Exploring next-generation sequencing in clinical microbiology: identification, characterization and typing of pathogens

    Research output: ThesisThesis fully internal (DIV)

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    Abstract

    Rapid and accurate detection of pathogens is a fundamental step in infection management and ensuring an optimum antimicrobial therapy is provided to the patient, ultimately reducing the antimicrobial resistance selection and medical costs of healthcare. Next-generation sequencing (NGS) technologies have transformed diagnostics in clinical microbiology by overcoming some of the challenges of conventional methods: culturing, relying on the growth of the pathogens, and molecular assays, limited by a restricted panel of pathogen targets at a time. NGS can provide detailed sequence information for specific genetic regions or the whole genome in a single assay. However, the
    interpretation of the sequence data requires sophisticated and robust bioinformatics pipelines to be standardized. In this thesis, we aimed at studying state-of-the-art molecular diagnostic techniques that strive for an accelerated microbial diagnosis. More specifically, we studied the application of several NGS approaches for different clinical applications and evaluated bioinformatic data analysis tools/approaches for pathogen detection,
    characterization, and typing.
    Original languageEnglish
    QualificationDoctor of Philosophy
    Awarding Institution
    • University of Groningen
    Supervisors/Advisors
    • Sinha, Bhanu, Supervisor
    • Rossen, John, Supervisor
    • Monge Gomes do Couto, Natacha, Co-supervisor
    Award date23-May-2022
    Place of Publication[Groningen]
    Publisher
    DOIs
    Publication statusPublished - 2022

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