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Just as microscopy opened up the worlds of microbiology by providing a tool with which to visualize microorganisms, technological advances in genomics are now providing microbiologists with powerful new methods with which to characterize the genetic map underlying all microbes with unprecedented resolution, thereby illuminating their complex and dynamic interactions with one another, the environment, and human health. The field of infectious disease genomics encompasses a vast frontier of active research that has the potential to transform clinical practice in relation to infectious diseases. While genetics has long played a key role in elucidating the process of infection and managing clinical infectious diseases, the ability to extend our thinking and our approaches beyond the study of single genes to an examination of the sequence, structure, and function of entire genomes is identifying new possibilities for research and opportunities to change clinical practice. From the development of diagnostics with unprecedented sensitivity, specificity, and speed to the design of novel public health interventions, technical and statistical genomic innovations are reshaping our understanding of the influence of the microbial world on human health and providing us with new tools to combat infection. This chapter explores the application of genomics methods to microbial pathogens and the infections they cause (Table 4-1). It discusses innovations that are driving the development of diagnostic approaches and the discovery of new pathogens; providing insight into novel therapeutic approaches and paradigms; and advancing methods in infectious disease epidemiology and the study of pathogen evolution that can inform infection control measures, public health responses to outbreaks, and vaccine development. We draw on examples in current practice and from the recent scientific literature as signposts that point toward the ways in which the insights from pathogen genomics may influence infectious diseases in the short and long terms. Table 4-2 provides definitions for a selection of important terms used in genomics.

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