[Interests of clinical metagenomic in infectious diseases]

INTERESTS OF CLINICAL METAGENOMICS IN INFECTIOUS DISEASES. Clinical metagenomics (CM) is a cutting-edge molecular biology technique that is now a valuable diagnostic tool for microbiologists. It enables the detection of all microorganisms present in a sample, without any prior assumption or bias. The CM approach can be applied to various types of samples and involves multiple steps, such as extraction, library preparation, Next Generation Sequencing, and bioinformatics analysis. CM has been implemented in the diagnosis of various conditions, including infections of the central nervous system, respiratory, digestive, ocular, skin infection, and sepsis. Moreover, CM provides a comprehensive analysis of the microbiome present in the sample, microbial transcripts, and the host response in a single analysis. However, further studies are necessary to determine its place in the diagnostic algorithm. Besides diagnosis, CM has proven useful in identifying resistance to antimicrobial treatments and in epidemiology. Although the cost of CM is still higher than conventional methods, the emergence of more affordable sequencers and commercial tests will enable its implementation in a larger number of laboratories in the future.