Metagenomics and Whole Genome Sequencing in Clinical Microbiology: A Narrative Review

The role of Whole Genome Sequencing (WGS) in clinical microbiology is increasing and is not restricted to molecular epidemiology alone. With the advent of third-generation sequencing technologies, its applications in infectious disease diagnostics have further expanded to include the direct identification of microorganisms from primary clinical samples, prediction of antimicrobial resistance (including antiviral resistance) by detecting resistance genes, and detection of virulence genes. Untargeted metagenomic sequencing of clinical samples can provide a promising platform for the comprehensive diagnosis of infections. This article outlines the applications and scope of WGS and metagenomic sequencing in routine clinical microbiology, along with the challenges and practical issues in their implementation.