Genomic methods are rapidly emerging as the gold standard for identifying, defining, and characterizing infectious agents of all types in both public health and biodefense settings, and the use of genomic-based approaches in the area of infectious disease is changing this field in a number of ways. This proposal outlines a book that will review the ways in which genomic methods are being applied to pathogen detection and diagnostics, investigation of disease outbreaks, the characterization of infectious agents, and the promises and challenges that lie ahead in the use of genomics within the field of infectious disease. This book will serve as a reference for scientists, clinicians and public health professionals seeking an immersive introduction to genomics-based analysis in infectious diseases, and as a roadmap for future research and development efforts in this area.