Table Of ContentThe Science and Applications of Microbial Genomics: Workshop Summary
Eileen R. Choffnes, LeighAnne Olsen, and Theresa Wizemann,
Rapporteurs
Forum on Microbial Threats
Board on Global Health
Copyright © National Academy of Sciences. All rights reserved.
The Science and Applications of Microbial Genomics: Workshop Summary
THE NATIONAL ACADEMIES PRESS 500 Fifth Street, NW Washington, DC 20001
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 Hu-
man Services: National Institutes of Health, National Institute of Allergy and Infectious
Diseases, Centers for Disease Control and Prevention, and the Food and Drug Administra-
tion; 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.
International Standard Book Number-13: 978-0-309-26819-6
International Standard Book Number-10: 0-309-26819-2
Additional copies of this report are available from the National Academies Press, 500
Fifth Street, NW, Keck 360, Washington, DC 20001; (800) 624-6242 or (202) 334-3313;
http://www.nap.edu.
For more information about the Institute of Medicine, visit the IOM home page at:
www.iom.edu.
Copyright 2013 by the National Academy of Sciences. All rights reserved.
Printed in the United States of America
The serpent has been a symbol of long life, healing, and knowledge among almost all
cultures and religions since the beginning of recorded history. The serpent adopted as a
logotype by the Institute of Medicine is a relief carving from ancient Greece, now held by
the Staatliche Museen in Berlin.
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 rep-
resentation 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.
Copyright © National Academy of Sciences. All rights reserved.
The Science and Applications of Microbial Genomics: Workshop Summary
“Knowing is not enough; we must apply.
Willing is not enough; we must do.”
—Goethe
Advising the Nation. Improving Health.
Copyright © National Academy of Sciences. All rights reserved.
The Science and Applications of Microbial Genomics: Workshop Summary
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.
The National Academy of Engineering was established in 1964, under the charter of
the National Academy of Sciences, as a parallel organization of outstanding engineers.
It is autonomous in its administration and in the selection of its members, sharing with
the National Academy of Sciences the responsibility for advising the federal government.
The National Academy of Engineering also sponsors engineering programs aimed at
meeting national needs, encourages education and research, and recognizes the superior
achievements of engineers. Dr. Charles M. Vest is president of the National Academy of
Engineering.
The Institute of Medicine was established in 1970 by the National Academy of Sciences
to secure the services of eminent members of appropriate professions in the examina-
tion of policy matters pertaining to the health of the public. The Institute acts under the
responsibility given to the National Academy of Sciences by its congressional charter to
be an adviser to the federal government and, upon its own initiative, to identify issues of
medical care, research, and education. Dr. Harvey V. Fineberg is president of the Institute
of Medicine.
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 Na-
tional 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.
www.national-academies.org
Copyright © National Academy of Sciences. All rights reserved.
The Science and Applications of Microbial Genomics: Workshop Summary
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
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.
v
Copyright © National Academy of Sciences. All rights reserved.
The Science and Applications of Microbial Genomics: Workshop Summary
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
1 Institute of Medicine Forums and Roundtables do not issue, review, or approve individual docu-
ments. 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.
vi
Copyright © National Academy of Sciences. All rights reserved.
The Science and Applications of Microbial Genomics: Workshop Summary
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
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.
vii
Copyright © National Academy of Sciences. All rights reserved.
The Science and Applications of Microbial Genomics: Workshop Summary
IOM Staff
EILEEN CHOFFNES, Scholar and Director
LEIGHANNE OLSEN, Program Officer
KATHERINE McCLURE, Senior Program Associate
REBEKAH HUTTON, Research Associate
PAMELA BERTELSON,8 Senior Program Assistant
8 Staff member until February 15, 2013.
viii
Copyright © National Academy of Sciences. All rights reserved.
The Science and Applications of Microbial Genomics: Workshop Summary
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
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.
ix
Copyright © National Academy of Sciences. All rights reserved.
