Christoffel J Opperman, Salim Ben Amor, Greshan Kisten, Brendon C Mann, Janré Steyn, Sarishna Singh, Yonas Ghebrekristos, Robin Warren, Wynand Goosen
{"title":"鸟分枝杆菌DNA提取：NTM鉴定和扩增子测序的意义。","authors":"Christoffel J Opperman, Salim Ben Amor, Greshan Kisten, Brendon C Mann, Janré Steyn, Sarishna Singh, Yonas Ghebrekristos, Robin Warren, Wynand Goosen","doi":"10.4102/sajid.v40i1.717","DOIUrl":null,"url":null,"abstract":"<p><p>This study evaluated six DNA (Deoxyribonucleic acid) extraction methods for <i>Mycobacterium avium</i>, focusing on cost, procedure time, yield, quality, DNA integrity, and suitability for amplicon-based sequencing. The extracted DNA was used in the GenoType<sup>®</sup> Mycobacterium Common Mycobacterium (CM) line probe assay (LPA), which is routinely used for nontuberculous mycobacteria (NTM) identification in South Africa.</p><p><strong>Contribution: </strong>The findings demonstrate that the currently used DNA extraction method, GenoLyse<sup>®</sup> Version 1.0, remains the fastest, simplest, and most cost-effective approach for routine NTM identification, despite lower DNA yields. GenoLyse also shows potential for implementation in amplicon-based sequencing of NTM, specifically when amplifying the 16S rRNA gene.</p>","PeriodicalId":44007,"journal":{"name":"Southern African Journal of Infectious Diseases","volume":"40 1","pages":"717"},"PeriodicalIF":1.4000,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12135763/pdf/","citationCount":"0","resultStr":"{\"title\":\"<i>Mycobacterium avium</i> DNA extraction: Implications for NTM identification and amplicon sequencing.\",\"authors\":\"Christoffel J Opperman, Salim Ben Amor, Greshan Kisten, Brendon C Mann, Janré Steyn, Sarishna Singh, Yonas Ghebrekristos, Robin Warren, Wynand Goosen\",\"doi\":\"10.4102/sajid.v40i1.717\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>This study evaluated six DNA (Deoxyribonucleic acid) extraction methods for <i>Mycobacterium avium</i>, focusing on cost, procedure time, yield, quality, DNA integrity, and suitability for amplicon-based sequencing. The extracted DNA was used in the GenoType<sup>®</sup> Mycobacterium Common Mycobacterium (CM) line probe assay (LPA), which is routinely used for nontuberculous mycobacteria (NTM) identification in South Africa.</p><p><strong>Contribution: </strong>The findings demonstrate that the currently used DNA extraction method, GenoLyse<sup>®</sup> Version 1.0, remains the fastest, simplest, and most cost-effective approach for routine NTM identification, despite lower DNA yields. GenoLyse also shows potential for implementation in amplicon-based sequencing of NTM, specifically when amplifying the 16S rRNA gene.</p>\",\"PeriodicalId\":44007,\"journal\":{\"name\":\"Southern African Journal of Infectious Diseases\",\"volume\":\"40 1\",\"pages\":\"717\"},\"PeriodicalIF\":1.4000,\"publicationDate\":\"2025-05-27\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12135763/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Southern African Journal of Infectious Diseases\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.4102/sajid.v40i1.717\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2025/1/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"Q4\",\"JCRName\":\"INFECTIOUS DISEASES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Southern African Journal of Infectious Diseases","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.4102/sajid.v40i1.717","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/1/1 0:00:00","PubModel":"eCollection","JCR":"Q4","JCRName":"INFECTIOUS DISEASES","Score":null,"Total":0}
Mycobacterium avium DNA extraction: Implications for NTM identification and amplicon sequencing.
This study evaluated six DNA (Deoxyribonucleic acid) extraction methods for Mycobacterium avium, focusing on cost, procedure time, yield, quality, DNA integrity, and suitability for amplicon-based sequencing. The extracted DNA was used in the GenoType® Mycobacterium Common Mycobacterium (CM) line probe assay (LPA), which is routinely used for nontuberculous mycobacteria (NTM) identification in South Africa.
Contribution: The findings demonstrate that the currently used DNA extraction method, GenoLyse® Version 1.0, remains the fastest, simplest, and most cost-effective approach for routine NTM identification, despite lower DNA yields. GenoLyse also shows potential for implementation in amplicon-based sequencing of NTM, specifically when amplifying the 16S rRNA gene.
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