Diagnostic accuracy of loop-mediated isothermal amplification assay for extra-pulmonary tuberculosis in Indian population

Diagnosis of abdominal tuberculosis by multi-targeted (mpt64 and IS6110) loop-mediated isothermal amplification assay

BACKGROUND AND AIM

Diagnosis of abdominal TB is an exigent task due to variable anatomical sites and non-specific clinical manifestations that closely resemble other diseases. Most of the available diagnostic modalities yield low sensitivities and need expertise to handle the specialized equipment. Hence, there is an urgent need to develop a rapid and reliable diagnostic test, so as to reduce the unnecessary morbidity. Therefore, we designed a multi-targeted loop-mediated isothermal amplification (MT-LAMP) for diagnosing abdominal TB.

METHODS

We evaluated an MT-LAMP (using mpt64 and IS6110) to diagnose abdominal TB within ascitic fluids and intestinal/peritoneal biopsies and compared these results with multiplex-PCR (M-PCR) using the same targets. MT-LAMP products were analyzed by gel electrophoresis and visual detection methods, that is, hydroxy naphthol blue and SYBR Green I reaction.

RESULTS

Sensitivities of 80.9% and 84.6% were obtained in suspected (n = 42) and total abdominal TB (n = 52) cases, respectively by gel-based MT-LAMP, with 97.3% (n = 37) specificity in non-TB controls. Notably, sensitivities attained by gel-based/SYBR Green I MT-LAMP in both clinically suspected and total abdominal TB cases were significantly higher (P < 0.05) than M-PCR. Furthermore, sensitivity obtained with SYBR Green I was equivalent to that of gel-based MT-LAMP, while somewhat lesser specificity (94.6%) was attained with SYBR Green I, compared with gel-based MT-LAMP.

CONCLUSION

Both gel-based and SYBR Green MT-LAMP exhibited equivalent sensitivities to diagnose abdominal TB. Because SYBR Green LAMP is easier to perform than a gel-based assay, we are currently focused on improving the specificity of this assay so as to develop a diagnostic kit.

Insight into diagnosis of pleural tuberculosis with special focus on nucleic acid amplification tests

INTRODUCTION

Pleural tuberculosis (TB) is the archetype of extrapulmonary TB (EPTB), which mainly affects the pleural space and leads to exudative pleural effusion. Diagnosis of pleural TB is a difficult task predominantly due to atypical clinical presentations and sparse bacillary load in clinical specimens.

AREA COVERED

We reviewed the current literature on the globally existing conventional/latest modalities for diagnosing pleural TB. Bacteriological examination (smear/culture), tuberculin skin testing/interferon-γ release assays, biochemical testing, imaging and histopathological/cytological examination are the main modalities. Moreover, nucleic acid amplification tests (NAATs), i.e. loop-mediated isothermal amplification, PCR/multiplex-PCR, nested-PCR, real-time PCR and GeneXpert® MTB/RIF are being utilized. Currently, GeneXpert Ultra, Truenat MTB^TM, detection of circulating Mycobacterium tuberculosis (Mtb) cell-free DNA by NAATs, aptamer-linked immobilized sorbent assay and immuno-PCR (I-PCR) have also been exploited.

EXPERT OPINION

Routine tests are not adequate for effective pleural TB diagnosis. The latest molecular/immunological tests as discussed above, and the other tools, i.e. real-time I-PCR/nanoparticle-based I-PCR and identification of Mtb biomarkers within urinary/serum extracellular vesicles being utilized for pulmonary TB and other EPTB types may also be exploited to diagnose pleural TB. Reliable diagnosis and early therapy would reduce the serious complications associated with pleural TB, i.e. TB empyema, pleural fibrosis, etc.

Diagnostic Accuracy of Loop-Mediated Isothermal Amplification (TB-LAMP) for Tuberculosis in Children

BACKGROUND

Diagnosing tuberculosis (TB) in children is challenging due to its paucibacillary nature. Loop-mediated isothermal amplification (TB-LAMP) is a simple, rapid, and specific point-of-care molecular diagnostic test. However, evaluation of its performance remains limited in children. This study aimed to evaluate the diagnostic performance of Eiken TB-LAMP among children with presumed tuberculosis disease.

METHODS

Pulmonary and extrapulmonary specimens were collected from children under 18 years with presumed TB. Each specimen was tested by using TB-LAMP, acid-fast bacilli (AFB) smear microscopy, and one of the two molecular assays (polymerase chain reaction [PCR] or Xpert MTB/RIF). Sensitivity and specificity were estimated compared to mycobacterial culture as reference standard.

RESULTS

From January 2020 to January 2021, 75 participants with presumed TB were enrolled with median age of 7 years (IQR 2-12). Seventeen specimens from 16 (21.3%) children had bacteriologically confirmed TB: 10 pulmonary and 7 extrapulmonary specimens. Overall sensitivity and specificity of TB-LAMP was 76.5% (95% CI 50.1%-93.2%) and 100% (95% CI 94.3%-100%), respectively. It had significantly higher sensitivity than AFB (52.9%, 95% CI 27.8%-77.0%) and similar to other molecular assays; PCR 82.4% (95% CI 56.6%-96.2%), Xpert MTB/RIF 70.0% (95% CI 34.8%-93.3%). Sensitivity of TB-LAMP for pulmonary, lymph node tissue, and extrapulmonary fluid was 80% (95% CI 44.4%-97.5%), 100% (95% CI 39.8-100), and 33.3% (95% CI 0.8-90.6), respectively. TB-LAMP detected all smear-positive (N = 9) and 50% of smear-negative (N = 8) specimens.

CONCLUSIONS

TB-LAMP had higher sensitivity than AFB microscopy and accuracy similar to other molecular assays in both pulmonary and extrapulmonary specimens. These findings support using TB-LAMP as a point-of-care test in children.

Evaluation of TB-LAMP assay for detection of Mycobacterium tuberculosis in children

BACKGROUND

Paediatric tuberculosis remains a major public health problem in developing countries. The diagnosis of tuberculosis in children is challenging because of the paucibacillary nature of the disease, due to which more sensitive nucleic acid amplification tests are needed. In this study, we determined the accuracy of WHO endorsed TB-LAMP assay for detection of Mycobacterium tuberculosis in children.

METHODS

This was a prospective study conducted between March to July, 2018. A total of 177 samples from consecutive suspected TB children were received for microbiological diagnosis of TB. All tests for Mycobacterium tuberculosis detection were performed in parallel (smear microscopy, mycobacterial culture, Xpert MTB/RIF and TB-LAMP). The diagnostic accuracy of index test i.e. TB LAMP were determined using mycobacterial culture as a reference standard.

RESULTS

Of the 177 samples, 2 (1.1%) were excluded from the study. Among 175 samples, TB-LAMP and Xpert MTB/RIF were positive in 27 (15.4%) and 25 (14.3%) samples, respectively. The sensitivity of both Xpert MTB/RIF and TB-LAMP was same, i.e. 84% (95%CI: 63.9-95.5%), when culture was considered as the reference standard. The specificity, positive predictive value and negative predictive value of TB-LAMP assay was 96% (95%CI: 91.5-98.5%), 77.8% (95%CI: 61.1-88.6%) and 97.3% (95%CI: 93.6-98.9%), respectively.

CONCLUSION

For the detection of M. tuberculosis in paediatric samples, TB-LAMP showed a sensitivity and specificity comparable to Xpert MTB/RIF.

Multi-targeted loop mediated amplification PCR for diagnosis of extrapulmonary tuberculosis

AIMS

The present study was conceived to evaluate multi-targeted loop mediated amplification (MLAMP) for the rapid diagnosis of extrapulmonary tuberculosis (EPTB).

METHODS AND RESULTS

A total of 700 patients were included who were classified into 2 groups: Group 1 (n = 400) included a 100 culture confirmed EPTB patients and 300 culture negative, suspected EPTB patients. Group 2 (n = 300) included negative controls from non-tubercular patients. All samples were subjected to Ziehl-Neelsen microscopy, solid culture on Lowenstein Jensen media, Polymerase chain reaction (PCR) targeting IS6110 gene and LAMP targeting both IS6110 and MPB64 individually and as MLAMP. The overall sensitivity of microscopy, culture, IS6110 PCR, IS6110 LAMP, MPB64 LAMP and the MLAMP assay were 12%, 25%, 72.5%, 80% and 86.6% respectively and the specificity of all the tests was 100%.

CONCLUSION

MLAMP is a rapid robust tool for the diagnosis of EPTB and utilizing two targets for M. tuberculosis can improve the overall sensitivity and increase the yield of detection from extrapulmonary samples. The rapidity, ease of performance and low cost make MLAMP an excellent alternative in low-income, resource limited settings.

Magnetic bead flocculation test: Improving the diagnosis of tuberculous meningitis (TBM) in low-resource settings

BACKGROUND

Despite several recent advances in detection techniques, there is still an unmet need for simple tests for the diagnosis of tuberculous meningitis (TBM). Therefore, in an effort towards developing a simple and rapid diagnostic test for resource-poor settings, we designed an assay in which magnetic bead flocculation test (MBF) was used to detect the amplified DNA. Multi-targeted (using two multicopy gene targets IS6110 and IS1081) loop-mediated isothermal amplification (MLAMP) was used for amplification.

METHODS

MLAMP-MBF assay was performed on CSF samples of 600 patients, out of which 120 were definite TBM (culture confirmed), 280 were probable TBM and 200 were non-TB controls, based on Marais's criteria. The performance of assay was evaluated by comparing the result of definite TBM with culture and that of probable TBM with composite reference standard consisting of clinical, microbiological(smear/culture) and radiological parameters.

RESULTS

The overall sensitivity of MLAMP-MBF (using any of the two gene targets) was 89.5% and specificity was 100%. The sensitivity was 96.6% (116/120) in diagnosing definite TBM and 86.4% (242/280) in diagnosing probable TBM. The sensitivity of IS1081 was 88% and that of IS6110 was 83% in diagnosing TBM. Specificity of both the gene targets was 100%. There were 20 cases positive only by IS1081 LAMP and 6 cases positive only by IS6110; thus 26 of 400 (6.5%) TBM cases could be additionally detected following multi-targeted approach.

CONCLUSION

MLAMP-MBF is a sensitive, robust, cost-effective and promising technique for diagnosis of TBM in low-resource high-endemic settings.