Budowle / Schutzer / Breeze Microbial Forensics

2. Auflage 2010
ISBN: 978-0-12-382007-5
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 744 Seiten

Microbial Forensics is a rapidly evolving scientific discipline. In the last decade, and particularly due to the anthrax letter attacks in the United States, microbial forensics has become more formalized and has played an increasingly greater role in crime investigations. This has brought renewed interest, development and application of new technologies, and new rules of forensic and policy engagement. It has many applications ranging from biodefense, criminal investigations, providing intelligence information, making society more secure, and helping protect precious resources, particularly human life. A combination of diverse areas is investigated, including the major disciplines of biology, microbiology, medicine, chemistry, physics, statistics, population genetics, and computer science. Microbial Forensics, Second Edition is fully revised and updated and serves as a complete reference of the discipline. It describes the advances, as well as the challenges and opportunities ahead, and will be integral in applying science to help solve future biocrimes. - A collection of microbiology, virology, toxicology and mycology as it relates to forensics, in one reference - New and expanded content to include statistical analysis of forensic data and legal admissibility and the standards of evidence, to name a few - Includes research information and application of that research to crime scene analysis, which will allow practitioners to understand and apply the knowledge to their practice with ease

Autoren/Hrsg.

Budowle, Bruce

Schutzer, Steven E.

Breeze, Roger G.

Keim, Paul S.

Morse, Stephen A.

Inhaltsverzeichnis

1;FRONT COVER;1
2;MICROBIAL FORENSICS;4
3;COPYRIGHT PAGE;5
4;CONTENTS;6
5;CONTRIBUTORS;10
6;FOREWORD;16
7;ACKNOWLEDGMENTS;18
8;INTRODUCTION – The Rapidly Evolving Discipline of Microbial Forensics;20
9;PART 1 INVESTIGATIVE GENETICS;24
9.1;Section A: Criminal;26
9.1.1;CHAPTER 1 The Kameido Anthrax Incident: A Microbial Forensics Case Study;28
9.1.1.1;Introduction;28
9.1.1.2;The Aum Shinrikyo: A Brief History;28
9.1.1.3;The Kameido Anthrax Incident;31
9.1.1.4;Microbial Forensics Investigation;32
9.1.1.5;Epidemiological Investigation;33
9.1.1.6;Discussion;34
9.1.1.7;Challenges;35
9.1.1.8;References;36
9.1.2;CHAPTER 2 Microbial Forensic Investigation of the Anthrax-Letter Attacks;38
9.1.2.1;The Anthrax-Letter Event;38
9.1.2.2;Identifying the Attack Strain;41
9.1.2.3;Whole Genome Sequencing of the “Florida” Ames Strain;42
9.1.2.4;Development of Ames-Specific Assays;43
9.1.2.5;The FBI Repository;43
9.1.2.6;Morphological Variants;44
9.1.2.7;Conclusion and Remaining Issues;46
9.1.2.8;References;47
9.2;Section B: Civilian;50
9.2.1;CHAPTER 3 Food-Borne Outbreaks: What’s New, What’s Not, and Where Do We Go from Here?;52
9.2.1.1;Prologue;52
9.2.1.2;Food-borne Illness: an Old but Persistent Problem;53
9.2.1.3;The Changing Landscape of Food-Borne Outbreaks;54
9.2.1.4;Enteric Pathogens as Bioterrorism Agents;57
9.2.1.5;Epilogue;60
9.2.1.6;References;61
9.2.2;CHAPTER 4 Genotype and Geography: The Global Distribution of Bovine Tuberculosis;66
9.2.2.1;What Can Bacterial Genotyping Offer the Forensic Microbiologist?;66
9.2.2.2;Has This Strain Been Recently Imported?;67
9.2.2.3;Where Did This Strain Come From?;68
9.2.2.4;Bovine Tuberculosis;68
9.2.2.5;Geographical Localization of M. Bovis Genotypes in Great Britain;69
9.2.2.6;Bovine Tuberculosis in the British Isles;70
9.2.2.7;Global Distribution of M. Bovis Genotypes;71
9.2.2.8;Europe 1—A Globally Important Clonal Complex of M. Bovis;72
9.2.2.9;African 1—Dominant in West-Central Africa;74
9.2.2.10;African 2—Dominant in East Africa;76
9.2.2.11;Other Clonal Complexes of M. Bovis in Africa;76
9.2.2.12;“Of What Use Is A Baby?”;77
9.2.2.13;Can We Identify the Origin of Imported Strains?;78
9.2.2.14;Acknowledgment;78
9.2.2.15;References;78
9.2.3;CHAPTER 5 Tracing Meat Products through the Production and Distribution Chain from Farm to Consumer;82
9.2.3.1;Introduction;82
9.2.3.2;Meat Chain Structure and Complexity;82
9.2.3.3;Genetic Identification of the Host Animal and its Derived Products;85
9.2.3.4;Tracing Meat Products Through the Supply Chain;87
9.2.3.5;Washington State BSE-Positive Cow;90
9.2.3.6;Food Safety;93
9.2.3.7;Practical Limits;93
9.2.3.8;Summary and Future Directions;95
9.2.3.9;References;95
9.2.4;CHAPTER 6 Microbial Forensics of RNA Viruses: Foot-and-Mouth Disease Virus;98
9.2.4.1;Challenges Posed by RNA Viruses;98
9.2.4.2;A Case Study: Foot-and-Mouth Disease in the United Kingdom (2001);99
9.2.4.3;What Information is Needed;100
9.2.4.4;Where We are Now;103
9.2.4.5;What Needs to be Done;104
9.2.4.6;References;107
9.2.5;CHAPTER 7 Forensic Plant Pathology;112
9.2.5.1;Introduction;112
9.2.5.2;Naturally Caused Versus Intentional Introduction?;113
9.2.5.3;History of Agricultural Bioweapons;113
9.2.5.4;The Need for Forensic Plant Pathology;115
9.2.5.5;Pathogen Detection and Diagnostics;116
9.2.5.6;Epidemiology in Forensic Investigation;117
9.2.5.7;Mutation, Evolution, and Forensic Plant Pathology;118
9.2.5.8;Investigation;120
9.2.5.9;Roles and Responsibilities;121
9.2.5.10;Education and Outreach;123
9.2.5.11;Resources and Infrastructure;124
9.2.5.12;Gaps;125
9.2.5.13;Summary;126
9.2.5.14;References;126
10;PART 2 EMERGING INFECTIONS;130
10.1;CHAPTER 8 Influenza Forensics;132
10.1.1;Introduction;132
10.1.2;The Influenza Virus;133
10.1.3;Influenza a Genomics;133
10.1.4;Influenza Nomenclature;136
10.1.5;Time: The Major Foe of Influenza Forensics;139
10.1.6;A Brief History of Pandemic Influenza a in Humans;140
10.1.7;2009 H1N1 Pandemic;142
10.1.8;Outbreak Detection: Symptoms, Diagnostics, and Surveillance;145
10.1.9;Surveillance;147
10.1.10;Diagnostics;147
10.1.11;Influenza as a Bioweapon;149
10.1.12;Moving Forward;152
10.1.13;Acknowledgments;152
10.1.14;References;152
10.2;CHAPTER 9 Keeping Track of Viruses;160
10.2.1;Introduction;160
10.2.2;What is a Virus?;160
10.2.3;Virus Life Cycle;161
10.2.4;How Do You Identify A Virus?;163
10.2.5;Viral Diversity and Phylogenetics;169
10.2.6;Solving a Biocrime;171
10.2.7;Challenges That Remain;174
10.2.8;Acknowledgments;174
10.2.9;References;175
10.3;CHAPTER 10 Microbial Forensic Analysis of Trace and Unculturable Specimens;178
10.3.1;Introduction to Bioforensic Analysis of Trace DNA;178
10.3.2;Use of WGA for Microbial Forensic Analysis of Trace Environmental Specimens;181
10.3.3;Deep Sequence Analysis of Bacillus anthracis Sterne Strain by Roche 454 Genome Sequencing Technology;185
10.3.4;Microbial Forensic Sequence Analysis of Trace Specimens of Bacillus anthracis by Single Molecule Real-Time Sequencing;188
10.3.5;Conclusions and Remaining Challenges;191
10.3.6;Acknowledgments;192
10.3.7;References;192
10.4;CHAPTER 11 Molecular Microbial Surveillance and Discovery in Bioforensics;196
10.4.1;Fundamental Questions: What is it? How Did it Get There? What Can We do About it? Climate is What You Expect; Weather is What You Get…How Expectations…;196
10.4.2;Characterization of the Threat: What Kind of Bug is It?;198
10.4.3;Conclusion;204
10.4.4;Acknowledgments;204
10.4.5;References;205
11;PART 3 BIOSECURITY;210
11.1;CHAPTER 12 Assessment of the Threat;212
11.1.1;National Threat Assessment: Role of the Intelligence Community;212
11.1.2;Threat Credibility Assessments: Role of Law Enforcement and Public Health Officials;215
11.1.3;Conclusion;219
11.1.4;References;219
11.2;CHAPTER 13 Select Agent Regulations;222
11.2.1;Introduction;222
11.2.2;The Select Agent Regulations;229
11.2.3;Summary;241
11.2.4;Acknowledgments;242
11.2.5;References;242
11.3;CHAPTER 14 Biosurety in the Post-9/11 Era;244
11.3.1;Introduction: Amerithrax and the Focus on Biosurety;244
11.3.2;The Threat of Misuse of Biological Agents;245
11.3.3;Categories of Threats;248
11.3.4;The Challenge of Protecting Against Insider Threats;252
11.3.5;Conclusion;258
11.3.6;References;259
11.4;CHAPTER 15 Forensic Public Health: Epidemiologic and Microbiologic Investigations for Biosecurity;262
11.4.1;Introduction;262
11.4.2;Dynamics of Disease Transmission;262
11.4.3;Outbreak Investigation;264
11.4.4;Deliberate Introduction of a Biological Agent;265
11.4.5;Molecular Strain Typing;269
11.4.6;Summary;275
11.4.7;Acknowledgments;276
11.4.8;References;276
12;PART 4 SUBJECT AREAS;280
12.1;CHAPTER 16 Forensic Analysis in Bacterial Pathogens;282
12.1.1;Introduction;282
12.1.2;16S Sequences and Rapid Identification of Microbes;283
12.1.3;Forensic Signatures: Human Versus Bacterial Pathogens;283
12.1.4;Bacillus Anthracis: A Model System;284
12.1.5;Mutation Rates in Bacteria;286
12.1.6;Yersinia Pestis and Plague: Another Recently Emerged Pathogen;287
12.1.7;Francisella Tularensis;289
12.1.8;Brucella spp. and Brucellosis;290
12.1.9;Burkholderia Pseudomallei;292
12.1.10;Clostridium Botulinum;293
12.1.11;Conclusions;295
12.1.12;References;295
12.2;CHAPTER 17 Rickettsia and Coxiella;300
12.2.1;Introduction;300
12.2.2;Rocky Mountain Spotted Fever, Epidemic Typhus, and Q Fever: The Diseases;301
12.2.3;Epidemiology;302
12.2.4;Diagnosis/Detection in Clinical Samples;303
12.2.5;Detection in Environmental Samples;304
12.2.6;Rickettsia Strain Typing;305
12.2.7;Coxiella Strain Typing;308
12.2.8;Conclusions;310
12.2.9;References;310
12.3;CHAPTER 18 Forensics and Epidemiology of Fungal Pathogens;320
12.3.1;Introduction;320
12.3.2;The Kingdom Fungi;320
12.3.3;Pathogenic Fungi;321
12.3.4;Conclusions;333
12.3.5;Disclaimer;333
12.3.6;References;334
12.4;CHAPTER 19 Ricin Forensics: Comparisons to Microbial Forensics;338
12.4.1;Introduction;338
12.4.2;Background;339
12.4.3;Ricin Toxin Detection;342
12.4.4;Castor Bean Genotyping;344
12.4.5;Challenges;346
12.4.6;References;347
12.5;CHAPTER 20 Forensic Aspects of Biological Toxins;350
12.5.1;Introduction;350
12.5.2;Botulinum Neurotoxin and Botulism;350
12.5.3;Ricin;365
12.5.4;Staphylococcal Enterotoxin B;366
12.5.5;Clostridium Perfringens Epsilon Toxin;367
12.5.6;Summary;367
12.5.7;Acknowledgment;368
12.5.8;References;368
13;PART 5 METHODS;378
13.1;CHAPTER 21 Use of Host Factors in Microbial Forensics;380
13.1.1;Introduction and Background;380
13.1.2;General Concepts;382
13.1.3;Illustrative Concepts;385
13.1.4;Utility of Serologic Analysis of People Exposed to Anthrax: Strengths and Limitations;387
13.1.5;Considerations and Concerns Raised by Analysis of Other Infections;391
13.1.6;Possible Scenarios of Bioterrorism Attacks: Distinguishing Victims from Perpetrators;395
13.1.7;References;398
13.2;CHAPTER 22 Collection and Preservation of Microbial Forensic Samples;402
13.2.1;General Best Practices of Collection of Forensic Evidence;404
13.2.2;Collection Strategies and Methods for Microbial Forensic Sampling;407
13.2.3;Looking to the Future;411
13.2.4;References;412
13.3;CHAPTER 23 Sampling for Microbial Forensic Investigations;416
13.3.1;Introduction;416
13.3.2;Commonalties and Differences Between Microbial Epidemiological and Microbial Forensic Investigations;417
13.3.3;Problems Associated with Sampling Activities for Both Microbial Epidemiological and Microbial Forensic Investigations;418
13.3.4;Challenges for Microbial Epidemiological and Microbial Forensic Investigations;423
13.3.5;Conclusion;425
13.3.6;Disclaimer;425
13.3.7;References;426
13.4;CHAPTER 24 Toxin Analysis Using Mass Spectrometry;428
13.4.1;Introduction;428
13.4.2;Specific Analytical Methods for Toxins;435
13.4.3;Quality Control, Validation, and Data Review;439
13.4.4;Current Limitations to Toxin Analysis;440
13.4.5;References;441
13.5;CHAPTER 25 Electron Beam-Based Methods for Bioforensic Investigations;444
13.5.1;Introduction;444
13.5.2;Electron Beam-Based Characterization Techniques;445
13.5.3;Conventional and Advanced Methods of Microanalysis, Data Acquisition and Analysis;454
13.5.4;Sample Preparation for Sem and (S)Tem;458
13.5.5;Applications of Electron Beam Characterization in Bioforensics;462
13.5.6;Summary;467
13.5.7;Acknowledgments;469
13.5.8;References;469
13.6;CHAPTER 26 Proteomics Development and Application for Bioforensics;472
13.6.1;Introduction;472
13.6.2;Microbiology and Biochemistry;473
13.6.3;Protein Detection and Identification—Mass Spectrometry for Proteomics Analysis;475
13.6.4;Computational Sciences;477
13.6.5;Summary;479
13.6.6;References;480
13.7;CHAPTER 27 High-Throughput Sequencing;484
13.7.1;Initial DNA Sequencing Approaches;484
13.7.2;Microbial Genome Sequencing;486
13.7.3;Next-Generation Sequencing Technology;490
13.7.4;Assembly Methods for DNA Sequence;495
13.7.5;Resequencing;497
13.7.6;Conclusion;497
13.7.7;References;498
13.8;CHAPTER 28 Genomics;502
13.8.1;Sequencing Technologies;503
13.8.2;Bioinformatics Sequence Analysis;506
13.8.3;The Pregenomic Era;507
13.8.4;Comparative Genomics;508
13.8.5;High-Throughput Screening Assays;509
13.8.6;Metagenomics;510
13.8.7;Genome Architecture and Evolution;510
13.8.8;Future Challenges;511
13.8.9;Genomics and Microbial Forensics;512
13.8.10;References;513
13.9;CHAPTER 29 Design of Genomic Signatures for Pathogen Identification and Characterization;516
13.9.1;Genomic Signatures;516
13.9.2;Different Types and Resolutions of Genomic Signatures;517
13.9.3;Potential Target Organisms;517
13.9.4;Signature Resolution;518
13.9.5;Genomic Sequence Data: What To Use And Where To Get It;518
13.9.6;Identifying Conserved Sequence Among Targets;520
13.9.7;Identifying Sequences Unique to Targets;521
13.9.8;Mining for Signatures;522
13.9.9;How Kpath Signatures are Designed;522
13.9.10;RNA Viruses Present Additional Challenges;523
13.9.11;Signatures of Potential Bacterial Genetic Engineering;525
13.9.12;Viral and Bacterial Detection Array;527
13.9.13;The Future of Genomic Signatures;528
13.9.14;Disclaimer;530
13.9.15;References;530
13.10;CHAPTER 30 Nonbiological Measurements on Biological Agents;532
13.10.1;Introduction;532
13.10.2;Determining Manufacturing Method;533
13.10.3;Sample Matching;539
13.10.4;Remaining Research and Development Challenges;541
13.10.5;Preparing for Future Events;544
13.10.6;Concluding Remarks;545
13.10.7;Acknowledgments;545
13.10.8;Disclaimer;546
13.10.9;References;546
13.11;CHAPTER 31 Inferential Validation and Evidence Interpretation;550
13.11.1;The Need to Validate the Interpretation of Microbial Forensic Evidence;550
13.11.2;The Taxonomy of Validation;551
13.11.3;The ROC/LR Framework for Inferential Validation;554
13.11.4;Application to Chemical and Physical Analysis of Biological Agents;562
13.11.5;Conclusion;565
13.11.6;Disclaimer;565
13.11.7;References;565
13.12;CHAPTER 32 Microbial Forensic Investigations in the Context of Bacterial Population Genetics;568
13.12.1;Introduction and Background;568
13.12.2;A Microbial Forensic Paradigm;571
13.12.3;Calculating Match Probabilities;578
13.12.4;Reference Database;579
13.12.5;Discussion;580
13.12.6;References;581
13.13;CHAPTER 33 Population Genetic Considerations in Statistical Interpretation of Microbial Forensic Data in Comparision with Human DNA Forensic Standard;584
13.13.1;Introduction;584
13.13.2;Background of Some Major Pathogens;585
13.13.3;Statistical Paradigm of Source Attribution of Microbial Agents;586
13.13.4;Conclusions;596
13.13.5;References;597
13.14;CHAPTER 34 Biorepositories and Their Foundations—Microbial Forensic Considerations;604
13.14.1;Introduction: Role of Biorepositories and Systematics in Microbial Forensics;604
13.14.2;Operational Biorepository Collection Verification and Validation Concerns;608
13.14.3;Beyond MLST—Extended Range Ultraresolution Typing;613
13.14.4;Challenges;615
13.14.5;Acknowledgments;621
13.14.6;References;621
14;PART 6 NATIONAL LEVEL CAPABILITIES;626
14.1;CHAPTER 35 A U.S. Research Strategy for Microbial Forensics: From Genesis to Implementation;628
14.1.1;Introduction;628
14.1.2;The Pillars of Biodefense;630
14.1.3;Setting the Foundation for a Research Strategy;631
14.1.4;Implementing a Formal Government Research Strategy;633
14.1.5;A Comprehensive Microbial Forensic Strategy Emerges;634
14.1.6;Meeting the Research Strategic Goals—Microbial Forensic Research Program in DHS S&T;637
14.1.7;Conclusion;639
14.1.8;References;640
14.2;CHAPTER 36 The National Bioforensic Analysis Center;642
14.2.1;Introduction;642
14.2.2;History of the NBFAC;642
14.2.3;NBFAC Operational Components;644
14.2.4;NBFAC Biothreat Agent Bioforensic Capability Expansion and Vision for the Future;645
14.2.5;New NBACC Laboratory Building;646
14.2.6;Conclusion;647
14.2.7;References;647
14.3;CHAPTER 37 Microbial Forensics in Australia—The Australian Federal Police Perspective;650
14.3.1;Introduction;650
14.3.2;The Threat of Bioterrorism in Australia;652
14.3.3;The Australian CBRN Data Center;652
14.3.4;The Australian Federal Police and its Role in Preventing, Countering, and Investigating Terrorism;653
14.3.5;The Australian Federal Police Microbial Forensics Program;654
14.3.6;The Australian Federal Police Mobile and Triage Laboratories;657
14.3.7;National Regulatory Scheme for Biological Agents of Security Concern;664
14.3.8;Potential Expansions to the Australian Federal Police Microbial Forensic Capability;665
14.3.9;The Australian Federal Police in the Whole of Government Approach to Bioterrorism;665
14.3.10;Conclusion;668
14.3.11;Acknowledgment;669
14.3.12;References;669
14.4;CHAPTER 38 Validation of Microbial Forensics in Scientific, Legal, and Policy Contexts;672
14.4.1;Introduction;672
14.4.2;An Accepted Approach to Validation Exists;673
14.4.3;Validation as Part of the Quest for Quality in Forensic Science;675
14.4.4;Legal Validation of Novel Scientific Techniques in U.S. Courts;676
14.4.5;Observations of the National Academy of Sciences (2009);681
14.4.6;Validation: Science at Intersections of Legal and Policy Environments: Snapshot Illustrations;682
14.4.7;Challenges Ahead for Microbial Forensics;684
14.4.8;Disclaimer;684
14.4.9;References;684
15;PART 7 MICROBIAL FORENSICS CURRICULA AND TRAINING;688
15.1;CHAPTER 39 Microbial Forensics: Educating the Workforce and the Community;690
15.1.1;Microbial Forensics Curricula and Training;691
15.1.2;Basic Epidemiology;694
15.1.3;Molecular Epidemiology;695
15.1.4;Microbes and Their Products as Biological Weapons;695
15.1.5;Host Factors Including Immune Responses;696
15.1.6;Processes and Technology;696
15.1.7;Forensic Science;700
15.1.8;Case Histories;701
15.1.9;Legal Issues;701
15.1.10;Operational and Intelligence Issues;702
15.1.11;National-Level Capabilities and Resources;702
15.1.12;Conclusion;703
15.1.13;References;703
15.2;CHAPTER 40 So You Really Want to Be an Expert Witness? A Primer for the Occasional Expert Witness;704
15.2.1;Attorneys’ Roles;704
15.2.2;Discovery;706
15.2.3;Experts’ Roles;709
15.2.4;Consequences of Discovery Violation;710
15.2.5;Grant Solicitations/Applications;711
15.2.6;Peer Review Articles/Comments;712
15.2.7;References;714
15.3;CHAPTER 41 Microbial Forensics, What Next?;716
15.3.1;References;719
16;INDEX;720
16.1;A;720
16.2;B;721
16.3;C;724
16.4;D;725
16.5;E;727
16.6;F;728
16.7;G;729
16.8;H;730
16.9;I;731
16.10;J;733
16.11;K;733
16.12;L;733
16.13;M;733
16.14;N;735
16.15;O;736
16.16;P;736
16.17;Q;738
16.18;R;739
16.19;S;740
16.20;T;743
16.21;U;743
16.22;V;744
16.23;W;745
16.24;X;745
16.25;Y;745
16.26;Z;745
17;COLOR PLATES;746