The Potential Role of Clinical Metagenomics in Infectious Diseases: Therapeutic Perspectives

Abstract

Clinical metagenomics (CMg) is the process of sequencing nucleic acid of clinical samples to obtain clinically relevant information such as the identification of microorganisms and their susceptibility to antimicrobials. Over the last decades, sequencing and bioinformatic solutions supporting CMg have much evolved and an increasing number of case reports and series covering various infectious diseases have been published. Metagenomics is a new approach to infectious disease diagnosis that is currently being developed and is certainly one of the most promising for the coming years. However, most CMg studies are retrospective, and few address the potential impact CMg could have on patient management, including initiation, adaptation, or cessation of antimicrobials. In this narrative review, we have discussed the potential role of CMg in bacteriology, virology, mycology, and parasitology. Several reports and case-series confirm that CMg is an innovative tool with which one can (i) identify more microorganisms than with conventional methods in a single test, (ii) obtain results within hours, and (iii) tailor the antimicrobial regimen of patients. However, the cost-efficiency of CMg and its real impact on patient management are still to be determined.

Fig. 1

Schematic representation of an example of a clinical metagenomics bioinformatics pipeline from reads processing to clinical reporting. NTC no template control, RPKM reads per kilobase million, RPM reads per million (created with BioRender.com)

Fig. 2

Summary of the potential impact of clinical metagenomics (created with BioRender.com)