Overview of microbial NGS for clinical and public health microbiology

Next-generation sequencing (NGS) has revolutionised the way we perform clinical and public health microbiology. This technology combined with the bioinformatics research field has led to a deeper understanding of the mechanisms involved in the pathogenesis of clinical infections, antimicrobial-resistant determination and dissemination of microorganisms inside the hospital, in the community, in animals and the environment. New approaches, like machine-learning methods, will even further potentiate the understanding of the information that is generated through NGS. In this book chapter, we aim to show the possibilities for NGS, including whole-genome sequencing (WGS) and metagenomics, in the fields of clinical and public health microbiology and speculate on its future importance.