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Mycobacterium avium DNA extraction: Implications for NTM identification and amplicon sequencing

Article scientifique 2025 Anglais

Résumé

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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Opperman, C., Amor, S., Kisten, G., Mann, B., Steyn, J., Singh, S., Ghebrekristos, Y., Warren, R., Goosen, W. (2025). Mycobacterium avium DNA extraction: Implications for NTM identification and amplicon sequencing. https://doi.org/10.4102/sajid.v40i1.717

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Auteur(s)

Christoffel J. Opperman Salim Ben Amor Greshan Kisten Brendon C. Mann Janré Steyn Sarishna Singh Yonas Ghebrekristos Robin M. Warren Wynand J. Goosen

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