Single Clinical Metagenomics Assay Targeting ‎Microbes from Different Taxa Based on a ‎Comparative Study of Extraction Methods. Establishment of Next-Generation Sequencing ‎Assay as a Diagnostic Tool for Infectious ‎Diseases ‎

Clinical metagenomics is a promising field that helps to find etiological agents in cases of ‎unidentified infections. For efficient detection of an unknown pathogen, a careful choice of the ‎extraction method is needed for the maximum recovery of nucleic acid from different ‎microorganisms. The aim of this study was to choose and optimize an extraction assay that had the ‎ability to isolate nucleic acids from different types of pathogens with good quality and quantity ‎followed with a single protocol for efficient use in clinical metagenomic identification. A mock ‎sample consisting of Cryptococcus neoformans‎, Staphylococcus aureus‎‎, Klebsiella pneumoniae‏,‏‎ ‎Adenovirus and Alkhumrah virus was prepared for the comparison of different commercial ‎extraction kits targeting DNA and/or RNA. The extracted nucleic acids were used in RNA-Seq ‎and/or DNA-Seq library preparation and run on the MiSeq platform. The generated data were ‎analyzed to extract the number of reads and the percent coverage of the pathogen genomes ‎included in the mock sample.