Metagenomics for Clinical Infectious Disease Diagnostics Steps Closer to Reality

Metagenomics approaches based on shotgun next-generation sequencing hold promise for infectious disease diagnostics. Despite substantial challenges that remain, work done over the past few years justifies excitement about the potential for these approaches to transform how clinical pathogen identification and analysis are performed. In an article in this issue of the Journal of Clinical Microbiology, M. I. Ivy et al. (J Clin Microbiol 56:e00402-18, 2018, https://doi.org/10.1128/JCM.00402-18) have applied a shotgun metagenomics approach to the diagnosis of prosthetic joint infections directly from synovial fluid. The results from this work demonstrate both the potentials and challenges of this approach applied in the clinical microbiology laboratory.