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Exploring next-generation sequencing in clinical microbiology

Identification, characterization and typing of pathogens
PhD ceremony:N. (Nilay) Peker
When:May 23, 2022
Supervisors:prof. dr. B.N.M. (Bhanu) Sinha, prof. dr. J.W.A. (John) Rossen
Co-supervisor:N. (Natacha) Monge Gomes do Couto
Where:Academy building RUG
Faculty:Medical Sciences / UMCG
Exploring next-generation sequencing in clinical microbiology

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.