Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens.

ABSTRACT: High throughput sequencing has been proposed as a one-stop solution for diagnostics and molecular typing directly from patient samples, allowing timely and appropriate implementation of measures for treatment, infection prevention and control. However, it is unclear how the variety of available methods impacts the end results. We applied shotgun metagenomics on diverse types of patient samples using three different methods to deplete human DNA prior to DNA extraction. Libraries were prepared and sequenced with Illumina chemistry. Data was analyzed using methods likely to be available in clinical microbiology laboratories using genomics. The results of microbial identification were compared to standard culture-based microbiological methods. On average, 75% of the reads corresponded to human

SUBMITTER: Couto N 

PROVIDER: S-EPMC6137123 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature