Evaluation of different DNA extraction methods and loop-mediated isothermal amplification primers for the detection of Mycobacterium ulcerans in clinical specimens

Autor:	Joseph Mathu Ndung'u, Isra Cruz, Dziedzom K. de Souza, Sandra A. King, Evans Ahotor, Charles A. Narh, Anthony Ablordey
Přispěvatelé:	Swiss Agency for Development and Cooperation, UBS Optimus Foundation
Jazyk:	angličtina
Rok vydání:	2021
Předmět:	Buruli ulcer DNA Bacterial Computer science Point-of-care testing Point-of-Care Systems Loop-mediated isothermal amplification Computational biology Infectious and parasitic diseases RC109-216 Sensitivity and Specificity Loop mediated isothermal amplification Sensitivity medicine Humans Buruli Ulcer DNA extraction Point of care DNA Primers biology Mycobacterium ulcerans Dna amplification biology.organism_classification medicine.disease Infectious Diseases Molecular Diagnostic Techniques DNA Transposable Elements Specificity Primer (molecular biology) Nucleic Acid Amplification Techniques Research Article
Zdroj:	BMC Infectious Diseases, Vol 21, Iss 1, Pp 1-8 (2021) Repisalud Instituto de Salud Carlos III (ISCIII) BMC Infectious Diseases
ISSN:	1471-2334
Popis:	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.
Databáze:	OpenAIRE
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