The Genomics of Emerging Pathogens

Globalization and industrialization have dramatically altered the vulnerability of human and animal populations to emerging and reemerging infectious diseases while shifting both the scale and pace of disease outbreaks. Fortunately, the advent of high-throughput DNA sequencing platforms has also increased the speed with which such pathogens can be detected and characterized as part of an outbreak response effort. It is now possible to sequence the genome of a pathogen rapidly, inexpensively, and with high sensitivity, transforming the fields of diagnostics, surveillance, forensic analysis, and pathogenesis. Here, we review advances in methods for microbial discovery and characterization, as well as strategies for testing the clinical and public health significance of microbe-disease associations. Finally, we discuss how genetic data can inform our understanding of the general process of pathogen emergence.