@article{24c1f5ebbdb745479533332f00cad38b,
title = "Understanding the promises and hurdles of metagenomic next-generation sequencing as a diagnostic tool for infectious diseases",
abstract = "Agnostic metagenomic next-generation sequencing (mNGS) has emerged as a promising single, universal pathogen detection method for infectious disease diagnostics. This methodology allows for identification and genomic characterization of bacteria, fungi, parasites, and viruses without the need for a priori knowledge of a specific pathogen directly from clinical specimens. Although there are increasing reports of mNGS successes, several hurdles need to be addressed, such as differentiation of colonization from infection, extraneous sources of nucleic acid, method standardization, and data storage, protection, analysis, and interpretation. As more commercial and clinical microbiology laboratories develop mNGS assays, it is important for treating practitioners to understand both the power and limitations of this method as a diagnostic tool for infectious diseases.",
keywords = "Bioinformatics, Diagnosis, Metagenomics, Next-generation sequencing",
author = "Simner, {Patricia J.} and Steven Miller and Carroll, {Karen C.}",
note = "Funding Information: Diagnostics, Curetis, BD Diagnostics, and GenePOC; personal fees from Roche Molecular, McGraw-Hill, American Society for Microbiology, and Elsevier. P. J. S. reports grants from Accelerate Diagnostics, BD Diagnostics, bioM{\'e}rieux, Cellex, Check-Points Diagnostics, BV, and Hardy Diagnostics; and personal fees from the American Society for Microbiology and Accelerate Diagnostics. S. M. has a patent for the SURPI pipeline issued to UCSF, a patent for microbial standard reference materials for pathogen detection pending to UCSF, and a patent for historic contaminant database for mNGS applications pending to UCSF. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed. Publisher Copyright: {\textcopyright} The Author(s) 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved.",
year = "2018",
month = mar,
doi = "10.1093/cid/cix881",
language = "English (US)",
volume = "66",
pages = "778--788",
journal = "Clinical Infectious Diseases",
issn = "1058-4838",
publisher = "Oxford University Press",
number = "5",
}