Microbial Forensics (eBook)

FRONT COVER 1
MICROBIAL FORENSICS 4
COPYRIGHT PAGE 5
CONTENTS 6
CONTRIBUTORS 10
FOREWORD 16
ACKNOWLEDGMENTS 18
INTRODUCTION – The Rapidly Evolving Discipline of Microbial Forensics 20
PART 1 INVESTIGATIVE GENETICS 24
Section A: Criminal 26
CHAPTER 1 The Kameido Anthrax Incident: A Microbial Forensics Case Study 28
Introduction 28
The Aum Shinrikyo: A Brief History 28
The Kameido Anthrax Incident 31
Microbial Forensics Investigation 32
Epidemiological Investigation 33
Discussion 34
Challenges 35
References 36
CHAPTER 2 Microbial Forensic Investigation of the Anthrax-Letter Attacks 38
The Anthrax-Letter Event 38
Identifying the Attack Strain 41
Whole Genome Sequencing of the “Florida” Ames Strain 42
Development of Ames-Specific Assays 43
The FBI Repository 43
Morphological Variants 44
Conclusion and Remaining Issues 46
References 47
Section B: Civilian 50
CHAPTER 3 Food-Borne Outbreaks: What’s New, What’s Not, and Where Do We Go from Here? 52
Prologue 52
Food-borne Illness: an Old but Persistent Problem 53
The Changing Landscape of Food-Borne Outbreaks 54
Enteric Pathogens as Bioterrorism Agents 57
Epilogue 60
References 61
CHAPTER 4 Genotype and Geography: The Global Distribution of Bovine Tuberculosis 66
What Can Bacterial Genotyping Offer the Forensic Microbiologist? 66
Has This Strain Been Recently Imported? 67
Where Did This Strain Come From? 68
Bovine Tuberculosis 68
Geographical Localization of M. Bovis Genotypes in Great Britain 69
Bovine Tuberculosis in the British Isles 70
Global Distribution of M. Bovis Genotypes 71
Europe 1—A Globally Important Clonal Complex of M. Bovis 72
African 1—Dominant in West-Central Africa 74
African 2—Dominant in East Africa 76
Other Clonal Complexes of M. Bovis in Africa 76
“Of What Use Is A Baby?” 77
Can We Identify the Origin of Imported Strains? 78
Acknowledgment 78
References 78
CHAPTER 5 Tracing Meat Products through the Production and Distribution Chain from Farm to Consumer 82
Introduction 82
Meat Chain Structure and Complexity 82
Genetic Identification of the Host Animal and its Derived Products 85
Tracing Meat Products Through the Supply Chain 87
Washington State BSE-Positive Cow 90
Food Safety 93
Practical Limits 93
Summary and Future Directions 95
References 95
CHAPTER 6 Microbial Forensics of RNA Viruses: Foot-and-Mouth Disease Virus 98
Challenges Posed by RNA Viruses 98
A Case Study: Foot-and-Mouth Disease in the United Kingdom (2001) 99
What Information is Needed 100
Where We are Now 103
What Needs to be Done 104
References 107
CHAPTER 7 Forensic Plant Pathology 112
Introduction 112
Naturally Caused Versus Intentional Introduction? 113
History of Agricultural Bioweapons 113
The Need for Forensic Plant Pathology 115
Pathogen Detection and Diagnostics 116
Epidemiology in Forensic Investigation 117
Mutation, Evolution, and Forensic Plant Pathology 118
Investigation 120
Roles and Responsibilities 121
Education and Outreach 123
Resources and Infrastructure 124
Gaps 125
Summary 126
References 126
PART 2 EMERGING INFECTIONS 130
CHAPTER 8 Influenza Forensics 132
Introduction 132
The Influenza Virus 133
Influenza a Genomics 133
Influenza Nomenclature 136
Time: The Major Foe of Influenza Forensics 139
A Brief History of Pandemic Influenza a in Humans 140
2009 H1N1 Pandemic 142
Outbreak Detection: Symptoms, Diagnostics, and Surveillance 145
Surveillance 147
Diagnostics 147
Influenza as a Bioweapon 149
Moving Forward 152
Acknowledgments 152
References 152
CHAPTER 9 Keeping Track of Viruses 160
Introduction 160
What is a Virus? 160
Virus Life Cycle 161
How Do You Identify A Virus? 163
Viral Diversity and Phylogenetics 169
Solving a Biocrime 171
Challenges That Remain 174
Acknowledgments 174
References 175
CHAPTER 10 Microbial Forensic Analysis of Trace and Unculturable Specimens 178
Introduction to Bioforensic Analysis of Trace DNA 178
Use of WGA for Microbial Forensic Analysis of Trace Environmental Specimens 181
Deep Sequence Analysis of Bacillus anthracis Sterne Strain by Roche 454 Genome Sequencing Technology 185
Microbial Forensic Sequence Analysis of Trace Specimens of Bacillus anthracis by Single Molecule Real-Time Sequencing 188
Conclusions and Remaining Challenges 191
Acknowledgments 192
References 192
CHAPTER 11 Molecular Microbial Surveillance and Discovery in Bioforensics 196
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…
Characterization of the Threat: What Kind of Bug is It? 198
Conclusion 204
Acknowledgments 204
References 205
PART 3 BIOSECURITY 210
CHAPTER 12 Assessment of the Threat 212
National Threat Assessment: Role of the Intelligence Community 212
Threat Credibility Assessments: Role of Law Enforcement and Public Health Officials 215
Conclusion 219
References 219
CHAPTER 13 Select Agent Regulations 222
Introduction 222
The Select Agent Regulations 229
Summary 241
Acknowledgments 242
References 242
CHAPTER 14 Biosurety in the Post-9/11 Era 244
Introduction: Amerithrax and the Focus on Biosurety 244
The Threat of Misuse of Biological Agents 245
Categories of Threats 248
The Challenge of Protecting Against Insider Threats 252
Conclusion 258
References 259
CHAPTER 15 Forensic Public Health: Epidemiologic and Microbiologic Investigations for Biosecurity 262
Introduction 262
Dynamics of Disease Transmission 262
Outbreak Investigation 264
Deliberate Introduction of a Biological Agent 265
Molecular Strain Typing 269
Summary 275
Acknowledgments 276
References 276
PART 4 SUBJECT AREAS 280
CHAPTER 16 Forensic Analysis in Bacterial Pathogens 282
Introduction 282
16S Sequences and Rapid Identification of Microbes 283
Forensic Signatures: Human Versus Bacterial Pathogens 283
Bacillus Anthracis: A Model System 284
Mutation Rates in Bacteria 286
Yersinia Pestis and Plague: Another Recently Emerged Pathogen 287
Francisella Tularensis 289
Brucella spp. and Brucellosis 290
Burkholderia Pseudomallei 292
Clostridium Botulinum 293
Conclusions 295
References 295
CHAPTER 17 Rickettsia and Coxiella 300
Introduction 300
Rocky Mountain Spotted Fever, Epidemic Typhus, and Q Fever: The Diseases 301
Epidemiology 302
Diagnosis/Detection in Clinical Samples 303
Detection in Environmental Samples 304
Rickettsia Strain Typing 305
Coxiella Strain Typing 308
Conclusions 310
References 310
CHAPTER 18 Forensics and Epidemiology of Fungal Pathogens 320
Introduction 320
The Kingdom Fungi 320
Pathogenic Fungi 321
Conclusions 333
Disclaimer 333
References 334
CHAPTER 19 Ricin Forensics: Comparisons to Microbial Forensics 338
Introduction 338
Background 339
Ricin Toxin Detection 342
Castor Bean Genotyping 344
Challenges 346
References 347
CHAPTER 20 Forensic Aspects of Biological Toxins 350
Introduction 350
Botulinum Neurotoxin and Botulism 350
Ricin 365
Staphylococcal Enterotoxin B 366
Clostridium Perfringens Epsilon Toxin 367
Summary 367
Acknowledgment 368
References 368
PART 5 METHODS 378
CHAPTER 21 Use of Host Factors in Microbial Forensics 380
Introduction and Background 380
General Concepts 382
Illustrative Concepts 385
Utility of Serologic Analysis of People Exposed to Anthrax: Strengths and Limitations 387
Considerations and Concerns Raised by Analysis of Other Infections 391
Possible Scenarios of Bioterrorism Attacks: Distinguishing Victims from Perpetrators 395
References 398
CHAPTER 22 Collection and Preservation of Microbial Forensic Samples 402
General Best Practices of Collection of Forensic Evidence 404
Collection Strategies and Methods for Microbial Forensic Sampling 407
Looking to the Future 411
References 412
CHAPTER 23 Sampling for Microbial Forensic Investigations 416
Introduction 416
Commonalties and Differences Between Microbial Epidemiological and Microbial Forensic Investigations 417
Problems Associated with Sampling Activities for Both Microbial Epidemiological and Microbial Forensic Investigations 418
Challenges for Microbial Epidemiological and Microbial Forensic Investigations 423
Conclusion 425
Disclaimer 425
References 426
CHAPTER 24 Toxin Analysis Using Mass Spectrometry 428
Introduction 428
Specific Analytical Methods for Toxins 435
Quality Control, Validation, and Data Review 439
Current Limitations to Toxin Analysis 440
References 441
CHAPTER 25 Electron Beam-Based Methods for Bioforensic Investigations 444
Introduction 444
Electron Beam-Based Characterization Techniques 445
Conventional and Advanced Methods of Microanalysis, Data Acquisition and Analysis 454
Sample Preparation for Sem and (S)Tem 458
Applications of Electron Beam Characterization in Bioforensics 462
Summary 467
Acknowledgments 469
References 469
CHAPTER 26 Proteomics Development and Application for Bioforensics 472
Introduction 472
Microbiology and Biochemistry 473
Protein Detection and Identification—Mass Spectrometry for Proteomics Analysis 475
Computational Sciences 477
Summary 479
References 480
CHAPTER 27 High-Throughput Sequencing 484
Initial DNA Sequencing Approaches 484
Microbial Genome Sequencing 486
Next-Generation Sequencing Technology 490
Assembly Methods for DNA Sequence 495
Resequencing 497
Conclusion 497
References 498
CHAPTER 28 Genomics 502
Sequencing Technologies 503
Bioinformatics Sequence Analysis 506
The Pregenomic Era 507
Comparative Genomics 508
High-Throughput Screening Assays 509
Metagenomics 510
Genome Architecture and Evolution 510
Future Challenges 511
Genomics and Microbial Forensics 512
References 513
CHAPTER 29 Design of Genomic Signatures for Pathogen Identification and Characterization 516
Genomic Signatures 516
Different Types and Resolutions of Genomic Signatures 517
Potential Target Organisms 517
Signature Resolution 518
Genomic Sequence Data: What To Use And Where To Get It 518
Identifying Conserved Sequence Among Targets 520
Identifying Sequences Unique to Targets 521
Mining for Signatures 522
How Kpath Signatures are Designed 522
RNA Viruses Present Additional Challenges 523
Signatures of Potential Bacterial Genetic Engineering 525
Viral and Bacterial Detection Array 527
The Future of Genomic Signatures 528
Disclaimer 530
References 530
CHAPTER 30 Nonbiological Measurements on Biological Agents 532
Introduction 532
Determining Manufacturing Method 533
Sample Matching 539
Remaining Research and Development Challenges 541
Preparing for Future Events 544
Concluding Remarks 545
Acknowledgments 545
Disclaimer 546
References 546
CHAPTER 31 Inferential Validation and Evidence Interpretation 550
The Need to Validate the Interpretation of Microbial Forensic Evidence 550
The Taxonomy of Validation 551
The ROC/LR Framework for Inferential Validation 554
Application to Chemical and Physical Analysis of Biological Agents 562
Conclusion 565
Disclaimer 565
References 565
CHAPTER 32 Microbial Forensic Investigations in the Context of Bacterial Population Genetics 568
Introduction and Background 568
A Microbial Forensic Paradigm 571
Calculating Match Probabilities 578
Reference Database 579
Discussion 580
References 581
CHAPTER 33 Population Genetic Considerations in Statistical Interpretation of Microbial Forensic Data in Comparision with Human DNA Forensic Standard 584
Introduction 584
Background of Some Major Pathogens 585
Statistical Paradigm of Source Attribution of Microbial Agents 586
Conclusions 596
References 597
CHAPTER 34 Biorepositories and Their Foundations—Microbial Forensic Considerations 604
Introduction: Role of Biorepositories and Systematics in Microbial Forensics 604
Operational Biorepository Collection Verification and Validation Concerns 608
Beyond MLST—Extended Range Ultraresolution Typing 613
Challenges 615
Acknowledgments 621
References 621
PART 6 NATIONAL LEVEL CAPABILITIES 626
CHAPTER 35 A U.S. Research Strategy for Microbial Forensics: From Genesis to Implementation 628
Introduction 628
The Pillars of Biodefense 630
Setting the Foundation for a Research Strategy 631
Implementing a Formal Government Research Strategy 633
A Comprehensive Microbial Forensic Strategy Emerges 634
Meeting the Research Strategic Goals—Microbial Forensic Research Program in DHS S& T
Conclusion 639
References 640
CHAPTER 36 The National Bioforensic Analysis Center 642
Introduction 642
History of the NBFAC 642
NBFAC Operational Components 644
NBFAC Biothreat Agent Bioforensic Capability Expansion and Vision for the Future 645
New NBACC Laboratory Building 646
Conclusion 647
References 647
CHAPTER 37 Microbial Forensics in Australia—The Australian Federal Police Perspective 650
Introduction 650
The Threat of Bioterrorism in Australia 652
The Australian CBRN Data Center 652
The Australian Federal Police and its Role in Preventing, Countering, and Investigating Terrorism 653
The Australian Federal Police Microbial Forensics Program 654
The Australian Federal Police Mobile and Triage Laboratories 657
National Regulatory Scheme for Biological Agents of Security Concern 664
Potential Expansions to the Australian Federal Police Microbial Forensic Capability 665
The Australian Federal Police in the Whole of Government Approach to Bioterrorism 665
Conclusion 668
Acknowledgment 669
References 669
CHAPTER 38 Validation of Microbial Forensics in Scientific, Legal, and Policy Contexts 672
Introduction 672
An Accepted Approach to Validation Exists 673
Validation as Part of the Quest for Quality in Forensic Science 675
Legal Validation of Novel Scientific Techniques in U.S. Courts 676
Observations of the National Academy of Sciences (2009) 681
Validation: Science at Intersections of Legal and Policy Environments: Snapshot Illustrations 682
Challenges Ahead for Microbial Forensics 684
Disclaimer 684
References 684
PART 7 MICROBIAL FORENSICS CURRICULA AND TRAINING 688
CHAPTER 39 Microbial Forensics: Educating the Workforce and the Community 690
Microbial Forensics Curricula and Training 691
Basic Epidemiology 694
Molecular Epidemiology 695
Microbes and Their Products as Biological Weapons 695
Host Factors Including Immune Responses 696
Processes and Technology 696
Forensic Science 700
Case Histories 701
Legal Issues 701
Operational and Intelligence Issues 702
National-Level Capabilities and Resources 702
Conclusion 703
References 703
CHAPTER 40 So You Really Want to Be an Expert Witness? A Primer for the Occasional Expert Witness 704
Attorneys’ Roles 704
Discovery 706
Experts’ Roles 709
Consequences of Discovery Violation 710
Grant Solicitations/Applications 711
Peer Review Articles/Comments 712
References 714
CHAPTER 41 Microbial Forensics, What Next? 716
References 719
INDEX 720
A 720
B 721
C 724
D 725
E 727
F 728
G 729
H 730
I 731
J 733
K 733
L 733
M 733
N 735
O 736
P 736
Q 738
R 739
S 740
T 743
U 743
V 744
W 745
X 745
Y 745
Z 745
COLOR PLATES 746