Abstract
Metagenomic next-generation sequencing (mNGS) has the theoretical capacity to detect any microbe present in a host. mNGS also has the potential to infer a pathogen's phenotypic characteristics, including the ability to colonize humans, cause disease, and resist treatment. Concurrent host nucleic acid sequencing can assess the infected individual's physiological state, including characterization and appropriateness of the immune response. When the pathogen cannot be identified, host RNA sequencing may help infer the organism's nature. While the full promise of mNGS remains far from realization, the potential ability to identify all microbes in a complex clinical sample, assess each organism's virulence and antibiotic susceptibility traits, and simultaneously characterize the host's response to infection provide opportunities for mNGS to supplant existing technologies and become the primary method of infectious diseases diagnostics.
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