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

Baikunje, Nandakishore; Behera, Digambar; Rajwanshi, Arwind; Sharma, Megha; Sharma, Aman; Sharma, Kusum

doi:10.1016/j.mcp.2019.101459

Cited by 9 publications

(3 citation statements)

References 23 publications

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“…Loop-mediated isothermal amplification (LAMP) stands out as a simpler yet powerful alternative to PCR of exceptional specificity since it employs 4–6 primers which recognize 6–8 different regions in the target sequence 7 . LAMP can be performed at a constant temperature (60–65 °C) eliminating the need for thermal cycling 8 , 9 , is faster 10 , 11 and less affected by inhibitors commonly present in biological samples 12 , 13 . LAMP amplification can be monitored in real-time primarily through fluorescence or turbidimetry providing quantitative information 14 – 16 .…”

Section: Introductionmentioning

confidence: 99%

Portable real-time colorimetric LAMP-device for rapid quantitative detection of nucleic acids in crude samples

Papadakis

Pantazis

Fikas

et al. 2022

Sci Rep

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Loop-mediated isothermal amplification is known for its high sensitivity, specificity and tolerance to inhibiting-substances. In this work, we developed a device for performing real-time colorimetric LAMP combining the accuracy of lab-based quantitative analysis with the simplicity of point-of-care testing. The device innovation lies on the use of a plastic tube anchored vertically on a hot surface while the side walls are exposed to a mini camera able to take snapshots of the colour change in real time during LAMP amplification. Competitive features are the rapid analysis (< 30 min), quantification over 9 log-units, crude sample-compatibility (saliva, tissue, swabs), low detection limit (< 5 copies/reaction), smartphone-operation, fast prototyping (3D-printing) and ability to select the dye of interest (Phenol red, HNB). The device’s clinical utility is demonstrated in cancer mutations-analysis during the detection of 0.01% of BRAF-V600E-to-wild-type molecules from tissue samples and COVID-19 testing with 97% (Ct < 36.8) and 98% (Ct < 30) sensitivity when using extracted RNA and nasopharyngeal-swabs, respectively. The device high technology-readiness-level makes it a suitable platform for performing any colorimetric LAMP assay; moreover, its simple and inexpensive fabrication holds promise for fast deployment and application in global diagnostics.

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Section: Introductionmentioning

confidence: 99%

Portable real-time colorimetric LAMP-device for rapid quantitative detection of nucleic acids in crude samples

Papadakis

Pantazis

Fikas

et al. 2022

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Loop-mediated isothermal amplification (LAMP) stands out as a simpler yet powerful alternative to PCR of exceptional specificity in the case of sequence-specific amplification since it employs 4 to 6 primers which recognize 6 to 8 different regions in the target sequence 7 . LAMP can be performed at a constant temperature (60-65 o C) eliminating the need for thermal cycling 8,9 , is faster 10,11 and less affected by inhibitors commonly present in biological samples 12,13 . LAMP amplification can be monitored in real-time primarily through fluorescence or turbidimetry providing quantitative information [14][15][16] .…”

mentioning

confidence: 99%

Portable real-time colorimetric LAMP-device for rapid quantitative detection of nucleic acids in crude samples

Papadakis

Pantazis

Fikas

et al. 2020

Preprint

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Most methods applied to nucleic acids’ detection at the point-of-care require either expensive and mostly bench-top instruments or simpler inexpensive systems providing qualitative results. Truly decentralized approaches to reliable, quantitative and affordable diagnostics are still missing. Here, we report the development of real-time quantitative colorimetric LAMP based on a portable and cost-effective device, the use of which requires minimal training. Main advantages of the method are the rapid analysis time (<30min); quantification over a large dynamic range (9 log units); ability to work with crude samples (saliva, tissue); demonstrated low detection limit (1-10 copies); smartphone-operation and fast prototyping (3D-printing). The system’s broad detection capability is demonstrated during infectious diseases-testing for COVID-19 and pharmacogenetics for BRAF V600E mutation testing. Validation studies showed 97.4% and 100% agreement with qRT-PCR for SARS-CoV-2 RNA detection extracted from positive and negative patients’ samples (89), respectively; and 100% agreement with ddPCR and Sanger sequencing for BRAF V600E mutation detection from 12 clinical biopsy samples. The new methodology provides a needed solution for affordable healthcare at the point-of-care, with emphasis on global diagnostics.

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“…On the other hand, studies using LAMP without Au-Np as a diagnostic tool are abundant and show the applicability of LAMP in different countries of different conditions. In several multicenter studies, LAMP is applicable in China [42,61,63,66,83,86], India [74,77,84,87], Sri Lanka [79], Nepal [85], Thailand [12,15,72,88], Vietnam [70,76], Indonesia [90], Malawi [71], South Africa [76,78], Ethiopia [75], Gambia [80], Zambia [73], Uganda [82,84], Peru [76,84], Brazil [76], Japan [68,89], and Korea [81]. Most studies about LAMP were carried out in developing countries that aim to solve the diagnostic problem of TB in burdened countries.…”

Section: Crs and Culture As Referencementioning

confidence: 99%

Combining LAMP and Au-Nanoprobe to detect INH-RIF resistance accurately in tuberculosis: an evidence-based review

Habiburrahman

Ariq

Handayani

2021

J Infect Dev Ctries

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Approximately 1.41 million people die annually due to tuberculosis. One of the main problems in Tuberculosis eradication is the development of resistance to various antibiotics. However, current efforts to detect resistances face challenges such as limited equipment, budget, and time. This evidence-based review investigated loop-mediated isothermal amplification, an alternative molecular diagnostic tool with promising performance and applicability in developing countries, and its use combined with Au-Nanoprobe to detect antibiotic resistance in tuberculosis. The literature search was conducted through four databases (Proquest, EBSCOhost, Scopus, and Pubmed) for useful articles on loop-mediated isothermal amplification and Au-Nanoprobe in detecting tuberculosis and tuberculosis resistance. After filtering the result with inclusion and exclusion criteria, the search produced three papers that best answer the clinical question. Loop-mediated isothermal amplification amplifies a target sequence, and Au-Nanoprobe responds to the DNA specific to the target mutant, producing an observable color change. Loop-mediated isothermal amplification and Au-Nanoprobe showed 100% sensitivity and specificity in detecting rifampicin and isoniazid resistance. Another study investigated its viability to detect tuberculosis and found 98.2% sensitivity and 88.2% specificity. Combining loop-mediated isothermal amplification and Au-Nanoprobe had a shorter time to get results and should also be relatively cheaper because it does not need a high temperature to work and requires less equipment. In conclusion, loop-mediated isothermal amplification and Au-Nanoprobe can be used as an efficient and accurate method to detect isoniazid and rifampicin-resistant tuberculosis strains. The new technology is promising for developing countries due to their high disease burden but facing several healthcare barriers.

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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

Cited by 9 publications

References 23 publications

Portable real-time colorimetric LAMP-device for rapid quantitative detection of nucleic acids in crude samples

Portable real-time colorimetric LAMP-device for rapid quantitative detection of nucleic acids in crude samples

Portable real-time colorimetric LAMP-device for rapid quantitative detection of nucleic acids in crude samples

Combining LAMP and Au-Nanoprobe to detect INH-RIF resistance accurately in tuberculosis: an evidence-based review

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