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NOTICE: The project that is the subject of this report was approved by the Governing Board of the National Research Council, whose members are drawn from the councils of the National Academy of Sciences, the National Academy of Engineering, and the Institute of Medicine.
Financial support for this project was provided by the U.S. Department of Health and Human Services: National Institutes of Health, National Institute of Allergy and Infectious Diseases, Centers for Disease Control and Prevention, and the Food and Drug Administration; U.S. Department of Defense, Department of the Army: Global Emerging Infections Surveillance and Response System, Medical Research and Materiel Command, and the Defense Threat Reduction Agency; U.S. Department of Veterans Affairs; U.S. Department of Homeland Security; U.S. Agency for International Development; Uniformed Services University of the Health Sciences; the Alfred P. Sloan Foundation, American Society for Microbiology; sanofi pasteur; Burroughs Wellcome Fund; GlaxoSmithKline; Infectious Diseases Society of America; and the Merck Company Foundation. The views presented in this publication do not necessarily reflect the views of the organizations or agencies that provided support for this project.
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Cover image: Derivation of genome trees from the comparative analyses of complete genomes. (2005) PLoS Computational Biology Issue Image | Vol. 1(7) December 2005. PLoS Comput Biol 1(7): ev01.i07. doi:10.1371/image.pcbi.v01.i07. Genome graphic representation completed with GenomeViz software, provided by Rohit Ghai. Fractal tree obtained with the FractalTrees X software, provided by Simon Woodside. Compiled by Edouard Yeramian.
Suggested citation: IOM (Institute of Medicine). 2013. The Science and Applications of Microbial Genomics: Workshop Summary. Washington, DC: The National Academies Press.
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The National Academy of Sciences is a private, nonprofit, self-perpetuating society of distinguished scholars engaged in scientific and engineering research, dedicated to the furtherance of science and technology and to their use for the general welfare. Upon the authority of the charter granted to it by the Congress in 1863, the Academy has a mandate that requires it to advise the federal government on scientific and technical matters. Dr. Ralph J. Cicerone is president of the National Academy of Sciences.
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The National Research Council was organized by the National Academy of Sciences in 1916 to associate the broad community of science and technology with the Academy’s purposes of furthering knowledge and advising the federal government. Functioning in accordance with general policies determined by the Academy, the Council has become the principal operating agency of both the National Academy of Sciences and the National Academy of Engineering in providing services to the government, the public, and the scientific and engineering communities. The Council is administered jointly by both Academies and the Institute of Medicine. Dr. Ralph J. Cicerone and Dr. Charles M. Vest are chair and vice chair, respectively, of the National Research Council.
PLANNING COMMITTEE FOR A WORKSHOP ON THE
SCIENCE AND APPLICATIONS OF MICROBIAL GENOMICS1
BRUCE BUDOWLE, University of North Texas Health Science Center, Fort Worth, Texas
ARTURO CASADEVALL, Albert Einstein College of Medicine, Bronx, New York
JONATHAN EISEN, University of California, Davis, California
CLAIRE FRASER, University of Maryland School of Medicine, Baltimore, Maryland
PAUL KEIM, Northern Arizona University, Flagstaff, Arizona
DAVID RELMAN, Stanford University, Stanford, California
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1 Institute of Medicine planning committees are solely responsible for organizing the workshop, identifying topics, and choosing speakers. The responsibility for the published workshop summary rests solely with the workshop rapporteurs and the institution.
FORUM ON MICROBIAL THREATS1
DAVID A. RELMAN (Chair), Stanford University, and Veterans Affairs Palo Alto Health Care System, Palo Alto, California
JAMES M. HUGHES (Vice-Chair), Global Infectious Diseases Program, Emory University, Atlanta, Georgia
LONNIE J. KING (Vice-Chair), The Ohio State University, Columbus, Ohio
KEVIN ANDERSON, Biological and Chemical Defense Division, Science and Technology Directorate, Department of Homeland Security, Washington, DC
ENRIQUETA C. BOND, Burroughs Wellcome Fund (Emeritus), QE Philanthropic Advisors, Marshall, Virginia
ROGER G. BREEZE, Lawrence Livermore National Laboratory, Livermore, California
PAULA R. BRYANT,2 Defense Threat Reduction Agency, Medical S&T Division, Fort Belvoir, Virginia
JOHN E. BURRIS, Burroughs Wellcome Fund, Research Triangle Park, North Carolina
ARTURO CASADEVALL, Albert Einstein College of Medicine, Bronx, New York
ANDREW CLEMENTS,3 U.S. Agency for International Development, Washington, DC
PETER DASZAK, EcoHealth Alliance, New York, New York
JEFFREY S. DUCHIN, Public Health–Seattle and King County, Seattle, Washington
JONATHAN EISEN, Genome Center, University of California, Davis, California
RALPH L. ERICKSON, Walter Reed Army Institute of Research, Silver Spring, Maryland
MARK B. FEINBERG, Merck Vaccine Division, Merck & Co., Inc., West Point, Pennsylvania
JACQUELINE FLETCHER, Oklahoma State University, Stillwater, Oklahoma
CLAIRE FRASER, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland
JESSE L. GOODMAN, Food and Drug Administration, Rockville, Maryland
EDUARDO GOTUZZO, Instituto de Medicina Tropical–Alexander von Humbolt, Universidad Peruaña Cayetano Heredia, Lima, Peru
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1 Institute of Medicine Forums and Roundtables do not issue, review, or approve individual documents. The responsibility for the published workshop summary rests with the workshop rapporteurs and the institution.
2 Forum member until February 8, 2013.
3 Forum member since January 1, 2013.
CAROLE A. HEILMAN, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
DAVID L. HEYMANN, Health Protection Agency, London, United Kingdom
ZHI HONG, GlaxoSmithKline, Research Triangle Park, North Carolina
PHILIP HOSBACH, sanofi pasteur, Swiftwater, Pennsylvania
STEPHEN ALBERT JOHNSTON, Arizona BioDesign Institute, Arizona State University, Tempe, Arizona
KENT KESTER, Uniformed Services University of the Health Sciences, Bethesda, Maryland
GERALD T. KEUSCH, Boston University School of Medicine and Boston University School of Public Health, Boston, Massachusetts
RIMA F. KHABBAZ, Centers for Disease Control and Prevention, Atlanta, Georgia
STANLEY M. LEMON, School of Medicine, University of North Carolina, Chapel Hill, North Carolina
MARGARET McFALL-NGAI, University of Wisconsin, Madison, Wisconsin
EDWARD McSWEEGAN, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
MARK A. MILLER,4 Fogarty International Center, Bethesda, Maryland
PAULA J. OLSIEWSKI,5 the Alfred P. Sloan Foundation, New York, New York
JULIE PAVLIN, Armed Forces Health Surveillance Center, Silver Spring, Maryland
GEORGE POSTE, Complex Adaptive Systems Initiative, Arizona State University, Tempe, Arizona
DAVID RIZZO, Department of Plant Pathology, University of California, Davis, California
GARY A. ROSELLE, Veterans Health Administration, Department of Veterans Affairs, Cincinnati, Ohio
ALAN S. RUDOLPH,6 Defense Threat Reduction Agency, Fort Belvoir, Virginia
KEVIN RUSSELL, Armed Forces Health Surveillance Center, Silver Spring, Maryland
JANET SHOEMAKER, American Society for Microbiology, Washington, DC
P. FREDERICK SPARLING, University of North Carolina, Chapel Hill, North Carolina
MURRAY TROSTLE,7 U.S. Agency for International Development, Washington, DC
MARY E. WILSON, Harvard School of Public Health, Harvard University, Boston, Massachusetts
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4 Forum member until August 31, 2012.
5 Forum member since January 30, 2013.
6 Forum member until February 8, 2013.
7 Forum member until December 31, 2012.
BOARD ON GLOBAL HEALTH1
RICHARD GUERRANT (Chair), Thomas H. Hunter Professor of International Medicine and Director, Center for Global Health, University of Virginia School of Medicine, Charlottesville, Virginia
JO IVEY BOUFFORD (IOM Foreign Secretary), President, New York Academy of Medicine, New York, New York
CLAIRE V. BROOME, Adjunct Professor, Division of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
JACQUELYN C. CAMPBELL, Anna D. Wolf Chair, and Professor, Johns Hopkins University School of Nursing, Baltimore, Maryland
THOMAS J. COATES, Michael and Sue Steinberg Professor of Global AIDS, Research Co-Director, UC Global Health Institute, David Geffen School of Medicine, University of California, Los Angeles, California
GARY DARMSTADT, Director, Family Health Division, Global Health Program, Bill & Melinda Gates Foundation, Seattle, Washington
VALENTIN FUSTER, Director, Wiener Cardiovascular Institute Kravis Cardiovascular Health Center Professor, Cardiology, Mount Sinai School of Medicine, Mount Sinai Medical Center, New York, New York
JACOB A. GAYLE, Vice President, Community Affairs, Executive Director, Medtronic Foundation, Minneapolis, Minnesota
GLENDA E. GRAY, Executive Director, Perinatal HIV Research Unit, Chris Hani Baragwanath Hospital, University of the Witwatersrand, Diepkloof, South Africa
STEPHEN W. HARGARTEN, Professor and Chair, Emergency Medicine, Director, Medical College of Wisconsin, Milwaukee, Wisconsin
JAMES HOSPEDALES, Coordinator, Chronic Disease Project, Health Surveillance and Disease Management Area, Pan American Health Organization and World Health Organization, Washington, DC
PETER J. HOTEZ, Professor and Chair, Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University, Washington, DC
CLARION JOHNSON, Global Medical Director, Medicine and Occupational Medicine Department, Exxon Mobil, Fairfax, Virginia
FITZHUGH MULLAN, Professor, Department of Health Policy, The George Washington University, Washington, DC
OLUFUNMILAYO F. OLOPADE, Walter L. Palmer Distinguished Service Professor of Medicine, The University of Chicago, Chicago, Illinois
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1 Institute of Medicine boards do not review or approve individual workshop summaries. The responsibility for the content of the workshop summary rests with the workshop rapporteurs and the institution.
GUY PALMER, Regents Professor of Pathology and Infectious Diseases, Director of the School for Global Animal Health, Washington State University, Pullman, Washington
THOMAS C. QUINN, Associate Director for International Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Professor of Medicine, International Health, Epidemiology, and Molecular Biology and Immunology, Johns Hopkins University School of Medicine, Baltimore, Maryland
JENNIFER PRAH RUGER, Associate Professor, Division of Health Policy and Administration, Yale University School of Public Health, New Haven, Connecticut
IOM Staff
PATRICK KELLEY, Director
ANGELA CHRISTIAN, Program Associate
This workshop summary has been reviewed in draft form by individuals chosen for their diverse perspectives and technical expertise, in accordance with procedures approved by the National Research Council’s Report Review Committee. The purpose of this independent review is to provide candid and critical comments that will assist the institution in making its published workshop summary as sound as possible and to ensure that the workshop summary meets institutional standards for objectivity, evidence, and responsiveness to the study charge. The review comments and draft manuscript remain confidential to protect the integrity of the process. We wish to thank the following individuals for their review of this workshop summary:
Roger G. Breeze, Lawrence Livermore National Laboratory, Livermore, California
James M. Hughes, Rollins School of Public Health, Emory University, Atlanta, Georgia
Tim Stearns, Department of Biology, Stanford University, Department of Genetics, Stanford School of Medicine, Stanford, California
Mary E. Wilson, Harvard School of Public Health, Harvard University, Boston, Massachusetts
Although the reviewers listed above have provided many constructive comments and suggestions, they did not see the final draft of the workshop summary before its release. The review of this workshop summary was overseen by Dr.
Melvin Worth. Appointed by the Institute of Medicine, he was responsible for making certain that an independent examination of this workshop summary was carried out in accordance with institutional procedures and that all review comments were carefully considered. Responsibility for the final content of this workshop summary rests entirely with the rapporteurs and the institution.
The Forum on Emerging Infections was created by the Institute of Medicine (IOM) in 1996 in response to a request from the Centers for Disease Control and Prevention (CDC) and the National Institutes of Health (NIH). The purpose of the Forum is to provide structured opportunities for leaders from government, academia, and industry to regularly meet and examine issues of shared concern regarding research, prevention, detection, and management of emerging, reemerging, and novel infectious diseases in humans, plants, and animals. In pursuing this task, the Forum provides a venue to foster the exchange of information and ideas, identify areas in need of greater attention, clarify policy issues by enhancing knowledge and identifying points of agreement, and inform decision makers about science and policy issues. The Forum seeks to illuminate issues rather than resolve them. For this reason, it does not provide advice or recommendations on any specific policy initiative pending before any agency or organization. Its value derives instead from the diversity of its membership and from the contributions that individual members make throughout the activities of the Forum. In September 2003, the Forum changed its name to the Forum on Microbial Threats.
The Forum on Microbial Threats and the IOM wish to express their warmest appreciation to the individuals and organizations who gave their valuable time to provide information and advice to the Forum through their participation in the planning and execution of this workshop. A full list of presenters, and their biographical information, may be found in Appendixes B and E, respectively.
The Forum gratefully acknowledges the contributions of the members of the planning committee1: Bruce Budowle (University of North Texas Health Science Center), Arturo Casadevall (Albert Einstein College of Medicine), Jonathan Eisen (University of California, Davis), Claire Fraser (University of Maryland School of Medicine, Baltimore), Paul Keim (Northern Arizona University), and David Relman (Stanford University).
The Forum is also indebted to the IOM staff who tirelessly contributed throughout the planning and execution of the workshop and the production of this workshop summary report. On behalf of the Forum, we gratefully acknowledge these efforts led by Dr. Eileen Choffnes, Scholar and Director of the Forum; Dr. LeighAnne Olsen, Program Officer; Katherine McClure, Senior Program Associate; Rebekah Hutton, Research Associate; and Pamela Bertelson,2 Senior Program Assistant, for dedicating much effort and time to developing this workshop’s agenda and for their thoughtful and insightful approach and skill in planning for the workshop and in translating the workshop’s proceedings and discussion into this workshop summary report. We would also like to thank the following IOM staff and consultants for their valuable contributions to this activity: Daniel Bethea, Laura Harbold DeStefano, Julie Wiltshire, Theresa Wizemann, and Sarah Ziegenhorn.
Finally, the Forum wishes to recognize the sponsors that supported this activity. Financial support for this project was provided by the U.S. Department of Health and Human Services: National Institutes of Health, National Institute of Allergy and Infectious Diseases, Centers for Disease Control and Prevention, and the Food and Drug Administration; U.S. Department of Defense, Department of the Army: Global Emerging Infections Surveillance and Response System, Medical Research and Materiel Command, and the Defense Threat Reduction Agency; U.S. Department of Veterans Affairs; U.S. Department of Homeland Security; U.S. Agency for International Development; Uniformed Services University of the Health Sciences; the Alfred P. Sloan Foundation; American Society for Microbiology; sanofi pasteur; Burroughs Wellcome Fund; GlaxoSmithKline; Infectious Diseases Society of America; and the Merck Company Foundation. The views presented in this workshop summary are those of the workshop participants and have been summarized by the rapporteurs. They do not necessarily reflect the views of the Forum on Microbial Threats, its sponsors, or the IOM.
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1 Institute of Medicine planning committees are solely responsible for organizing the workshop, identifying topics, and choosing speakers. The responsibility for the published workshop summary rests solely with the workshop rapporteurs and the institution.
2 Staff member until February 15, 2013.
A1 The Microbial Forensics Pathway for Use of Massively Parallel Sequencing Technologies
Bruce Budowle, Sarah E. Schmedes, and Randall S. Murch
A2 Microbial Virulence as an Emergent Property: Consequences and Opportunities
Arturo Casadevall, Ferric C. Fang, and Liise-anne Pirofski
A3 Microbial Genome Sequencing to Understand Pathogen Transmission
A5 Design Considerations for Home and Hospital Microbiome Studies
Daniel P. Smith, John C. Alverdy, Jeffrey A. Siegel, and Jack A. Gilbert
A6 Sequencing Errors, Diversity Estimates, and the Rare Biosphere
Susan M. Huse, David B. Mark Welch, and Mitchell L. Sogin
A7 Phylogeography and Molecular Epidemiology of Yersinia pestis in Madagascar
Folker Meyer and Elizabeth M. Glass
A9 High-Throughput Bacterial Genome Sequencing: An Embarrassment of Choice, A World of Opportunity
A10 Evidence for Several Waves of Global Transmission in the Seventh Cholera Pandemic
A11 Multi-Partner Interactions in Corals in the Face of Climate Change
Koty H. Sharp and Kim B. Ritchie
A12 Genomic Transition to Pathogenicity in Chytrid Fungi
Suzanne Joneson, Jason E. Stahich, Shin-Han Shiu, and Erica Bree Rosenblum
A14 Genomic Approaches to Studying the Human Microbiota
A15 Sequence Analysis of the Human Virome in Febrile and Afebrile Children
Characteristics of Bacteria, Microbial Eukaryotes, and Viruses in the Human Microbiome |
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