challenge because of its pauci-bacillary nature. The aim of the study was to evaluate the role of a multiplex PCR assay in the diagnosis of extrapulmonary tuberculosis and to compare the efficiency of two targets, IS6110 and MPB64 to detect Mycobacterium tuberculosis.

Methods

150 extrapulmonary samples (61 pus/aspirate, 46 tissue, 32 body fluids, and 11 urine) from clinically suspected cases of tuberculosis were included in the study. All the samples were subjected to direct fluorescent microscopy, TB culture (BacT/ALERT 3D, biomerieux, Durham, North Carolina, USA) and a Multiplexed Tandem PCR targeting two mycobacterial DNA sequences, IS6110 and MPB64. Master-Mix reagents and primers were prepared by AusDiagnostics Pvt. Ltd (Alexandria, New South Wales, Australia). The performance of the assay was assessed using a composite gold standard, which included clinical characteristics, microbiology smear as well as culture, histopathology, cytology, radiology, and response to antitubercular therapy.

Results

20.3%, 23.6%, and 45.3% of specimens were positive by smear, culture, and PCR, respectively. The sensitivity and specificity of the multiplex PCR was 91.9% and 88.4%, respectively, using the composite gold standard. Positive and negative predictive values of the PCR were estimated as 85.1% and 93.8%, respectively. Higher positivity was observed with target IS6110 (44.6%) as compared to target MPB64 (18.9%). The sensitivities of IS6110 and MPB64 individual targets were 90.3% and 64.5%, respectively, and specificities were 88.4% and 97.7%, respectively.

Conclusion

PCR can play an important role in rapid and accurate diagnosis of extrapulmonary tuberculosis. IS6110 alone is an effective target in our part of the country.

Comparative Evaluation of Several Gene Targets for Designing a Multiplex-PCR for an Early Diagnosis of Extrapulmonary Tuberculosis

PURPOSE

Diagnosis of extrapulmonary tuberculosis (EPTB) poses serious challenges. A careful selection of appropriate gene targets is essential for designing a multiplex-polymerase chain reaction (M-PCR) assay.

MATERIALS AND METHODS

We compared several gene targets of Mycobacterium tuberculosis, including IS6110, devR, and genes encoding MPB-64 (mpb64), 38kDa (pstS1), 65kDa (hsp65), 30kDa (fbpB), ESAT-6 (esat6), and CFP-10 (cfp10) proteins, using PCR assays on 105 EPTB specimens. From these data, we chose the two best gene targets to design an M-PCR.

RESULTS

Among all gene targets tested, mpb64 showed the highest sensitivity (84% in confirmed cases and 77.5% in clinically suspected cases), followed by IS6110, hsp65, 38kDa, 30kDa, esat6, cfp10, and devR. We used mpb64+IS6110 for designing an M-PCR assay. Our M-PCR assay demonstrated a high sensitivity of 96% in confirmed EPTB cases and 88.75% in clinically suspected EPTB cases with a high specificity of 100%, taking clinical diagnosis as the gold standard.

CONCLUSION

These M-PCR results along with the clinical findings may facilitate an early diagnosis of EPTB patients and clinical management of disease.