Various “omics” methods have recently revolutionized molecular diagnostics. Next-generation sequencing (NGS) makes it possible to sequence a human genome in just one day. Whole genome sequencing (WGS) greatly improves the ability to investigate the outbreaks of numerous pathogens. Metagenomics helps to analyze the microbiome, which aids greatly in identifying the pathogenesis of infectious diseases. Proteomic-based methods, namely matrix-assisted laser desorption-ionization time of flight mass spectrometry (MALDI-TOF-MS), have a promising role in identifying myctobacteria and fungi, and predicting antimicrobial resistance. While there are numerous scientific publications on “omics” applications for microbiology, there are relatively few books that review this topic from a clinical diagnostics perspective. This book looks at this field from a holistic viewpoint, instead of limiting by type of “omics” technology, in order to cover the body of knowledge needed for practitioners and academics interested in clinical and public health microbiology. Additionally, it addresses the management, economical, regulatory and operational aspects of integrating these technologies into routine diagnostics.