The implementation of 16S-23S Next Generation Sequencing (NGS) for the detection of pathogens in clinical samples is an emerging area in clinical diagnostics. Certe and the UMCG have developed a novel, culture independent, method that detects and identifies bacterial species directly from clinical samples by targeted NGS of the 16S-23S rDNA region.
A barrier is the ratio of eukaryote to pathogen DNA isolated from samples with a low pathogen load. DNA extraction methods that feature selective lysis of eukaryote cells and subsequent degradation of the released eukaryote DNA followed by isolation of purified microbial DNA could improve the sensitivity of 16S-23S rDNA NGS.
We compared the MolYsis SelectNA plus DNA extraction kit (Molzym) and QIAamp DNA Microbiome DNA extraction kit (Qiagen), both featuring eukaryote DNA depletion, with the Purelink Genomic DNA mini kit (Invitrogen) which extracts total DNA, for sensitivity and depletion of eukaryote DNA using 16S-23S rDNA NGS.
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