Use of Diagnostic Metagenomics in the Clinical Microbiology Laboratory

Abstract

Next Generation Sequencing (NGS)-based assays have recently entered the realm of the clinical microbiology laboratory's capacity, providing an exciting potential for improvement in infectious disease detection and identification. There are many diagnostic applications of NGS, such as targeted or amplicon NGS and metagenomic NGS (mNGS). mNGS has received the most attention for diagnostics due to its unbiased nature and "hypothesis free" testing approach. While mNGS may have improved pathogen detection compared to conventional culture-based testing, and has shown clinically utility in some specific cases, the application of this technology is still investigational and many barriers and limitations remain to be overcome. This review will cover both the advantages and limitations of mNGS, and addresses the need for and incorporation of new technologist skillsets in the clinical microbiology laboratory to successfully implement mNGS diagnostics.