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WGS for Bacterial Identification and Susceptibility Testing in the Clinical Lab

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

Abstract

Two decades after the first bacterial genome sequencing by Fleischmann et al. in 1995, bacterial genomics gained an important role both in the identification and antimicrobial susceptibility testing of bacterial pathogens. Continuous advances in high throughput sequencing (Next Generation Sequencing, NGS) technologies have empowered today’s clinical microbiology laboratory with vast potential in pathogen detection, identification and characterisation. Bacterial whole-genome sequencing (WGS) is the most promising aspect of these technologies. Most clinical microbiology laboratories are not currently ready to adopt and implement WGS in their routine, mostly because of costs, time to results and data interpretation issues and it is currently applied in specific niches, such as molecular epidemiology and outbreak investigations, as well as identification and susceptibility testing of difficult-to-grow yet clinically important pathogens, such as Mycobacterium tuberculosis. In this chapter, the application of WGS in the routine clinical microbiology laboratories for identification and susceptibility testing of common and fastidious bacteria will be discussed with specific emphasis on mycobacteria as an example of utilisation of NGS technologies on clinically important slow-growing pathogens.

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Authors and Affiliations

  1. Laboratory of Clinical Microbiology, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece

    Sophia Vourli, Fanourios Kontos & Spyridon Pournaras

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  1. Sophia Vourli
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  2. Fanourios Kontos
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  3. Spyridon Pournaras
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Correspondence to Sophia Vourli or Spyridon Pournaras .

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  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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Vourli, S., Kontos, F., Pournaras, S. (2021). WGS for Bacterial Identification and Susceptibility Testing in the Clinical 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_3

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