ena-STUDY-King Fahd Medical Research Centre-29-05-2020-14:17:46:781-241
Single Clinical Metagenomics Assay Targeting ?Microbes from Different Taxa Based on a ?Comparative Study of Extraction Methods
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.
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.