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Integrating Metagenomics in the Routine Lab

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Application and Integration of Omics-powered Diagnostics in Clinical and Public Health Microbiology

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Abstract

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.

This chapter aims at describing current common hurdles encountered when attempting to utilise CMg to clinical samples (such as sample preparation and wet lab issues and bioinformatic challenges) and discuss ways to overcome them. We will also review the current experience with using CMg in clinical samples from different anatomical sites.

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Authors and Affiliations

  1. Laboratoire de Bactériologie, Université de Paris, Hôpital Bichat, Paris, France

    Etienne Ruppé

  2. Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland

    Yannick Charretier, Vladimir Lazarevic & Jacques Schrenzel

  3. Bacteriology Laboratory, Service of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland

    Jacques Schrenzel

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  1. Etienne Ruppé
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Correspondence to Jacques Schrenzel .

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Editors and Affiliations

  1. Ben-Gurion University of the Negev, Beer Sheva, Israel

    Jacob Moran-Gilad

  2. Ben-Gurion University of the Negev, Beer-Sheva, Israel

    Yael Yagel

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Ruppé, E., Charretier, Y., Lazarevic, V., Schrenzel, J. (2021). Integrating Metagenomics in the Routine Lab. In: Moran-Gilad, J., Yagel, Y. (eds) Application and Integration of Omics-powered Diagnostics in Clinical and Public Health Microbiology . Springer, Cham. https://doi.org/10.1007/978-3-030-62155-1_8

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