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commonplace to sort through the genomes of dozens of strains of a single microbial species or to conduct “metagenomic” analyses of vast communities of the microbiota from a wide variety of environments. These technical advancements and concurrent investments in the fields of microbial ecology, evolution, forensics, and epidemiology have transformed our ability to use genomic sequence information to explore the origins, evolution, and catalysts associated with historical, emergent, and reemergent disease outbreaks. The ability to “read” the nucleic acid sequence of microbial genomes has provided important insights into this previously hidden, unculturable world by revealing the vast diversity and complexity of microbial life around us, and their myriad interactions with their abiotic and biotic environmental niches.

Recent examples of the use of “whole genome” sequencing to investigate outbreaks of emerging, reemerging, and novel infectious diseases illustrate the potential of these methods for enhancing disease surveillance, detection, and response efforts. Using slight sequence differences between isolates to discriminate between closely related strains, investigators have tracked the evolution of isolates in a disease outbreak, traced person-to-person transmission of a communicable disease, and identified point sources of disease outbreaks. When genomic information about related strains or past disease outbreaks is available, the genome sequence of outbreak strains has proved useful in identifying factors that may contribute to the emergence, virulence, or spread of pathogens, as well as in speeding diagnostic tool development. In a recent development, fast genome sequencing was used to halt the spread of a methicillin-resistant Staphylococcus aureus (MRSA) infection in a neonatal ward in a hospital in Cambridge, United Kingdom (Harris et al., 2012)

Statement of Task

On June 12 and 13, 2012, the Institute of Medicine’s (IOM’s) Forum on Microbial Threats convened a public workshop in Washington, DC, to discuss the scientific tools and approaches being used for detecting and characterizing microbial species, and the roles of microbial genomics and metagenomics to better understand the culturable and unculturable microbial world around us.3 Through invited presentations and discussions, participants examined the use of microbial genomics to explore the diversity, evolution, and adaptation of microorganisms in

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3 A public workshop will be held to explore new scientific tools and methods for detecting and characterizing microbial species and for understanding the origins, nature, and spread of emerging, reemerging, and novel infectious diseases of humans, plants, domestic animals, and wildlife. Topics to be discussed may include microbial diversity, evolution, and adaptation; microbial genomic, epidemiology, and forensic tools and technologies; infectious disease detection and diagnostic platforms in clinical medicine, veterinary medicine, plant pathology, and wildlife epidemiology; development of microbial genomic and proteomic databases; and strategies for predicting, mitigating, and responding to emerging infectious diseases.



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