Application of Next-Generation Sequencing in Microbiology: from Clinical Diagnostics to One Health Surveillance

Next-generation sequencing (NGS) is a process of massively parallel sequencing of nucleic acids. It can be applied to single pathogens from a pure culture to determine the whole genome but also directly to clinical, animal, and environmental samples to detect microorganisms and antimicrobial resistance markers without a priori knowledge of the target sequences. Genomic identification and characterization of microorganisms in humans and animals are about to become a game-changer for diagnosing, monitoring, and controlling infectious diseases. This thesis aimed to assess the application of culture-dependent and culture-independent NGS approaches in diagnosing and monitoring infectious diseases within and outside the hospital.