Microbial Forensics

499 Pages·2019·13.9 MB·English

by  Bruce Budowle (editor), Steven E. Schutzer (editor), Stephen A. Morse (editor)

MICROBIAL
FORENSICS
THIRD EDITION
Edited by
Bruce Budowle
Steven Schutzer
Stephen Morse
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Contributors
M.W. Allard Division of Microbiology, Office of Robert L. Bull FBI Laboratory, Quantico, VA,
Regulatory Science, CFSAN, US FDA, College UnitedStates
Park,MD,UnitedStates James Burans National Bioforensic and Analysis
JonathanAllen LawrenceLivermore NationalLab- Center,Frederick,MD,UnitedStates
oratory,Livermore,CA,UnitedStates David O. Carter Laboratory of Forensic
Philip S. Amara College of Public Health, Univer- Taphonomy, Forensic Sciences Unit, Division of
sity of Nebraska Medical Center, Omaha, NE, Natural Sciences and Mathematics, Chaminade
UnitedStates University of Honolulu, Honolulu, HI, United
Neel G. Barnaby FBI Laboratory, Quantico, VA, States
UnitedStates Angela Choi Department of Microbiology, Icahn
John R. Barr Centers for Disease Control and Pre- School of Medicine at Mount Sinai, New York,
NY,UnitedStates
vention,NationalCenterforEnvironmentalHealth,
Division of Laboratory Sciences, Atlanta, GA, Brooke L. Deatherage Kaiser Pacific Northwest
UnitedStates NationalLaboratory,Richland,WA,UnitedStates
Aeriel Belk Animal Sciences, Colorado State Uni- R.ScottDecker Bio-LogicSecurity,LLC,LasVegas,
versity,FortCollins,CO,UnitedStates NV,UnitedStates
Nicholas H. Bergman National Bioforensic and HeatherDeel AnimalSciences,ColoradoStateUni-
AnalysisCenter,Frederick,MD,UnitedStates versity,FortCollins,CO,UnitedStates
Christopher A. Bidwell Federation of American David M. Engelthaler TGen North, Translational
Scientists,Washington,DC,UnitedStates GenomicsResearchInstitute,Flagstaff,AZ,United
DawnBirdsell ThePathogenandMicrobiomeInsti- States
tute, Northern Arizona University, Flagstaff, AZ, Hector F. Espitia-Navarro School of Biological Sci-
UnitedStates ences, Georgia Institute of Technology, Atlanta,
Thomas A. Blake Centers for Disease Control and GA, United States; PanAmerican Bioinformatics
Institute,Cali,ValledelCauca,Colombia
Prevention, National Center for Environmental
Health, Division of Laboratory Sciences, Atlanta, Jacqueline Fletcher Department of Entomology &
GA,UnitedStates Plant Pathology, National Institute for Microbial
E.W.Brown DivisionofMicrobiology,OfficeofReg- Forensics & Food and Agricultural Biosecurity,
OklahomaStateUniversity,Stillwater,OK,United
ulatory Science, CFSAN, US FDA, College Park,
MD,UnitedStates States
Sibyl Bucheli Department of Biological Sciences, Jeffrey T. Foster The Pathogen and Microbiome
Institute, Northern Arizona University, Flagstaff,
Sam Houston State University, Huntsville, TX,
AZ,UnitedStates
UnitedStates
Bruce Budowle Center for Human Identification, Adolfo García-Sastre Department of Microbiology,
Department of Microbiology, Immunology and Icahn School of Medicine at Mount Sinai, New
York,NY,UnitedStates; DepartmentofMedicine,
Genetics,UniversityofNorthTexasHealthScience
Center,FortWorth,TX,UnitedStates IcahnSchoolofMedicineatMountSinai,NewYork,
xi
xii
Contributors
NY, United States; Global Health and Emerging Rob Knight Department of Pediatrics, Department
Pathogens Institute, Icahn School of Medicine at ofComputerScienceandEngineering,Microbiome
Mount Sinai, New York, NY, United States; The Innovation Center, University of California, San
Tisch Cancer Institute, Icahn School of Medicine at Diego,CA,UnitedStates
MountSinai,NewYork,NY,UnitedStates Asja Korajkic U.S. Environmental Protection
Jennifer S. Goodrich National Bioforensic and Agency, Office of Research and Development,
AnalysisCenter,Frederick,MD,UnitedStates Cincinnati,OH,UnitedStates
BradleyHart LawrenceLivermoreNationalLabora- StevenB.Lee InternationalForensicResearchInsti-
tory,Livermore,CA,UnitedStates tute, Florida International University, Miami, FL,
DavidR.Hodge DepartmentofHomelandSecurity, UnitedStates; ForensicScienceProgram,Depart-
ment of Justice Studies, San Jose State University,
Washington,DC,UnitedStates
SanJose,CA,UnitedStates
PaulJ.Jackson AdjunctProfessor,Nonproliferation
and Terrorism Studies, James Martin Center for Anastasia P. Litvintseva Mycotic Diseases Branch,
Centers for Disease Control and Prevention,
Nonproliferation Studies, Middlebury Institute of
Atlanta,GA,UnitedStates
International Studies at Monterey, Monterey, Cali-
fornia,UnitedStates Douglas G. Luster USDA ARS, Foreign Disease -
CrystalJaing LawrenceLivermoreNationalLabora- Weed Science Research Unit, Fort Detrick, MD,
UnitedStates
tory,Livermore,CA,UnitedStates
Rudolph C. Johnson Centers for Disease Control Aaron Lynne Department of Biological Sciences,
Sam Houston State University, Huntsville, TX,
andPrevention,NationalCenterforEnvironmental
UnitedStates
Health, Division of Laboratory Sciences, Atlanta,
GA,UnitedStates Leonard W. Mayer PanAmerican Bioinformatics
I.KingJordan Schoolof BiologicalSciences,Geor- Institute,Cali,ValledelCauca,Colombia; Applied
Bioinformatics Laboratory, Atlanta, GA, United
gia Institute of Technology, Atlanta, GA, United
States
States; PanAmerican Bioinformatics Institute,
Cali,ValledelCauca,Colombia; AppliedBioin- UlrichMelcher OklahomaStateUniversity,Depart-
formaticsLaboratory,Atlanta,GA,UnitedStates ment of Biochemistry & Molecular Biology, Still-
Suzanne R. Kalb Centers for Disease Control and water,OK,UnitedStates
Prevention, National Center for Environmental EricD.Merkley PacificNorthwestNationalLabora-
Health, Division of Laboratory Sciences, Atlanta, tory,Richland,WA,UnitedStates
GA,UnitedStates Jessica L. Metcalf Animal Sciences, Colorado State
Arnold F. Kaufmann United States Public Health University,FortCollins,CO,UnitedStates
Service,StoneMountain,GA,UnitedStates DeEtta K. Mills International Forensic Research
PaulKeim ThePathogenandMicrobiomeInstitute, Institute, Florida International University, Miami,
NorthernArizonaUniversity,Flagstaff,AZ,United FL,UnitedStates
States StephenA.Morse IHRC,Inc.,Atlanta,GA,United
TerryL.Kerns Bio-LogicSecurity,LLC,LasVegas, States
NV,UnitedStates Ted D. Mullins American Type Culture Collection
AliS.Khan CollegeofPublicHealth,Universityof (ATCC),Manassas,VA,UnitedStates
Nebraska Medical Center, Omaha, NE, United Randall Murch Virginia Polytechnic Institute and
States StateUniversity,Arlington,VA,UnitedStates
Rachel E. Kieser Center for Human Identification, ForrestW.Nutter,Jr. IowaStateUniversity,Depart-
GraduateSchoolofBiomedicalSciences,University
ment of Plant Pathology and Microbiology, Ames,
ofNorthTexasHealthScienceCenter,FortWorth,
IA,UnitedStates
TX,UnitedStates
xiii
Contributors
Francisco M. Ochoa Corona Department of Ento- Orin C. Shanks U.S. Environmental Protection
mology & Plant Pathology, National Institute for Agency, Office of Research and Development,
Microbial Forensics & Food and Agricultural Bio- Cincinnati,OH,UnitedStates
security, Oklahoma State University, Stillwater, Frank P. Simione American Type Culture Collec-
OK,UnitedStates tion(ATCC),Manassas,VA,UnitedStates
Sam Ogden Animal Sciences, Colorado State Uni- Tom Slezak Lawrence Livermore National Labora-
versity,FortCollins,CO,UnitedStates tory,Livermore,CA,UnitedStates
RichardT.Okinaka ThePathogenandMicrobiome JeniferA.L.Smith DistrictofColumbiaDepartment
Institute, Northern Arizona University, Flagstaff, ofForensicSciences,Washington,DC,UnitedStates
AZ,UnitedStates
Carla S. Thomas University of California, Plant
Talima Pearson The Pathogen and Microbiome PathologyDepartment,Davis,CA,UnitedStates
Institute, Northern Arizona University, Flagstaff,
Stephan P. Velsko Lawrence Livermore National
AZ,UnitedStates
Laboratory,Livermore,CA,UnitedStates
BernardR.Quigley IHRC,Inc.,Atlanta,GA,United
RichardR.Vines AmericanTypeCultureCollection
States
(ATCC),Manassas,VA,UnitedStates
Lavanya Rishishwar School of Biological Sciences,
Amy Vogler The Pathogen and Microbiome Insti-
Georgia Institute of Technology, Atlanta, GA,
tute, Northern Arizona University, Flagstaff, AZ,
UnitedStates; PanAmericanBioinformaticsInsti-
UnitedStates
tute, Cali, Valle del Cauca, Colombia; Applied
Bioinformatics Laboratory, Atlanta, GA, United David M. Wagner The Pathogen and Microbiome
States Institute, Northern Arizona University, Flagstaff,
AZ,UnitedStates
JasonW.Sahl ThePathogenandMicrobiomeInsti-
tute, Northern Arizona University, Flagstaff, AZ, Karen L. Wahl Pacific Northwest National Labora-
UnitedStates tory,Richland,WA,UnitedStates
StephenA.Saltzburg WallaceandBeverleyUniver- Charles H. Williamson The Pathogen and Micro-
sity Professor, The George Washington University biome Institute, Northern Arizona University,
LawSchool,UnitedStates Flagstaff,AZ,UnitedStates
Harald Scherm University of Georgia, Department Mark Wilson MRW Analytics, LLC, Fredericks-
ofPlantPathology,Athens,GA,UnitedStates burg,VA,UnitedStates
David G. Schmale, III Virginia Tech University, August Woerner Center for Human Identification,
SchoolofPlantandEnvironmentalSciences,Blacks- University of North Texas Health Science Center,
burg,VA,UnitedStates Fort Worth, TX, United States; Department of
Microbiology, Immunology and Genetics, Univer-
Sarah E. Schmedes Association of Public Health
sity of North Texas Health Science Center, Fort
Laboratories,SilverSpring,MD,UnitedStates
Worth,TX,UnitedStates
Steven E. Schutzer Department of Medicine,
David S. Wunschel Pacific Northwest National
Rutgers New Jersey Medical School, Newark, NJ,
Laboratory,Richland,WA,UnitedStates
UnitedStates
Foreword
Iamhonoredthattheauthorshaveaskedme Banburyalreadyhadheldaseriesofmeetings
tocontributetheforewordtothethirdeditionof on what was still a “newly emerged” disease,
Microbial Forensics. My connection to the book Lyme disease. The first meeting was held in
and to the field in general was as a facilitator 1991, only nine years after Willy Burgdorfer
rather than as a researcher, and it was in the had identified the previously unknown path-
distant past, 20 years ago! ogen, the spirochete, Borrelia burgdorferi. I put
MicrobialForensicsreceivedinputanddirection Suzanne in touch with the organizers of those
inaseriesofmeetingsheldattheBanburyCenter, meetings, Steve Schutzer and Ben Luft, and the
aconferencecenteratColdSpringHarborLabo- three organized the April 2000 meeting “Strate-
ratory. Indeed, some meetings held at the Ban- giesforDetectionandIdentificationofUnknown
bury, which predate the emergence of Microbial Pathogens.”
Forensics as a formalized discipline, laid some The primary focus of this meeting was
ofthegroundworkforthismust-neededforensic health, and the word “forensic” did not appear.
field.Banburyhasaninternationalreputationfor However, one of the participants was Roger
intensivediscussionmeetingswithfewerthan30 Breeze,thenwiththeUSDepartmentofAgricul-
participants of topics in the life sciences that ture.Whilethetitleofthemeetingheorganized
would benefit from critical review, topics that in October 2000 had the rather innocuous title
are frequently controversial and often involve “The Challenge of Infectious Diseases in the
issuesofpolicyaswellasscience. 21st Century,” his view of unrecognized infec-
In 1999, Suzanne Vernon and Bill Reeves of tious disease was quite definitely forensic; the
the Centers for Disease Control (CDC) invitation referred to the need for strategies to
approached me about a meeting to be funded dealwithnewandemergingthreats“.ofwhich
by CDC to discuss how it would be possible to biological terrorism is the latest.”
detect and develop tests for unknown patho- Finally, in November 2002, Schutzer and
gens. CDC was interested because it had been Breeze with Bruce Budowle (then with the FBI
proposed that chronic fatigue syndrome (CFS) LaboratoryinQuantico)organizedthefirst“Mi-
was an infectious disease, but the pathogen crobial Forensics” meeting, followed by addi-
detection techniques used by CDCdserology, tional four meetings. The final meeting in 2010
culture, PCRdhad failed to identify an infec- wason“MicrobialForensicsintheEraofGeno-
tious agent associated with CFS. By 1999, new mics,” which reviewed techniques for DNA
techniques were coming online, and CDC sequencingandbioinformaticsthatwereunfath-
wanted to review how these might be used to omable mere eightyearsearlier.
findnovel orpreviouslyuncharacterizedpatho- Despitetheseandotherdramaticadvancesin
gens associatedwith CFS. technology, it is not surprising that the same
xvi
Foreword
broad issues remain, some of which are identi- it becameapowerful toolforthe justicesystem.
fied in the authors’ introduction, for example, I am proud to recall that a Banbury Center
thedifferingneedsoftheworldsofpublichealth meeting in 1988 (attended by Bruce Budowle)
and forensics; the latter required meeting the contributed to cementing this technology as the
legal standards for evidence that might be used gold standard of the forensicsciences.
in the court. Finally, I fully endorse the authors’ closing
The authors refer to the issue of whether mi- remarks.Scientificevidencecarriesgreatauthor-
crobialforensicswillbecentralized,forexample, ity over and above its evidentiary value. This
at the National Bioforensics Analysis Center, or responsibility requires that those employing
become distributed. If the latter, adequate scientifictechniquesintheserviceofforensicsci-
resourcesegraining and infrastructureewill be ence do so to the highest standards possible. It
needed, but this may be hard to justify for took several years for DNA fingerprinting to
what one hopes will berare events. reach that position, and it will take the same
In some ways, I am reminded of the early commitment for microbial forensics to attain
days of forensic DNA fingerprinting. The tech- the same level of credibility and acceptance.
niques and associated population genetic ana- But without a doubt, it will be well worthwhile
lyses had been developed in academic as this burgeoning discipline continues to fulfill
laboratories, and there were many obstacles to its promise.
be overcome before DNA fingerprinting was
accepted. It required training in techniques and Jan AWitkowski PhD
theory, as well as an acceptance by the public, Professor
law enforcement, and defense attorneys, before Cold Spring Harbor Laboratory
Introduction
Stephen A. Morse1, Bruce Budowle2, Steven E. Schutzer3
1IHRC,Inc., Atlanta, GA, UnitedStates; 2Center forHuman Identification,University of North Texas
Health Sciences Center, FortWorth, TX,UnitedStates; 3Department ofMedicine, RutgersNew Jersey
Medical School, Newark,NJ, UnitedStates
Deliberatedisseminationofabiologicalagent Microbialforensicinvestigationsandmolecu-
viaseveraldifferentroutes,includingair,water, lar epidemiologic investigations share many
food, infected vectors, and manmade avenues, aspects but are performed for different reasons.
presents a challenge to global health and secu- An epidemiologic investigation aims to identify
rity. The ability to identify the perpetrator(s) in the source of an outbreak and to understand
an expeditious and effective manner is of para- routesoftransmissioninordertopreventfurther
mount importance as both a deterrent and for spread and reduce the risk of future outbreaks
gauging an appropriate response. Eliminating througheffectivepreventivemeasures.Amicro-
those individuals who are falsely associated bialforensicinvestigationisundertakentoiden-
withevidenceoracrimeisofequalimportance. tifytheperpetratorofacrimeandtogatherhigh
The past decade has seen major advances in qualityevidencethatcanbeusedforindictment
the scientific discipline of microbial forensics, and conviction of perpetrators or to help deci-
whose core objective is attribution: the inves- sion makers prepare an appropriate response
tigative process aimed at identifying the perpe- to an attack. A microbial forensic investigation
trators of a biowarfare, bioterrorism, or hasbeendescribedasconsistingofthreeinterre-
biocrime event and bringing them to justice. lated stages: identification of the biological
This highly interdisciplinary field, which has agent(s) responsible for an event; characteriza-
largely emerged through US initiatives (Tucker tion of the event as intentional, unintentional
and Koblentz, 2009; U.S., 2010), encompasses (e.g.,duetonegligenceorcarelessness),ornatu-
traditionallawenforcementandforensicinvesti- rally occurring; and, if the event is deemed
gativemethodsaswellasthedetailedcharacter- illegitimate (i.e., intentional or unintentional),
ization of samples containing biological agents. attribution of use to a specific perpetrator(s)
Moreover, with the advent of high throughput (Koblentz and Tucker, 2010). Additionally,
technologies, such as massively parallel analyses may be used to determine the pro-
sequencing, microbial forensics as a discipline cess(es) used to produce a bioweapon, which
has expanded beyond its primary focus on can provide additional forensic evidence and
microbes and their products involved in bioter- insight into the sophistication of the production
rorism and biocrimes to other applications such process. Regardless if an event was intentional
asexploiting thehumanmicrobiomeforhuman or accidental, an immediate goal is to prevent
identification, human geolocation, and deter- additional attacks and protect the public.
mining post mortem interval.
xviii
Introduction
Many of the questions asked during the first detection and identification and did not include
two stages of a microbial forensic investigation detailed characterization and comparative ana-
are identical to those of anepidemiologic inves- lyses. Thus,the first edition was developed as a
tigation,andthesamemethodsandtechnologies foundational text to stimulate scientists, legal
aregenerallyusedtoanswerthem(Sjodinetal., experts, and decision makers responsible for
2013).However,theattributionstepisuniqueto analyzing and interpreting evidence from an
microbial forensics. In addition to traditional actofbiologicalwarfare,bioterrorism,biocrime,
forensic analyses of recovered evidence from or inadvertent release of a microorganism or
thecrimescene(analysisofhumanDNA,finger- toxinforattributionpurposesandtodescribethe
prints, fibers, etc.), detailed analyses are con- discipline. In addition, the initial edition of this
ducted of the responsible biologic agent book discussed some of the future opportunities
(bacterium,virus,fungus,ortoxin).Itispossible and challenges for the microbial forensic field.
thattheresultsofanepidemiologicinvestigation The secondedition of this book,published in
maysuggestadeliberateorunintentionalrelease 2011,containedseveralchaptersthatbroughtthe
of a biological agent and thus lead to the initia- Amerithrax investigation to a conclusion. The
tion of a microbial forensic investigation. The anthrax mail investigation, one of the most
intentional release of a biological agent can be intense and expansive investigations to date by
done overtly, in which case the perpetrators the Federal Bureau of Investigation and US
will announce their responsibility, or covertly, Postal Service (http://www.fbi.gov/antrhrax/
in which case they will not call attention to the amerithraxlinks.htm), is now considered closed.
release of a biological agent (Budowle et al., However, the third edition of this book revisits
2005).Itislikelythatmostunintentionalreleases this case and provides a first-hand account of
willbecovert-likeinnature(ZimmerandBurke, the investigation as well as lessons learned on
2009). what should be done in microbial forensics to
Sincethepublicationofthefirsteditionofthis support an investigation and equally important
bookin2005,thefieldofmicrobialforensicshas whatshould be avoided.
evolvedsubstantiallyinitsabilitytoattributethe Many of the elements discussed in the first
source of microorganisms and toxins that have and second editions of this book are echoed in
been used in cases of bioterrorism and in bio- the 2009 US National Research and Develop-
crimes. The 2001 anthrax mail attack (often ment Strategy for Microbial Forensics (U.S.,
referredtoas“Amerithrax”)fortunatelyremains 2010),whichidentifiesthreatawareness,preven-
theworstandbest-knownexampleofsuccessful tion and protection, surveillance and detection,
bioterrorism on US soil (Chapters 2 and 3). At and response and recovery as the essential pil-
the time, the US was ill prepared to investigate lars of US national biodefense policy.
the unique types of microbiological evidence “Attribution”dthe investigative process by
forattributionthatweregeneratedbythatinves- which the US government links the identity of
tigation, although traditional types of forensic a perpetrator or perpetrators of illicit activity
evidence could readily be collected, analyzed, andthepathwayleadingtocriminalactivitydis
andinterpretedwithintheframeworkofastatis- part of the surveillance and detection pillar.
tically sound scientific foundation. The first Making a determination of attribution for a
edition of this book had only limited reference planned or actual perpetrated biological attack
to the anthrax mail attack because much of the would be the culmination of a complex investi-
scientific examination was still in progress and gative process drawing on many different sour-
methodologies were still under development. ces of information, including traditional
Early capabilities were initially limited to forensic analysis of material evidence collected