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Committee on Science Needs for Microbial Forensics: Developing an Initial International Roadmap Board on Life Sciences Division on Earth and Life Studies In cooperation with The Croatian Academy of Sciences and Arts The U.K. Royal Society and The International Union of Microbiological Societies

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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 Gov- erning Board of the National Research Council, whose members are drawn from the councils of the National Academy of Sciences, the National Academy of Engi- neering, and the Institute of Medicine. The members of the committee responsible for the report were chosen for their special competences and with regard for appropriate balance. This study was supported by the Naval Postgraduate School’s Project on Advanced Systems and Concepts for Countering Weapons of Mass Destruction (PASCC) via Assistance Grant No. N00244-13-1-0026 awarded by the NAVSUP Fleet Logistics Center San Diego (NAVSUP FLC San Diego) to the National Academy of Sci- ences, by purchase order SAQMMA13M2120 from the U.S. Department of State to the National Academy of Sciences, and by internal support from the National Academy of Sciences. The views expressed in this publication and/or made by speakers, moderators, and presenters do not necessarily reflect the official policies of the Naval Postgraduate School nor does mention of trade names, commercial practices, or organizations imply endorsement by the U.S. Government. Any opin- ions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the views of the organizations or agencies that provided support for the project. International Standard Book Number-13:  978-0-309-30245-6 International Standard Book Number-10:  0-309-30245-5 Additional copies of this report are available for sale from The National Acade- mies Press, 500 Fifth Street, N.W., Keck 360, Washington, DC 20001; (800) 624-6242 or (202) 334-3313; Internet, http://www.nap.edu/. Copyright 2014 by the National Academy of Sciences. All rights reserved. Printed in the United States of America

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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 govern- ment 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 mem- bers, sharing with the National Academy of Sciences the responsibility for advis- ing 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. C. D. Mote, Jr., 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 examination 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. Victor J. Dzau 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 National Academy of Engineering in pro- viding 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. C. D. Mote, Jr., are chair and vice chair, respectively, of the National Research Council. www.national-academies.org

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COMMITTEE ON SCIENCE NEEDS FOR MICROBIAL FORENSICS: DEVELOPING AN INITIAL INTERNATIONAL ROADMAP Members JOHN D. CLEMENTS (Chair), Tulane University, New Orleans, Louisiana MUNIRUL ALAM, International Center for Diarrhoeal Diseases Research, Dhaka, Bangladesh BRUCE BUDOWLE, Institute of Applied Genetics, University of North Texas Health Science Center, Fort Worth JONGSIK CHUN, Seoul National University, Seoul, South Korea RITA R. COLWELL, University of Maryland, College Park NANCY D. CONNELL, Rutgers New Jersey Medical School, Rutgers University, Newark PAUL KEIM, Northern Arizona University, Flagstaff JUNCAI MA, WFCC-MIRCEN World Data Center of Microorganisms (WDCM), Institute of Microbiology, Chinese Academy of Sciences, Beijing, China ALEMKA MARKOTIĆ, University Hospital for Infectious Diseases, Zagreb, Croatia GEOFFREY SMITH, Imperial College London, London, United Kingdom Staff FRANCES E. SHARPLES, Study Director and Director, Board on Life Sciences JO L. HUSBANDS, Scholar/Senior Project Director, Board on Life Sciences CARL ANDERSON, Program Associate, Board on Life Sciences JENNA OGILVIE, Senior Program Assistant, Board on Life Sciences BENJAMIN RUSEK, Program Officer, Committee on International Security and Arms Control KRISTIN WHITE, Consultant Writer v

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BOARD ON LIFE SCIENCES Members JAMES P. COLLINS (Chair), Arizona State University, Tempe ENRIQUETA C. BOND, Burroughs Wellcome Fund (retired), Marshall, Virginia ROGER D. CONE, Vanderbilt University Medical Center, Nashville, Tennessee SEAN EDDY, HHMI Janelia Farm Research Campus, Ashburn, Virginia SARAH C. R. ELGIN, Washington University, St. Louis, Missouri DAVID R. FRANZ, Former Cdr USAMRIID; Consultant, Frederick, Maryland LOUIS J. GROSS, University of Tennessee, Knoxville ELIZABETH HEITMAN, Vanderbilt University Medical Center, Nash- ville, Tennessee JOHN G. HILDEBRAND, University of Arizona, Tucson RICHARD A. JOHNSON, Arnold & Porter, LLC, Washington, D.C. JUDITH KIMBLE, University of Wisconsin, Madison CATO T. LAURENCIN, University of Connecticut Health Center, Farmington ALAN I. LESHNER, American Association for the Advancement of Sci- ence, Washington, D.C. KAREN E. NELSON, J. Craig Venter Institute, Rockville, Maryland ROBERT M. NEREM, Georgia Institute of Technology, Atlanta CAMILLE PARMESAN, University of Texas, Austin ALISON G. POWER, Cornell University, Ithaca, New York MARGARET RILEY, University of Massachusetts, Amherst JANIS C. WEEKS, University of Oregon, Eugene MARY WOOLLEY, Research!America, Alexandria, Virginia Staff FRANCES E. SHARPLES, Director JO L. HUSBANDS, Scholar/Senior Project Director JAY B. LABOV, Senior Scientist/Program Director for Biology Education KATHERINE W. BOWMAN, Senior Program Officer INDIA HOOK-BARNARD, Senior Program Officer MARILEE K. SHELTON-DAVENPORT, Senior Program Officer KEEGAN SAWYER, Program Officer BETHELHEM MEKASHA, Financial Associate ANGELA KOLESNIKOVA, Administrative Assistant JENNA OGILVIE, Senior Project Assistant LAUREN SONI, Senior Project Assistant vi

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Preface In September 2001, shortly after the terrorist attacks on the World Trade Center and the Pentagon, someone placed letters containing Bacil- lus anthracis spores into a mailbox in Trenton, New Jersey. Those letters were addressed to several media outlets, including ABC, NBC, CBS, the New York Post, and American Media, Inc. in Boca Raton, Florida. The recipients of one of the letters, Mr. Robert Stevens, was the first person to die in what has become known as the anthrax letters attack and des- ignated as the “Amerithrax” investigation by the FBI. At first, diagnosis of Mr. Stevens’ illness was complicated by the absence of any suspicion that would make anthrax part of the differential diagnosis for a 63-year- old man in Boca Raton. Once a diagnosis of anthrax was made, health care workers and epidemiologists began trying to understand how an office worker could come in contact with B. anthracis, the causative agent of the disease anthrax. One possible, though unlikely, scenario that was widely touted at the time was that he had come across an infected ani- mal, perhaps a beaver, while on a recent hiking trip. The receipt of an array of letters filled with white powder soon confirmed that this was a bioterrorist attack and not a natural occurrence. In early October, the perpetrator mailed a second set of letters containing a more highly refined preparation of spores, this time addressed to Senators Tom Daschle and Patrick Leahy. Once it was clear that there was an ongoing threat, exten- sive efforts were begun to identify the source and characteristics of the material used in the attack. What became immediately clear in the midst of heroic efforts to discern the cause and source of the anthrax mailings vii

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viii PREFACE was that we were unprepared to analyze the microbial forensic evidence associated with this attack. At the time, most diagnostic and epidemiological characterizations of infectious diseases were based on illness, culture, serology, physical characteristics, and metabolic profiles of infectious organisms—processes that take time and require pure cultures of viable microorganisms. There was a nascent field of microbial forensics, which had begun in the United States in the preceding decade with the formation of the Federal Bureau of Investigation’s Hazardous Materials Response Unit. The Unit was cre- ated in part to support suspected or known bioterrorism investigations by providing investigative leads and supporting prosecutions or exon- erations with scientific evidence. The Unit was a law enforcement opera- tion designed to employ forensic science principles and practices to pro- duce evidence that would be admissible in court according to U.S. legal requirements and standards. The Amerithrax investigation accelerated the development of the field of microbial forensics, resulting in remark- able development and applications of new techniques and approaches for using laboratory tools to pinpoint the identity of a microbial agent. Microbial forensics became an essential part of the scientific investiga- tion, which was combined with physicochemical analyses as well as other nonscientific types of evidence to narrow the search for the source of the B. anthracis used in the attacks. Today we find ourselves with a complex infrastructure of govern- ment agencies, Select Agent registries, regulated research, environmental monitoring in designated cities, federal and state regulations—all result- ing from one more or less successful biological attack on the United States. The Amerithrax attack with highly refined material produced by a knowl- edgeable expert (presumably in a U.S. bioweapons laboratory) resulted in 22 illnesses and 5 deaths. Approximately 4 g of material were used in the Amerithrax attack. At that time, the United States planned and pre- pared as best it could for an attack involving 50 kg of weaponized anthrax spores released on a city with a population of 500,000, anticipating 125,000 casualties. However, it is unlikely that a nonstate entity would be able to produce that quality or quantity of material undetected. Moreover, aside from B. anthracis, there are few (if any) biological agents that can be grown in quantity, viably maintained, stabilized, processed to the appropriate size, and delivered in an aerosolizable form except by a few special- ized bioweapons facilities and certainly not by terrorists in a garage or cave. Most exotic microorganisms are just too difficult to grow and keep alive, even in the most sophisticated facility. In addition, the technology involved in weaponizing biological materials is complex, demanding, and requires substantial expertise. The more likely scenario is someone having access to a small amount of unrefined material that he/she uses to make

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PREFACE ix a few individuals ill (causing perhaps a few deaths), the consequence of which will be a nation paralyzed with fear, not illness. In that context, microbial forensics becomes more important than ever. How does one differentiate a natural outbreak from an accidental release from a legitimate laboratory, or the use of biological material to commit a crime, bioterrorism, and all-out biological warfare? How can this be accomplished quickly enough to inform law enforcement, the intelligence community, policy makers, and the public in a timely fashion? The traditional clinical laboratory sciences of culture identification, serol- ogy, etc. are inadequate for these purposes. It was with this background that the workshop in Zagreb, Croatia, was held in October 2013 with the intent to identify the scientific challenges that must be met to improve the capability of microbial forensics to investigate suspected outbreaks and to provide evidence of sufficient quality to support responses, legal proceedings, and the development of government policies. The workshop also was designed to increase awareness of microbial forensics among the members of the larger international scientific communities and to engage these communities in the development of a plan on how to address sci- entific challenges. One of the more important concepts discussed during the workshop was that the techniques of microbial forensics could aid not only law enforcement and policy makers, but also public health workers, in trying to identify the existence and source of natural outbreaks. Indeed, as we saw in the Amerithrax attack, the public health system will likely be the first to encounter and the first line of defense against a biological attack. Most infectious diseases develop gradually, with individual patients seek- ing medical care through their local health care providers. People vary in their susceptibility to infectious diseases, and subtle clues may signal an attack, such as an increase in frequency of a naturally occurring infectious disease, unusual seasonality, unexpected resistance to antimicrobials, or unusual age distribution. These features are likely to be recognized first in the public health arena, and the more common the tools and techniques are between law enforcement and public health, the more likely that a true attack will be identified early, perhaps in time to administer prophylactic antibiotics or vaccines or prevent a second release. Moreover, the further we get from an actual attack, the less inclined policy makers are to pro- vide financial support for continuing the research necessary to prepare for an attack. As noted in the 2013 President’s Report for the Global Partner- ship Against the Spread of Weapons and Materials of Mass Destruction (U.K. Foreign and Commonwealth Office, 2013): Many of the capabilities required for detecting and responding to the whole spectrum of natural, intentional, and man-made events are es- sentially the same. Systems and networks that might be created for rare

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x PREFACE events will atrophy through lack of use, whereas systems created for addressing natural, man-made and accidental outbreaks of infectious disease are likely to be used frequently. Relying on tools and systems that are compatible with both rare and common occurrences means that in an instance of a rare event, detection and response will not be delayed by lack of familiarity with the tools or systems of reporting. On behalf of the entire committee, I wish to extend our sincere grati- tude to the excellent staff at the National Academies. It is because of the dedication and extraordinary efforts of Fran Sharples, Director of the Board on Life Sciences at the National Academy of Sciences (NAS), that we were able to complete this ambitious task in so short a time. The committee also wishes to thank Jo Husbands from the NAS staff and our colleagues at the Croatian Academy of Sciences and Arts, Jelena Dukic, the Director of International Cooperation, and Ninja Ivanus from her staff, for their outstanding contributions to the design and organization of the workshop. Our colleagues from the U.K. Royal Society and the Interna- tional Union of Microbiological Societies provided important support and ideas throughout the process. I also want to thank my fellow committee members for their commitment that made the workshop and writing of this report an enjoyable and rewarding opportunity. John D. Clements, Chair

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Acknowledgments This report has been reviewed in draft form by individuals chosen for their diverse perspectives and technical expertise, in accordance with procedures approved by the National Academies’ Report Review Com- mittee. The purpose of this independent review is to provide candid and critical comments that will assist the institution in making its published report as sound as possible and to ensure that the report meets institu- tional 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 report: Kenneth Berns, University of Florida Aaron Darling, University of Technology, Sydney, Australia Sean Eddy, HHMI Janelia Farm Research Campus Jens Kuhn, Integrated Research Facility, Fort Detrick, National Institutes of Health Ian Lipkin, Columbia University Stephen Morse, Columbia University Karen Nelson, J. Craig Venter Institute Tom Slezak, Lawrence Livermore National Laboratory Tim Trevan, International Council for the Life Sciences David Walt, Tufts University xi

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xiv CONTENTS 7 BIOINFORMATICS AND DATA 143 8 FINDINGS AND CONCLUSIONS: INITIAL PRIORITIZED SCIENCE NEEDS FOR MICROBIAL FORENSICS 157 REFERENCES 179 APPENDIXES A COMMITTEE BIOGRAPHIES 191 B CONVENING ORGANIZATIONS 199 C AGENDA 205 D LIST OF PARTICIPANTS 211 E LIST OF PRESENTATIONS 215 F SPEAKER BIOGRAPHIES 219

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Boxes, Figures, and Tables BOXES S-1 Priority Categories for Microbial Forensics Needs, 4 1-1 Statement of Task, 8 1-2 Questions Forensics Can Help Answer, 13 1-3 Forensic Science Methods and System Elements, 16 1-4 Murch’s Scenario 1—Unknown Outbreak, No Indigenous Capability, 21 1-5 Murch’s Scenario 2—Viral Outbreak: Bioattack? Genetic Engineering? Multiple Countries Involved, 22 1-6 Murch’s Scenario 3—Alleged Strategic Attack, 23 1-7 Relevant Articles of the Biological Weapons Convention, 25 3-1 Epidemiological Clues That May Signal a Biological or Chemical Terrorist Attack, 61 3-2 Rapid NGS Diagnostic Applications and Public Health Microbiology, 68 5-1 Sampling and Handling Goals, 100 5-2 Sample Matrices for Evidence Collection, 101 5-3 Potential Food and Agriculture Targets, 105 5-4 Plants Are Vulnerable and Efficacious Targets for Agroterrorism, 106 xv

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xvi BOXES, FIGURES, AND TABLES 5-5 Sampling Strategy, 107 5-6 Comprehensive Plan for Sampling and Collection, 107 6-1 Validation for the Analysis Stage, 123 6-2 Interpretation of Results, 129 6-3 Challenges for Any Target: Source Exclusion, Association, and Attribution, 130 6-4 Microbial Forensics Questions: Genetics, 131 6-5 A Bioinformatics Toolbox for Microbial Forensics, 133 6-6 Inference and Error Issues, 134 6-7 Gaps in Standard Reference Materials (SRMs), 136 6-8 Databases and Resources, 137 6-9 Databases and Resources: The World Data Centre for Microorganisms (WDCM), 140 6-10 Proposed Global Catalogue for Microbial Forensics, 142 FIGURES 1-1 Spectrum of risks due to biological agents, 10 1-2 The forensic continuum, 15 1-3 Time-risk continuum, 33 2-1 Variants of representative colonies of each of the morphotypes of B. anthracis Ames, 42 2-2 Worldwide distribution of B. anthracis clonal lineages, 47 2-3 Three classifications of bacterial pathogens, 49 2-4 Distribution of Y. pestis, 50 2-5 Red lineages represent HIV sequences from the suspected perpetrator, 53 3-1 The microbial forensic process, 62 3-2 Events timeline of enterohemorrhagic E. coli O104:H4 outbreak, 65 3-3 A ranking of the discriminatory power of microbial typing approaches, 69 3-4 Four approaches to using whole-genome sequencing, 71 3-5 Differences from the Index Case in the NS5B region, 75 3-6 Maximum likelihood tree for cloned sequences in the E1-E2 region, 77 6-1 Process of implementing a test for diagnostic use, 124 6-2 Performance characteristics, error types, and measurement metrics, 126

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BOXES, FIGURES, AND TABLES xvii 6-3 Sample analysis flowchart, 126 7-1 Evolutionary phylogenetic tree of V. cholarae based on SNP analysis of 26 genomes, 148 TABLE 8-1 Priority Categories for Microbial Forensics Needs, 175

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List of Acronyms and Initialisms AAM American Academy of Microbiology ABC American Broadcasting Company ABC Analyzer of Bio-resource Citations ACD Advisory Committee to the Director AMD advanced molecular detection ANI Average Nucleotide Identity ASM American Society for Microbiology ASPR Assistant Secretary for Preparedness and Response ATCC American Type Culture Collection ATM atomic force microscopy AWS Amazon Web Services BEAST Bayesian evolutionary analysis by sampling trees BfR Bundesinstitut für Risikobewertung (Federal Institute of Risk Assessment, Germany) BGI Beijing Genomics Institute (People’s Republic of China) BLAST Basic Local Alignment Search Tool BSL biosafety level BWC Biological Weapons Convention canSNP canonical single-nucleotide polymorphism CAP College of American Pathologists xix

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xx LIST OF ACRONYMS AND INITIALISMS CAP Certified Authorization Professional CBRND chemical, biological, radiological, and nuclear defense CBS Columbia Broadcasting System (now operating as CBS Broadcasting, Inc.) CCINFO World Directory of Culture Collections CDC U.S. Centers for Disease Control and Prevention CEO chief executive officer CLIA Clinical Laboratory Improvement Amendments CODATA Committee on Data for Science and Technology CODIS Combined DNA Index System COMCOFs committees, commissions, and federations CPU central processing unit DGA French Ministry of Defense DHHS U.S. Department of Health and Human Services DNA deoxyribonucleic acid dNTP deoxynucleotide triphosphates DOE U.S. Department of Energy DTRA Defense Threat Reduction Agency (part of the U.S. Department of Defense) EAEC enteroaggregative Escherichia coli EBI European Bioinformatics Institute ECL electrochemiluminescence EDA Economic Development Administration EDC European Centre for Disease Prevention and Control (Sweden) EHEC enterohemorrhagic Escherichia coli ELISA enzyme-linked immunosorbent assay EM electron microscopy ENCODE Encyclopedia of DNA Elements env HIV retrovirus envelope gene EPA U.S. Environmental Protection Agency ESI electrospray ionization EU European Union FAO U.N. Food and Agriculture Organization FAZD National Center for Foreign Animal and Zoonotic Disease Defense FBI U.S. Federal Bureau of Investigation FCA Fellow of the Croatian Academy FDA U.S. Food and Drug Administration

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LIST OF ACRONYMS AND INITIALISMS xxi FEMA U.S. Federal Emergency Management Agency FOI Swedish Defense Research Agency GAO U.S. Government Accountability Office GCM Global Catalogue of Microorganisms GHDP genomically highly diversified pathogen GIDP genomically intermediately diversified pathogen GISAID Global Initiative on Sharing Avian Influenza Data GLEWS Global Early Warning System for Major Animal Diseases, Including Zoonoses GMMP genomically monomorphic pathogen GOARN Global Alert and Response Network GPHIN Global Public Health Intelligence Network GPU graphics processing unit HAZMAT hazardous materials and items HCV hepatitis C virus HFRS hemorrhagic fever with renal syndrome HHMI Howard Hughes Medical Institute HIV-1 human immunodeficiency virus 1 HMM Hidden Markov Model HMRU Hazardous Materials Response Unit HPA Health Protection Agency (United Kingdom) HPS hantavirus pulmonary syndrome HSPD Homeland Security Presidential Directive HUS hemolytic uremic syndrome HVAC heating, ventilation, and air conditioning HVR hypervariable region IAEA International Atomic Energy Agency IBD-BIOM Inflammatory Bowel Disease Biomarkers Program iBOL International Barcode of Life Project ICDDRB International Center for Diarrhoeal Diseases Research, Bangladesh ICFMH-WPCM Working Party on Culture Media of the International Committee on Food Microbiology and Hygiene ICRC International Committee for the Red Cross ICSU International Council of Science IDA Institute for Defense Analyses IHR International Health Regulations IMCAS Institute of Microbiology, Chinese Academy of Sciences

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xxii LIST OF ACRONYMS AND INITIALISMS IMG Integrated Microbial Genomes INTERPOL International Criminal Police Organization IOM Institute of Medicine ISABS International Society of Applied Biological Sciences ISO International Organization for Standardization IT information technology IUBS International Union of Biological Sciences IUMS International Union of Microbiological Societies IV intravenous JAMA Journal of the American Medical Association JGI Joint Genome Institute (U.S. Department of Energy) LPSN List of Prokaryotic Names with Standing in Nomenclature LRN Laboratory Response Network LT Life Technologies Group MALDI-TOF matrix-assisted laser desorption/ionization time-of-flight Mb megabyte MDS minimum datasets MERS Middle East Respiratory Syndrome MGIT mycobacterial growth indicator tube MG-RAST Metagenomics Rapid Annotations using Subsystems Technology MiSeq benchtop NGS instrument manufactured by Illumina MLST multilocus sequence typing MLST+ core-genome MLST MLVA multilocus VNTR analysis MPS massively parallel sequencing MRCA most recent common ancestor MRSA methicillin-resistant Staphylococcus aureus NAS U.S. National Academy of Sciences NATO North Atlantic Treaty Organization NAU Northern Arizona University NBACC National Biodefense Analysis and Countermeasures Center NBAS National Biosurveillance Advisory Committee NBC National Broadcasting Company

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LIST OF ACRONYMS AND INITIALISMS xxiii NBFAC National BioForensic Analysis Center NBTCC National Biological Threat Characterization Center NCBI National Center for Biotechnology Information NeCTAR National eResearch Tools and Resources NGO nongovernmental organization NGS next-generation gene sequencing NIAID National Institute of Allergy and Infectious Diseases, NIH NIH National Institutes of Health NIST National Institute of Standards and Technology NRC National Research Council NSTC National Science and Technology Council OIE World Organization for Animal Health OPCW Organization for the Prohibition of Chemical Weapons PATH Program for Appropriate Technology in Health PC personal computer PCR polymerase chain reaction PFGE pulsed-field gel electrophoresis PGM Ion Torrent Personal Genome Machine™ PHEIC Public Health Emergency of International Concern PI principal investigator PIXE particle-induced X-ray emission PLOS Public Library of Science PNAS Proceedings of the National Academy of Sciences Pol HIV retrovirus polymerase gene PPE personal protective equipment PS presumed source PUUV Puumala virus QA/QC quality assurance and quality control qPCR quantitative PCR RAPD random amplified polymorphic DNA RDS recommended datasets RFLP restriction fragment length polymorphism RIPL Rare and Imported Pathogens Laboratory RIVM Dutch National Institute for Public Health and the Environment RKI Robert Koch Institute (Germany) rMLST ribosomal MLST RNA ribonucleic acid

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xxiv LIST OF ACRONYMS AND INITIALISMS RNJMS Rutgers New Jersey Medical School rRNA ribosomal RNA R&D research and development SARS Severe Acute Respiratory Syndrome SEM scanning electron microscope SIMS secondary ion mass spectroscopy SMRT single-molecule real time SNP single-nucleotide polymorphism SOAP Short Oligonucleotide Analysis Package SOP standard operating protocols (or procedures) SRM Standard Reference Materials SSD solid-state disk S&T science and technology TB terabyte TEM transmission electron microscope TGen Translational Genomics Research Institute TIGR The Institute for Genomic Research TTP thrombotic thrombocytopenic purpura UHID University Hospital for Infectious Diseases U.K. United Kingdom UKM University Hospital Muenster (Germany) U.N. United Nations UNESCO United Nations Educational, Scientific and Cultural Organization UNICRI U.N. Interregional Crime and Justice Research Institute UNIDIR U.N. Institute for Disarmament Research U.S. United States of America USAMRIID U.S. Army Medical Research Institute of Infectious Diseases USDA U.S. Department of Agriculture VNTR variable number tandem repeat WDCM World Data Center of Microorganisms WFCC-MIRCEN World Federation for Culture Collections— Microbial Resources Centers Network WGS whole-genome sequencing WHO World Health Organization WIPO World Intellectual Property Organization WMD weapons of mass destruction