Evaluation of different DNA extraction methods and loop-mediated isothermal amplification primers for the detection of Mycobacterium ulcerans in clinical specimens
Abstract Background Early diagnosis and treatment of Buruli ulcer is critical in order to avoid the debilitating effects of the disease. In this regard, the development of new diagnostic and point of care tools is encouraged. The loop-mediated isothermal amplification for the detection of Mycobacter...
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| Format: | Article |
| Language: | English |
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BMC
2021-06-01
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| Series: | BMC Infectious Diseases |
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| Online Access: | https://doi.org/10.1186/s12879-021-06308-z |
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| author | Anthony Ablordey Evans Ahotor Charles A. Narh Sandra A. King Isra Cruz Joseph M. Ndung’u Dziedzom K. de Souza |
| author_facet | Anthony Ablordey Evans Ahotor Charles A. Narh Sandra A. King Isra Cruz Joseph M. Ndung’u Dziedzom K. de Souza |
| author_sort | Anthony Ablordey |
| collection | DOAJ |
| description | Abstract Background Early diagnosis and treatment of Buruli ulcer is critical in order to avoid the debilitating effects of the disease. In this regard, the development of new diagnostic and point of care tools is encouraged. The loop-mediated isothermal amplification for the detection of Mycobacterium ulcerans represents one of the new tools with a good potential of being developed into a point of care test. There is however the need to standardize the assays, reduce sample preparation times, improve the detection/visualization system and optimize them for high-throughput screening, adaptable to low resourced laboratories. Methods In this study, we assessed two DNA extraction protocols (modified Boom and EasyNAT methods), three previously published LAMP primer sets (BURULI, MU 2404 and BU-LAMP), and compared the sensitivity and specificity of LAMP assays on three DNA amplification platforms. Results Our results show that Buruli ulcer diagnosis using primers targeting IS2404 for the LAMP method is sensitive (73.75–91.49%), depending on the DNA extraction method used. Even though the modified Boom DNA extraction method provided the best results, its instrumentation requirement prevent it from being field applicable. The EasyNAT method on the other hand is simpler and may represent the best method for DNA extraction in less resourced settings. Conclusions For further work on the development and use of LAMP tests for Buruli diagnosis, it is recommended that the BURULI sets of primers be used, as these yielded the best results in terms of sensitivity (87.50–91.49%) and specificity (89.23–100%), depending on the DNA extraction methods used. |
| first_indexed | 2024-12-19T06:18:16Z |
| format | Article |
| id | doaj.art-ac99e4c328d54ae5966da14d738b94af |
| institution | Directory Open Access Journal |
| issn | 1471-2334 |
| language | English |
| last_indexed | 2024-12-19T06:18:16Z |
| publishDate | 2021-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Infectious Diseases |
| spelling | doaj.art-ac99e4c328d54ae5966da14d738b94af2022-12-21T20:32:47ZengBMCBMC Infectious Diseases1471-23342021-06-012111810.1186/s12879-021-06308-zEvaluation of different DNA extraction methods and loop-mediated isothermal amplification primers for the detection of Mycobacterium ulcerans in clinical specimensAnthony Ablordey0Evans Ahotor1Charles A. Narh2Sandra A. King3Isra Cruz4Joseph M. Ndung’u5Dziedzom K. de Souza6Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of GhanaNoguchi Memorial Institute for Medical Research, College of Health Sciences, University of GhanaNoguchi Memorial Institute for Medical Research, College of Health Sciences, University of GhanaNoguchi Memorial Institute for Medical Research, College of Health Sciences, University of GhanaFoundation for Innovative New DiagnosticsFoundation for Innovative New DiagnosticsNoguchi Memorial Institute for Medical Research, College of Health Sciences, University of GhanaAbstract Background Early diagnosis and treatment of Buruli ulcer is critical in order to avoid the debilitating effects of the disease. In this regard, the development of new diagnostic and point of care tools is encouraged. The loop-mediated isothermal amplification for the detection of Mycobacterium ulcerans represents one of the new tools with a good potential of being developed into a point of care test. There is however the need to standardize the assays, reduce sample preparation times, improve the detection/visualization system and optimize them for high-throughput screening, adaptable to low resourced laboratories. Methods In this study, we assessed two DNA extraction protocols (modified Boom and EasyNAT methods), three previously published LAMP primer sets (BURULI, MU 2404 and BU-LAMP), and compared the sensitivity and specificity of LAMP assays on three DNA amplification platforms. Results Our results show that Buruli ulcer diagnosis using primers targeting IS2404 for the LAMP method is sensitive (73.75–91.49%), depending on the DNA extraction method used. Even though the modified Boom DNA extraction method provided the best results, its instrumentation requirement prevent it from being field applicable. The EasyNAT method on the other hand is simpler and may represent the best method for DNA extraction in less resourced settings. Conclusions For further work on the development and use of LAMP tests for Buruli diagnosis, it is recommended that the BURULI sets of primers be used, as these yielded the best results in terms of sensitivity (87.50–91.49%) and specificity (89.23–100%), depending on the DNA extraction methods used.https://doi.org/10.1186/s12879-021-06308-zLoop mediated isothermal amplificationDNA extractionSensitivitySpecificity |
| spellingShingle | Anthony Ablordey Evans Ahotor Charles A. Narh Sandra A. King Isra Cruz Joseph M. Ndung’u Dziedzom K. de Souza Evaluation of different DNA extraction methods and loop-mediated isothermal amplification primers for the detection of Mycobacterium ulcerans in clinical specimens BMC Infectious Diseases Loop mediated isothermal amplification DNA extraction Sensitivity Specificity |
| title | Evaluation of different DNA extraction methods and loop-mediated isothermal amplification primers for the detection of Mycobacterium ulcerans in clinical specimens |
| title_full | Evaluation of different DNA extraction methods and loop-mediated isothermal amplification primers for the detection of Mycobacterium ulcerans in clinical specimens |
| title_fullStr | Evaluation of different DNA extraction methods and loop-mediated isothermal amplification primers for the detection of Mycobacterium ulcerans in clinical specimens |
| title_full_unstemmed | Evaluation of different DNA extraction methods and loop-mediated isothermal amplification primers for the detection of Mycobacterium ulcerans in clinical specimens |
| title_short | Evaluation of different DNA extraction methods and loop-mediated isothermal amplification primers for the detection of Mycobacterium ulcerans in clinical specimens |
| title_sort | evaluation of different dna extraction methods and loop mediated isothermal amplification primers for the detection of mycobacterium ulcerans in clinical specimens |
| topic | Loop mediated isothermal amplification DNA extraction Sensitivity Specificity |
| url | https://doi.org/10.1186/s12879-021-06308-z |
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