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Microbial Typing by Machine Learned DNA Melt Signatures

There is still an ongoing demand for a simple broad-spectrum molecular diagnostic assay for pathogenic bacteria. For this purpose, we developed a single-plex High Resolution Melt (HRM) assay that generates complex melt curves for bacterial identification. Using internal transcribed spacer (ITS) regi...

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Detalles Bibliográficos
Autores principales: Andini, Nadya, Wang, Bo, Athamanolap, Pornpat, Hardick, Justin, Masek, Billie J., Thair, Simone, Hu, Anne, Avornu, Gideon, Peterson, Stephen, Cogill, Steven, Rothman, Richard E., Carroll, Karen C., Gaydos, Charlotte A., Wang, Jeff Tza-Huei, Batzoglou, Serafim, Yang, Samuel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5292719/
https://www.ncbi.nlm.nih.gov/pubmed/28165067
http://dx.doi.org/10.1038/srep42097
Descripción
Sumario:There is still an ongoing demand for a simple broad-spectrum molecular diagnostic assay for pathogenic bacteria. For this purpose, we developed a single-plex High Resolution Melt (HRM) assay that generates complex melt curves for bacterial identification. Using internal transcribed spacer (ITS) region as the phylogenetic marker for HRM, we observed complex melt curve signatures as compared to 16S rDNA amplicons with enhanced interspecies discrimination. We also developed a novel Naïve Bayes curve classification algorithm with statistical interpretation and achieved 95% accuracy in differentiating 89 bacterial species in our library using leave-one-out cross-validation. Pilot clinical validation of our method correctly identified the etiologic organisms at the species-level in 59 culture-positive mono-bacterial blood culture samples with 90% accuracy. Our findings suggest that broad bacterial sequences may be simply, reliably and automatically profiled by ITS HRM assay for clinical adoption.