Microbial Forensics

430 Pages·2005·14.552 MB·English

by  Roger G. Breeze, BVMS, PhD, MRCVS, Bruce Budowle, PhD, and Steven E. Schutzer, MD (Eds.)

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CONTRIBUTORS
Numbers in parentheses indicate the pages on which the author’s contribution
begins.
GRAHAM BENCH (251), Center for Accelerator Mass Spectrometry, Energy
and Environment Directorate, Lawrence Livermore National Laboratory,
Livermore, California 94551
ROGER G. BREEZE(1, 27), Centaur Science Group, Washington, DC 20007
BRUCE BUDOWLE(1), Federal Bureau of Investigation, Laboratory Division,
Quantico, Virginia 22135
JAMES P. BURANS (1), National Bioforensic Analysis Center, Department of
Homeland Security, Frederick, Maryland
JOSEPH M. CAMPOS (371), Department of Laboratory Medicine, Children’s
National Medical Center; Professor of Pediatrics, Pathology, and Microbiology/
Tropical Medicine, George Washington University Medical, Washington, DC
20037
CONSUELO CARRILLO(173), Plum Island Animal Disease Center, Agricul-
tural Research Service, U.S. Department of Agriculture, Greenport, New York
11944
RANAJIT CHAKRABORTY(1), Department of Environmental Health, Centre
for Genome Information, University of Cincinnati College of Medicine,
Cincinnati, Ohio 45267
CHARLES L. COOKE JR. (233), Bristow, VA 20136
MARC A. CUBETA (109), Department of Plant Pathology, North Carolina
State University, Raleigh, North Carolina 27695-7567
xiii
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xiv CONTRIBUTORS
JAMES J. DEYOREO (251), BioSecurity and Nanosciences Laboratory,
Chemistry and Materials Science Directorate, Lawrence Livermore National
Laboratory, Livermore, California 94551
TONY ESPOSITO(251), BioSecurity and Nanosciences Laboratory, Chemistry
and Materials Science Directorate, Lawrence Livermore National Laboratory,
Livermore, California 94551
JOHN W. EZZELL (213), U.S. Army Medical Research Institute of Infectious
Diseases, Fort Detrick, Maryland 21702-5001
DAVID P. FERGENSON (251), BioSecurity and Nanosciences Laboratory,
Chemistry and Materials Science Directorate, Lawrence Livermore National
Laboratory, Livermore, California 94551
JAMES FERREIRA (251), Materials Science and Technology Division,
Chemistry and Materials Science Directorate, Lawrence Livermore National
Laboratory, Livermore, California 94551
ERIC GARD(251), BioSecurity and Nanosciences Laboratory, Chemistry and
Materials Science Directorate, Lawrence Livermore National Laboratory,
Livermore, California 94551
PATRICK GRANT (251), Center for Accelerator Mass Spectrometry, Energy
and Environment Directorate, Lawrence Livermore National Laboratory,
Livermore, California 94551
HOLLY L. HANSON (55), Laboratory of Virology and Infectious Disease,
Center for the Study of Hepatitis C, The Rockefeller University, New York, New
York 10021
ROCKNE HARMON (381), Alameda County District Attorney’s Office,
Oakland, California 94612
JACK HIETPAS(55), Laboratory of Virology and Infectious Disease, Center for
the Study of Hepatitis C, The Rockefeller University, New York, New York 10021
CHRISTOPHER HOLLARS (251), BioSecurity and Nanosciences Laboratory,
Chemistry and Materials Science Directorate, Lawrence Livermore National
Laboratory, Livermore, California 94551
JOANNE HORN (251), Energy and Environment Directorate, Lawrence
Livermore National Laboratory, Livermore, California 94551
THOMAS HUSER(251), BioSecurity and Nanosciences Laboratory, Chemistry
and Materials Science Directorate, Lawrence Livermore National Laboratory,
Livermore, California 94551
MICHAELE KASHGARIAN(251), Center for Accelerator Mass Spectrometry,
Energy and Environment Directorate, Lawrence Livermore National Labora-
tory, Livermore, California 94551
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CONTRIBUTORS xv
PAUL KEIM (99, 355), Department of Biological Sciences, Northern Arizona
University, Flagstaff, Arizona 86011-5640
LYNDA COLLINS KELLEY (187), U.S. Department of Agriculture, Food
Safety and Inspection Service, Office of Public Health Science, Russell Research
Center, Athens, Georgia 30604
ALI S. KHAN(157), Division of Parasitic Diseases, National Center for Infec-
tious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
30333
JOHN KNEZOVICH(251), Center for Accelerator Mass Spectrometry, Energy
and Environment Directorate, Lawrence Livermore National Laboratory,
Livermore, California 94551
STEPHEN M. LANE (251), BioSecurity and Nanosciences Laboratory,
Chemistry and Materials Science Directorate, Lawrence Livermore National
Laboratory, Livermore, California 94551
RICHARD E. LENSKI (355), Department of Microbiology and Molecular
Genetics, Michigan State University, East Lansing, Michigan 48825-4320
ALEXANDER J. MALKIN (251), BioSecurity and Nanosciences Laboratory,
Chemistry and Materials Science Directorate, Lawrence Livermore National
Laboratory, Livermore, California 94551
JAMES D. MARKS (131), Department of Anesthesia and Pharmaceutical
Chemistry, University of California, San Francisco, San Francisco General
Hospital, San Francisco, California 94110
LAURA K. MCMULLAN(55), Laboratory of Virology and Infectious Disease,
Center for the Study of Hepatitis C, The Rockefeller University, New York, New
York 10021
DAVID P. MINDELL (55), Department of Ecology and Evolutionary Biology,
Museum of Zoology, University of Michigan, Ann Arbor, Michigan 48109-1079
STEPHEN A. MORSE (157), Bioterrorism and Response Program, National
Center for Infectious Diseases, Centers for Disease Control and Prevention,
Atlanta, Georgia 30333
GARY A. PAYNE (109), Department of Plant Pathology, North Carolina State
University, Raleigh, North Carolina 27695-7567
MAURICE PITESKY (251), BioSecurity and Nanosciences Laboratory,
Chemistry and Materials Science Directorate, Lawrence Livermore National
Laboratory, Livermore, California 94551
CHARLES M. RICE (55), Laboratory of Virology and Infectious Disease,
Center for the Study of Hepatitis C, The Rockefeller University, New York, New
York 10021
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xvi CONTRIBUTORS
DANIEL L. ROCK (173), Plum Island Animal Disease Center, Agricultural
Research Service, U.S. Department of Agriculture, Greenport, New York 11944
STEVEN L. SALZBERG (313), Center for Bioinformatics and Computational
Biology, University of Maryland, College Park, Maryland; The Institute for
Genomic Research, Rockville, Maryland 20878
CHARLENE M. SCHALDACH (251), BioSecurity and Nanosciences Labora-
tory, Chemistry and Materials Science Directorate, Lawrence Livermore
National Laboratory, Livermore, California 94551
STEVEN E. SCHUTZER (295), Department of Medicine, University of
Medicine and Dentistry of New Jersey—New Jersey Medical School, Newark,
New Jersey 07103
TOM R. SLEZAK(313), BioSecurity and Nanosciences Laboratory, Chemistry
and Materials Science Directorate, Lawrence Livermore National Laboratory,
Livermore, California 94551
CHAD TALLEY (251), BioSecurity and Nanosciences Laboratory, Chemistry
and Materials Science Directorate, Lawrence Livermore National Laboratory,
Livermore, California 94551
HERB J. TOBIAS(251), BioSecurity and Nanosciences Laboratory, Chemistry
and Materials Science Directorate, Lawrence Livermore National Laboratory,
Livermore, California 94551
STEPHAN P. VELSKO (251), BioSecurity and Nanosciences Laboratory,
Chemistry and Materials Science Directorate, and Nonproliferation, Arms
Control, and International Security Directorate, Lawrence Livermore National
Laboratory, Livermore, California 94551
MARK R. WILSON(1), Federal Bureau of Investigation, Laboratory Division,
Quantico, Virginia 22135
JEFFREY WILUSZ (41), Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado 80523-1619
BRUCE WOODS(251), BioSecurity and Nanosciences Laboratory, Chemistry
and Materials Science Directorate, Lawrence Livermore National Laboratory,
Livermore, California 94551
KUANG-JEAN WU (251), Materials Science and Technology Division,
Chemistry and Materials Science Directorate, Lawrence Livermore National
Laboratory, Livermore, California 94551
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FOREWORD
Kilmacthomas is a small town of some 7,500 inhabitants, not far from
Waterford in southern Ireland. In November 2001, the citizens of
Kilmacthomas found themselves subject to the same fears that swept commu-
nities from Washington, D.C., to Nairobi, Karachi, Beijing, and thousands of
other cities, towns and villages across the world. The Waterford News &
Star reported, together with the results of the whist drive in Ballylaneen, that
the Kilmacthomas post office had been closed after a white powder was found
in the mail box. Police, fire department, ambulance and the Army Disposal
Unit personnel were called to the scene to make the post office safe. The
powder did not contain anthrax but the incident shows how easily the fear
of bioterrorism paralyzes communities.
We have always lived in perilous times. Seemingly from nowhere, “new” or
new variants of infectious agents have appeared and afflicted human beings.
The Spanish flu of the 1918–1919 pandemic killed tens of millions; in 1984,
human immunodeficiency virus (HIV) was identified as the causative agent
of a new disease, acquired immunodeficiency disease syndrome (AIDS);
hantavirus pulmonary syndrome caused by the Hanta virus of rodents was
first identified in 1993; variant Creutzfeldt-Jakob disease was first diagnosed
in 1996; and severe acute respiratory syndrome (SARS) caused widespread
panic in 2003. This list does not include the devastating infections of agricul-
tural plants and animals—the 2001 foot-and-mouth disease outbreak in the
United Kingdom led to the slaughter of 11 million animals.
In 1991, Lyme disease was still a “newly emerged” infection; the bacterium
responsible had been identified only nine years earlier. In that year, the first
in a series of meetings on Lyme disease was held at the Banbury Center of the
Cold Spring Harbor Laboratory. It was chaired by Steve Schutzer. It highlighted
many diagnostic problems common to other newly emerging infections. How
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xviii FOREWORD
can one diagnose a previously-unknown infection? What laboratory tests can
detect an unknown pathogen? This book has its origins in that series of meet-
ings, which by 2000 had metamorphosed to embrace the wider problems of
novel infections in plants and animals, as well as human beings. It was during
the 2000 conference on Meeting the Challenge of Infectious Diseases in the
21st Century, chaired by Roger Breeze, that two sessions were devoted to
“Detection, Identification, Forensics and Diagnosis.” Then came the anthrax
terrorist attacks of 2001, when genuine threats were followed by many thou-
sands of hoaxes throughout the world. And so it was that the editors of this
book—Steve Schutzer, Roger Breeze, and Bruce Budowle, along with other
colleagues—organized Banbury Center meetings in 2002 and 2004 to examine
forensic approaches to microbial bioterrorism. This was not the first occasion
on which forensics had been discussed at Banbury. In 1988, there was what
turned out to be an historic meeting examining the early implementation of
human DNA fingerprinting. Bruce Budowle was one of the participants in that
meeting.
This book tackles many of the issues facing investigators of real or poten-
tial attacks employing microorganisms and toxins. How to identify rapidly
unknown substances? If there is an outbreak or even just one example of a
seemingly new disease, is it naturally occurring? If not, who is responsible?
What pathogen is involved? Has it been manipulated in any way? What advice
should be given to the officials and to the public? Microbial Forensicstakes us
from the fundamental biology of pathogenic organisms, through the investi-
gation of suspicious events, to the legal requirements for prosecution should
a felony have been committed. Such investigations require expertise in many
different fields and the authors of the chapters in the book are acknowledged
experts, bringing their knowledge and experience to bear on what continues
to be one of the most difficult challenges of the new, post September 11thworld.
Microbial Forensics provides a much needed resource for all those faced with
investigating mysterious white powders and unknown infections.
Jan Witkowski
Director, Banbury Center
Cold Spring Harbor Laboratory
New York
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PREFACE
Pathogenic microbes and their toxins have always posed a significant threat to
the health of humans, animals and plants that become exposed and infected
in the great scheme of Life. But now there is a new threat—the deliberate use
of pathogens and toxins as weapons in acts of bioterrorism or the commission
of biocrimes. Countering these weapons demands new tools and a new
scientific discipline, microbial forensics. We define microbial forensics as a
scientific discipline dedicated to analyzing evidence from a bioterrorism act,
biocrime, or inadvertent microorganism/toxin release for attribution purposes.
Epidemiologists, particularly those in public health fields, have used foren-
sic practices for decades to identify causative agents and the etiology of disease.
Some essential elements of this new discipline aimed at attribution have long
been growing in several government agencies. But microbial forensics could
not evolve into its own discipline because it was not considered a potential
deterrent and it seemed limited in its ability to attribute the source or to iden-
tify the perpetrator. However, over the last decade, and particularly after the
2001 anthrax letter attacks, microbial forensics has crystallized and become
more formalized. This has brought renewed interest, an influx of resources and
people, and new rules of engagement.
Scientists entering the field of microbial forensics and people who may
make political, administrative, or legal decisions or just would like to be better
informed have no single source to consult. This book was written to provide
such a resource, to introduce the discipline, and to describe some of the chal-
lenges and opportunities ahead. Not all possible topics are described. Instead,
representative examples are provided to initiate and educate the reader. We
hope that the book will serve as a foundation text to stimulate new genera-
tions of scientists and legal experts who will bring additional expertise to
the field. The book has this Preface and 18 other chapters that address: 1)
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xx PREFACE
definition of the discipline, select history of past bioterrorism and biocrime
events, challenges and direction; 2) synopses of the basic biology of viruses,
bacteria, fungi, and toxins; 3) epidemiology; 4) laboratory and technology con-
siderations; 5) host-pathogen interactions; 6) bioinformatics and population
genetics; 7) quality assurance; and 8) legal aspects. An appendix lists quality
assurance guidelines for microbial forensic laboratories that carry out ana-
lytical assays.
Over the past century, science has played an increasingly greater role in
criminal investigation. Microbial forensic science will continue this tradition
and assist in solving crimes by characterizing physical evidence found at a
crime scene for attribution purposes. A combination of diverse disciplines is
exploited to analyze evidence, including biology, microbiology, medicine,
chemistry, physics, statistics, population genetics, and computer science. New
techniques must be employed to get the most evidence from biological mate-
rials used in terrorist and criminal events, especially when more traditional
forms of evidence are either not available or very limited in content. These
concepts are explained in this book. Yet scientific analysis alone is not enough.
Forensic science should be integrated with other information. In practice, rig-
orous attention must be paid to steps that will assure admissibility of results
in a court of law. Admissibility rules, and legal expectations and consequences,
are described by citing past cases. We also stress quality control and quality
assurance as the means to ensure reliability. Practices such as adherence to
chain of custody procedures, documentation of activities, using tested
reagents, calibrated equipment, negative and known positive control samples,
validated procedures, standard operating procedures, and so on, are the ess-
ence of reliability and confidence. These in turn ensure admissibility.
The foundations described here should be strengthened, built upon,
and when appropriate remodeled. The driving force for the maturation of
microbial forensics will be our present and future colleagues. We look forward
to their input, interaction, and insight.
Bruce Budowle
Steven E. Schutzer
Roger G. Breeze
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ACKNOWLEDGMENTS
This book grew out of a meeting at Cold Spring Harbor Laboratory attended
by some 40 scientists who were enthusiastic about sharing their experiences
and ideas and anxious to see the new discipline of microbial forensics des-
cribed in a foundational reference text. But any editor who has ever awoken
the morning after such group excitement knows that euphoria soon fades, to
be replaced by hard realities and the relentless demands of other commitments.
In this case, the work could be shared equally among three editors who
brought different talents to the whole enterprise. However, two of us, Roger
Breeze and Bruce Budowle, would like to take this opportunity to recognize
the insight, tireless enthusiasm, optimism, discipline and leadership of Steve
Schutzer, without whom this volume would never have seen the light of day.
Steve was instrumental in putting the Cold Spring Harbor Laboratory-Banbury
Center meetings together, stimulating discussions during the formal meetings
and evening sessions, keeping manuscripts on track, and ensuring the other
editors met their obligations.
Two people played vital roles in establishing microbial forensics as a disci-
pline through vision, leadership, advocacy and pioneering accomplishments
from the early years: Janet Dorigan of the Office of Research and Development,
Central Intelligence Agency, and Randall Murch of the Laboratory Division of
the Federal Bureau of Investigation. On behalf of all the authors in this volume,
we would like to recognize their contributions and express our appreciation.
We extend the same sentiments and recognition to others at the same
agencies who have contributed substantially to the foundations of microbial
forensics but remain anonymous.
We also thank the contributors to this book, those who provided intellec-
tual input at Cold Spring Harbor Laboratory and Banbury Conference meet-
ings over the years, and the many others whose efforts have contributed to the
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xxii ACKNOWLEDGMENTS
foundation of microbial forensics. Government agencies whose support has
been invaluable include: the Department of Defense, the Intelligence commu-
nity, the Department of Justice and National Institute of Justice, the Depart-
ment of Homeland Security, the Department of Agriculture, the Department of
Energy, the Centers for Disease Control and Prevention, the National Institutes
of Health, and the Food and Drug Administration. The National Academy of
Sciences has contributed to this field and should be commended.
Bruce Budowle, on behalf of the Federal Bureau of Investigation, would like
to thank the members of the Scientific Working Group on Microbial Genetics
and Forensics for their contributions and continued efforts. He also would like
to acknowledge the efforts of his colleagues at the Chem-Bio Sciences Unit
at the Federal Bureau of Investigation, and the encouragement of his close
friends Arthur J. Eisenberg, Leonard Klevan, Jose A. Lorente, Randy Murch,
Antti Sajantila, and Rock Harmon.
Roger Breeze would like to acknowledge Hugh Pirie, Norman Whittle,
David C. Taylor, Mick Taylor, Leo Bustad, and Robert Wilson without whose
support and encouragement he would not have come to this day.
Steven Schutzer would like to thank friends, family, and colleagues. He par-
ticularly would like to thank Bruce Budowle and Roger Breeze for their vision
and the privilege of working with them. Special thanks to Jan Witkowski and
Jim Watson for providing the unique environment that helps launch new
endeavors.
Steven E. Schutzer
Roger G. Breeze
Bruce Budowle