Microbial Forensics (eBook)

CONTRIBUTORS 13
FOREWORD 17
PREFACE 19
ACKNOWLEDGMENTS 21
CHAPTER 1: Microbial Forensics 23
Introduction 23
The Threat 24
History 25
Forensic Science 28
Defining the Microbial Forensics Program 30
Carrying Out a Successful Microbial Forensics Program 33
SWGMGF 34
Epidemiology (A First Step in a Microbial Forensic Analysis) 38
Microbial Forensic Tools 39
Bioinformatics and Genetics 41
Forensic Case Examples 42
Education 43
Conclusion 45
Acknowledgment 45
References 45
CHAPTER 2: Infectious Diseases: Not Just a Health Matter Anymore 49
Introduction 49
Infectious Disease: The Classic Health Viewpoint 51
Infectious Disease: The Offensive Biological Weapons Viewpoint 53
Infectious Disease: New Players and New Threats 54
Infectious Disease: What Are the Threats? 58
Infectious Disease: Biosafety and Biosecurity 59
References 61
CHAPTER 3: The Fundamentals of Human Virology 63
Introduction 63
An Overview of the DNA Viruses 67
An Overview of the RNA Viruses 69
Positive-sense RNA Viruses 69
Negative-sense Single-Stranded RNA Viruses 71
Segmented RNA Viruses and the Retroviridae 72
The Application of Molecular Forensics and Epidemiology to Viral Infections 73
References 75
CHAPTER 4: Keeping Track of Viruses 77
Introduction 77
What Is a Virus? Basic Virology 78
Virus Lifecycle 79
Virus Classification 82
Generation of Viral Diversity 84
Introduction to Viral Kinetics and Outcome 85
How Do You Identify a Virus? 88
Examples of Naturally Emerging Viruses 98
Viral Forensics 112
Engineering Novel Viruses 114
Determining the Source of an Engineered Virus 116
Conclusion 117
Acknowledgments 117
References 117
CHAPTER 5: Bacterial Pathogens 121
DNA Regions of Value for Forensic Identification of Bacterial Pathogens 121
Bacterial Pathogens of Concern 124
References 128
CHAPTER 6: Biology and Detection of Fungal Pathogens of Humans and Plants 131
Introduction 132
Classification, Nomenclature, and Taxonomy of Fungi 133
Growth Habit and Reproduction 137
Pathogenicity 140
Epidemiology 145
Detection and Identification 147
References 150
CHAPTER 7: Forensic Aspects of Biologic Toxins 153
Introduction 153
Botulinum Neurotoxin and Botulism 154
Ricin 168
Staphylococcal Enterotoxin B 169
Clostridia perfringens Epsilon Toxin 170
Summary 171
References 171
CHAPTER 8: Epidemiologic Investigation for Public Health, Biodefense, and Forensic Microbiology 179
Introduction 179
Dynamics of Disease Transmission 180
Outbreak Investigation 181
Deliberate Introduction of a Biological Agen 181
Molecular Strain Typing 185
Summary 191
References 191
CHAPTER 9: Molecular Epidemiology and Forensics of RNA Viruses 195
Challenges Posed by RNA Viruses 196
A Case Study: Foot-and-Mouth Disease in the United Kingdom, 2001 197
What Needs To Be Done? 199
References 202
CHAPTER 10: Investigation of Suspicious Disease Outbreaks 209
Natural and Deliberate Disease 209
Importance of Disease Surveillance 212
Global Disease Reporting Systems 213
U.S. Disease Surveillance and Reporting Systems 214
Epidemiologic Investigation 216
Composition of an Outbreak Investigation Team 216
Epidemiologic Analysis 217
Evaluation of Clinical Findings 222
Investigation of Animal Disease Outbreaks 223
Investigation of Crop Disease Outbreaks 224
Specimen Collection 225
Environmental Sampling 225
Sample Handling 226
Specimen Storage 226
Laboratory Analysis 226
Serology 227
Evaluation of the Etiologic Agent 227
Analysis of Meteorological and Climatic Conditions 228
Economic Analysis 228
Media Reports 229
Available Documents 229
Evaluation of Scientific Literature 229
Training or Work Experience 230
Equipment or Potential Means of Delivery 230
Summary 231
References 231
CHAPTER 11: Forensic Handling of Biological Threat Samples in the Lab 235
Introduction 235
Use of Test Plans to Implement Operational Strategies 235
Biological and Physical Integrity of a Sample 240
Legal Concerns for Sample Handling and Data Records 241
Safety Issues 245
Sample Shipping Regulations 247
CDC/NIH Regulations 248
References 252
CHAPTER 12: Forensic Genetic Analysis of Microorganisms: Overview of Some Important Technical Concepts and Selected Genetic T 255
Introduction 255
Useful Definitions and Concepts 257
Taxonomy and Epidemiology 257
Genetic Considerations 258
Restriction Endonucleases and Polymerase Chain Reaction 259
Of Dendrograms and Phylogenetic Trees 262
Molecular Genetic Techniques for Strain Typing 263
Multilocus Sequence Typing 263
Restriction Fragment Length Polymorphism Typing 264
PCR-Based Genetic Typing 266
Viruses and Fungi 267
Conclusions 268
References 269
CHAPTER 13: Non-DNA Methods for Biological Signatures 273
Introduction 274
Intrinsic Molecular Properties: Fingerprints 279
A Multidisciplinary Approach to Biological Signatures 279
Overview of Characterization Techniques 280
Individual Methods in Detail 283
Results: Analysis of Bacillus globigii Spore Samples 308
Discussion and Future Directions 312
References 313
CHAPTER 14: Microbial Forensics Host Factors 317
General Concepts 318
Utility of Serologic Analysis of People Exposed to Anthrax: Strengths and Limitations 324
Considerations and Concerns Raised by Analysis of Other Infections 328
Possible Scenarios of Bioterrorism Attacks: Distinguishing Victims from Perpetrators 330
References 333
CHAPTER 15: Bioinformatics Methods for Microbial Detection and Forensic Diagnostic Design 335
A Working Definition of Bioinformatics 335
An Overview of Microbial Diagnostics 336
Detection Diagnostics 337
Nucleic Acid Detection Diagnostics 338
Chemistries for Nucleic Acid Detection 339
Protein Detection Diagnostics 341
Monoclonal Antibody 341
High-Affinity Ligands 342
Forensic Diagnostics 343
Large-Scale, Chip-Based Techniques 345
Protein Forensic Diagnostics 346
Genome Sequencing and Analysis Techniques 346
Basecalling and Accuracy 347
Draft versus Finished 349
Strategies for Bacterial and Viral Sequencing 350
Assembly 350
Annotation 352
Tools for Annotation 352
Annotation for Diagnostics versus Traditional Genomic Annotation 353
Comparative Genomics 354
Pairwise Comparison and Alignment 355
Multisequence and Multigenome Alignment 355
Common Substring Comparison 358
Comparative Genomic Tools 358
Protein Structure 360
Tools for Protein Structure Modeling 361
Tools for Protein Structure Analysis 363
Visualization 363
Other Forensic Techniques 364
Protein Mass Spectrometer Analysis 365
Image Analysis 365
Examples 365
Anthracis Analysis 366
Nucleic Acid Signature Pipeline 367
Determination of Target Pathogen Consensus Sequence 368
Fast, Scalable Sequence Comparison Programs to Locate Unique Sequence 369
Primer and Probe Selection and Acceptance 371
Protein Signature Pipeline 372
Acknowledgments 373
References 373
CHAPTER 16: Population Genetics of Bacteria in a Forensic Context 377
Introduction 377
DNA Forensics of Humans and Bacteria 378
Case Study of Bacillus anthracis 379
Conclusions 388
Recommendations 389
Acknowledgments 390
References 390
CHAPTER 17: Quality Management in Microbial Forensics Laboratories 393
Introduction 393
Laboratory Quality Management 395
A Few Definitions Are in Order at This Point 395
Laboratory Accreditation 396
Validation of Laboratory Tests 397
Proficiency Testing 397
Quality Control Testing 398
Quality Assurance Monitoring 398
Competency Assessment of Laboratory Employees 398
Procedure Manuals 399
Laboratory Reports 399
Laboratory Records 400
Laboratory Security 400
Conclusions 400
Bibliography 401
CHAPTER 18: Admissibility Standards for Scientific Evidence 403
Legal Admissibility 404
Background to the Daubert Decision 405
Analysis of the Daubert Decision 405
The DNA Admissibility Litigation 408
Fingerprint Admissibility Litigation Under Daubert 411
Observations 412
References 413
APPENDIX: Quality Assurance Guidelines for Laboratories Performing Microbial Forensic Work 415
SUBJECT INDEX 433