References
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. https://www.doi.org/10.1016/S0022-2836(05)80360-2
- Béland K, Dore-Nguyen M, Gagné MJ, Patey N, Brassard J, Alvarez F, Halac U. Torque Teno virus in children who underwent orthotopic liver transplantation: New insights about a common pathogen. J Infect Dis. 2014 Jan 15;209(2):247–254. https://www.doi.org/10.1093/infdis/jit423
- Blauwkamp TA, Thair S, Rosen MJ, Blair L, Lindner MS, Vilfan ID, Kawli T, Christians FC, Venkatasubrahmanyam S, Wall GD, et al. Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease. Nat Microbiol. 2019 Apr;4(4):663–674. https://www.doi.org/10.1038/s41564-018-0349-6
- Charalampous T, Kay GL, Richardson H, Aydin A, Baldan R, Jeanes C, Rae D, Grundy S, Turner DJ, Wain J, et al. Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection. Nat Biotechnol. 2019 Jul;37(7):783–792. https://www.doi.org/10.1038/s41587-019-0156-5
- Chiu CY, Miller SA. Clinical metagenomics. Nat Rev Genet. 2019 Jun;20(6):341–355. https://www.doi.org/10.1038/s41576-019-0113-7
- Grumaz S, Stevens P, Grumaz C, Decker SO, Weigand MA, Hofer S, Brenner T, von Haeseler A, Sohn K. Next-generation sequencing diagnostics of bacteremia in septic patients. Genome Med. 2016 Jul 1;8(1):73. https://www.doi.org/10.1186/s13073-016-0326-8
- Gu W, Miller S, Chiu CY. Clinical metagenomic next-generation sequencing for pathogen detection. Annu Rev Pathol. 2019 Jan 24;14:319–338. https://www.doi.org/10.1146/annurev-pathmechdis-012418-012751
- Horiba K, Kawada JI, Okuno Y, Tetsuka N, Suzuki T, Ando S, Kamiya Y, Torii Y, Yagi T, Takahashi Y, et al. Comprehensive detection of pathogens in immunocompromised children with bloodstream infections by next-generation sequencing. Sci Rep. 2018 Feb 28;8(1):3784. https://www.doi.org/10.1038/s41598-018-22133-y
- Laupland KB, Gregson DB, Zygun DA, Doig CJ, Mortis G, Church DL. Severe bloodstream infections: A population-based assessment. Crit Care Med. 2004 Apr;32(4):992–997. https://www.doi.org/10.1097/01.ccm.0000119424.31648.1e
- Long Y, Zhang Y, Gong Y, Sun R, Su L, Lin X, Shen A, Zhou J, Caiji Z, Wang X, et al. Diagnosis of sepsis with cell-free DNA by next-generation sequencing technology in ICU patients. Arch Med Res. 2016 Jul;47(5):365–371. https://www.doi.org/10.1016/j.arcmed.2016.08.004
- Miao Q, Ma Y, Wang Q, Pan J, Zhang Y, Jin W, Yao Y, Su Y, Huang Y, Wang M, et al. Microbiological diagnostic performance of metagenomic next-generation sequencing when applied to clinical practice. Clin Infect Dis. 2018 Nov 13;67(suppl_2):S231–S240. https://www.doi.org/10.1093/cid/ciy693
- Miller S, Naccache SN, Samayoa E, Messacar K, Arevalo S, Federman S, Stryke D, Pham E, Fung B, Bolosky WJ, et al. Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid. Genome Res. 2019 May;29(5):831–842. https://www.doi.org/10.1101/gr.238170.118
- Rutanga JP, Nyirahabimana T. Clinical significance of molecular diagnostic tools for bacterial bloodstream infections: A systematic review. Interdiscip Perspect Infect Dis. 2016;2016:6412085. https://www.doi.org/10.1155/2016/6412085
- Simner PJ, Miller S, Carroll KC. Understanding the promises and hurdles of metagenomic next-generation sequencing as a diagnostic tool for infectious diseases. Clin Infect Dis. 2018 Feb 10;66(5): 778–788. https://www.doi.org/10.1093/cid/cix881
- Walton AH, Muenzer JT, Rasche D, Boomer JS, Sato B, Brownstein BH, Pachot A, Brooks TL, Deych E, Shannon WD, et al. Reactivation of multiple viruses in patients with sepsis. PLoS One. 2014 Jun 11;9(2):e98819. https://www.doi.org/10.1371/journal.pone.0098819
- Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014 Mar 3; 15(3):R46. https://www.doi.org/10.1186/gb-2014-15-3-r46