Integrating Metagenomics in the Routine Lab

Clinical metagenomics (CMg), based on whole-genome sequencing of clinical samples, offers the potential to directly detect all microorganisms present in a sample. This approach could, therefore, provide potential unbiased detection of all microorganisms present in the sample, including those organisms that are fastidious or even cannot be cultivated. It constitutes a rapid and generic approach providing all medically-actionable information: the presence or the absence of microorganisms (detection), their identification to the species level or even beyond (speciation), the detection of antimicrobial resistance determinants, with the potential to guide antibiotic therapy and virulence-associated genes.