Metagenome of human blood from a patient with acute liver failure
The serum sample was first treated with a cocktail of Turbo DNase (Ambion) and Baseline-ZERO DNase (Epicentre) prior to nucleic acid extraction. Nucleic acid extraction was performed on the Qiagen EZ1 Advanced XL automated system using the EZ1 Virus Mini Kit v2.0 (Qiagen). Extracted nucleic acid was amplified with random hexamers to generate a cDNA library as previously described (Lee, et al. 2012, PloS One). NGS libraries were generated using the NexteraXT protocol (Illumina) and sequenced on the Illumina HiSeq. The sequencing reads were analyzed using SURPI ("sequence-based ultra-rapid pathogen identification"), a computational pipeline for comprehensive pathogen identification from metagenomic NGS data by comparison to microbial sequences in the National Center for Biotechnology Information (NCBI) NT database (Naccache, et al., 2014, Genome Research).