Microbial Forensics

Cover......Page 1
Microbial Forensics......Page 2
Copyright......Page 3
Contributors......Page 4
Foreword......Page 7
. Part 1 Introduction......Page 9
References......Page 12
The Aum Shinrikyo: a brief history......Page 13
The Kameido anthrax incident......Page 15
Microbial forensic investigation......Page 16
Discussion......Page 18
References......Page 20
Laboratory Response Network......Page 21
Post-9/11: the second wave of attack......Page 23
Quality of spore material—behavioral assessment......Page 25
Colony morphology and DNA sequencing......Page 26
Carbon-14 dating......Page 28
Flexographic print defects......Page 29
Bacterial contamination......Page 30
Operational concerns—collection and preservation of microbial evidence......Page 31
References......Page 32
Methods used to analyze the attack isolate......Page 34
Bacillus anthracis strain archives......Page 36
Analysis using today's advanced forensic methods......Page 37
Limits to sample analysis and other issues......Page 38
Conclusion......Page 39
References......Page 40
Whole genome sequencing for foodborne outbreaks......Page 42
Drivers for scientific development......Page 44
Regulatory framework and trends in standard setting......Page 47
Implications for developing and transitioning countries......Page 49
Key roles for international organizations......Page 50
References......Page 52
Further reading......Page 55
5 - Forensic plant pathology......Page 56
Naturally caused versus intentional introduction......Page 57
History of agricultural bioweapons......Page 58
The need for forensic plant pathology......Page 59
Pathogen detection and diagnostics......Page 60
Epidemiology in forensic investigation......Page 64
Natural versus deliberate introduction......Page 65
Mutation, evolution, and forensic plant pathology......Page 66
Investigation......Page 68
Roles and responsibilities......Page 69
Education and outreach......Page 70
Detection and diagnostics......Page 71
Gaps......Page 72
References......Page 73
The burden of human fecal pollution on public health and the economy......Page 78
Municipal stormwater discharge characterization......Page 79
Hazardous event response......Page 80
Development of the human-associated HF183 qPCR method......Page 81
Validation of the HF183 qPCR method......Page 82
HF183 qPCR analytical performance......Page 84
Interlaboratory performance......Page 85
Application-specific field demonstration......Page 86
Implementation of nonfully validated HF183 qPCR method......Page 87
Document performed procedures in detail......Page 88
Conclusions......Page 89
References......Page 90
Introduction......Page 95
Influenza A virus genome......Page 96
Antigenic drift and shift......Page 97
1918 H1N1 “Spanish Flu” pandemic......Page 98
2009 H1N1 “Swine Flu” pandemic......Page 99
H5N1 and H7N9 epidemics......Page 100
Antigenic and genetic characterization......Page 101
Protection against influenza......Page 102
Influenza virus vaccines......Page 103
Dual-use research......Page 104
The 1977 H1N1 “Russian Flu” outbreak: A laboratory escape?......Page 105
The reconstruction of the 1918 influenza virus......Page 106
Highly pathogenic avian influenza H5N1 virus......Page 107
References......Page 108
Introduction......Page 111
Dynamics of disease transmission......Page 112
Deliberate introduction of a biological agent......Page 114
Molecular strain typing......Page 119
Challenges......Page 125
References......Page 126
Introduction......Page 129
Bacillus anthracis: a model system......Page 130
The Sverdlovsk genome......Page 133
Yersinia pestis and plague: another recently emerged pathogen......Page 134
Francisella tularensis and tularemia......Page 136
Brucella spp. and brucellosis......Page 137
Botulinum neurotoxin–producing clostridium species......Page 139
References......Page 142
The kingdom fungi......Page 147
Pathogenic fungi......Page 148
Genetics and genomics of Coccidioides......Page 150
Molecular genotyping and forensics of Coccidioides......Page 151
Other pathogenic fungi......Page 152
Molecular epidemiology guides outbreak investigations: Fusarium and Bipolaris......Page 154
Sarocladium deaths in pediatric cancer patients......Page 155
Conclusions......Page 156
References......Page 157
Introduction......Page 161
Human microbiome......Page 163
Human identity testing......Page 164
Human host attribution......Page 165
Methodologies......Page 166
Targeted multiplex panel of clade-specific markers......Page 167
Conclusions......Page 170
References......Page 171
Further reading......Page 175
Introduction......Page 176
Stages of decomposition......Page 177
Estimating the postmortem interval......Page 179
Using decomposition studies to build regression models for predicting postmortem interval......Page 182
The use of mammalian model systems to develop a microbial clock......Page 185
Human decomposition studies......Page 186
Human body: externally accessible locations......Page 187
Human body: internally accessible locations......Page 188
Soil......Page 189
The effect of environmental variables on the microbial clock......Page 190
Adoption of technology......Page 191
Conclusions......Page 193
References......Page 194
13 - Select methods for microbial forensic nucleic acid analysis of trace and uncultivable specimens......Page 197
References......Page 206
Introduction and background......Page 208
General concepts......Page 210
Illustrative concepts......Page 211
Utility of serologic analysis of people exposed to anthrax: strengths and limitations......Page 214
Considerations and concerns raised by analysis of other infections......Page 217
Possible scenarios of bioterrorism attacks: distinguishing victims from perpetrators......Page 220
References......Page 222
Toxins......Page 225
Sample preparation......Page 229
Mass spectrometry......Page 230
Saxitoxin analysis......Page 231
Botulinum neurotoxin analysis......Page 232
Validation of toxin methods......Page 233
References......Page 236
Introduction......Page 240
History of castor beans......Page 241
Ricin poisoning......Page 242
Ricin toxin detection......Page 243
Castor bean genotyping......Page 245
Nuclear SNPs......Page 246
Challenges......Page 247
References......Page 248
Why proteomics?......Page 250
Proteomic analysis workflow......Page 252
Mass spectrometry......Page 253
Data analysis......Page 254
Distinguishing wild isolates from laboratory-adapted strains......Page 255
Elucidating methods of production: impacts of growth environment on endogenous protein expression......Page 256
Elucidating methods of production: exogenous proteomic signatures of production methods......Page 258
Protein toxin identification......Page 259
Complex and diverse samples......Page 260
Selection of search database......Page 261
References......Page 262
Molecular epidemiology and typing......Page 265
Multilocus sequence typing......Page 266
Impact of NGS on bacterial typing schemes......Page 268
Alignment-based computational methods......Page 269
Alignment-free computational methods......Page 271
Genome-enabled bacterial typing schemes......Page 274
Computational approaches to large-scale typing schemes......Page 275
Community adoption of genome-based bacterial typing......Page 276
References......Page 279
19 - Genomics......Page 281
Sanger sequencing: historic context......Page 282
Next-generation sequencing using pH mediation......Page 283
Next-generation sequencing using nanopores......Page 284
Bioinformatics sequence analysis......Page 285
The pregenomic era......Page 286
Comparative genomics......Page 287
Metagenomics......Page 288
Genome architecture and evolution......Page 289
Future challenges......Page 290
Genomics and microbial forensics......Page 291
References......Page 292
Genomic signatures......Page 296
Potential target organisms......Page 297
Genomic sequence data: what to use and where to get it......Page 298
Identifying conserved sequence among targets......Page 300
Mining for signatures......Page 301
RNA viruses present additional challenges......Page 302
Signatures of potential bacterial genetic engineering......Page 303
Viral and bacterial detection array signatures......Page 304
The future of genomic signatures......Page 305
Acknowledgments......Page 307
References......Page 308
21 - Collection and preservation of microbial forensic samples......Page 310
General best practices of collection of forensic evidence......Page 311
Collection strategies and methods for microbial forensic sampling......Page 314
Looking to the future......Page 317
References......Page 318
National threat assessment: role of the Intelligence Community......Page 320
Threat credibility assessments: role of law enforcement and public health officials......Page 324
Validation of biological agent detection assays......Page 328
Admission of scientific evidence......Page 330
References......Page 331
Introduction......Page 333
Considerations based on recent criticism of forensic science testimony......Page 334
Common practices in science communication may cause problems in testimony......Page 336
When can statistical language be justified?......Page 339
Microbial identification: asserting that an organism is a pathogenic strain......Page 342
Statements regarding uncertainty in identification......Page 344
Morph statistics—responding to criticisms of imperfect tests......Page 345
Genetic inference—avoiding the need for hedging or “inclusion” type testimony......Page 347
Trace DNA detection: discounting questions of background and contamination......Page 349
Can more liberal standards for expressing uncertainty in scientific testimony be justified?......Page 351
References......Page 352
Further reading......Page 354
Introduction......Page 355
Formalization of the idea of a “forensic test”......Page 357
Defining the hypotheses to be tested......Page 358
Defining the population......Page 359
Verifying the oracle......Page 360
Constructing estimators for error rate, probability, and likelihood ratio characterizations of degree of certainty......Page 361
More subtle issues with inferential validation......Page 362
Postmortem interval estimation......Page 366
Human source attribution......Page 367
Inferences about geolocation......Page 370
Concluding remarks......Page 371
References......Page 372
Further reading......Page 374
Introduction and background......Page 375
A microbial forensic paradigm......Page 378
Step 2—population genetic database development......Page 379
Step 4—hypothesis testing needs to be done in the context of a relevant reference population......Page 380
Step 6—inheritance mode: clonal replication......Page 381
Step 9—evaluation of analyses......Page 382
Calculating match probabilities......Page 383
Reference database......Page 384
Discussion......Page 385
References......Page 386
Introduction......Page 387
Historical drivers......Page 388
International considerations......Page 389
Competing timelines......Page 390
Microbial forensics in a legal context......Page 392
Admissibility......Page 393
Case precedent......Page 394
Microbial forensics evidence in comparison to other forensic disciplines (Bidwell and Bhatt, 2016)......Page 395
The CSI effect......Page 396
References......Page 397
The legal standard......Page 399
An unusual process: lay judges rule on the reliability of expert work......Page 401
The ultimate error......Page 404
Expert exaggeration: a particular example of the ultimate error......Page 405
An example of careful science and the lessons it teaches......Page 406
Judicial findings of reliability......Page 408
Expert credibility......Page 409
The importance of discovery......Page 410
Some tips for expert witnesses......Page 412
Cross-examination of government tanker expert......Page 413
Rule 706. Court-appointed expert witnesses......Page 414
Conclusion......Page 415
The select agent regulations......Page 416
Select agents and toxins......Page 417
Restricted experiments......Page 421
Exemptions......Page 423
Exclusions......Page 424
Transfers......Page 426
Biosafety/biocontainment......Page 428
References......Page 429
Managing microbial forensics biological resources......Page 431
Biological Resource Centers......Page 432
Creating value......Page 434
Sustainability......Page 435
Building a biological resource......Page 436
Assuring quality and standardization......Page 437
Data management and integration......Page 439
Acquisition......Page 440
Equitable access......Page 441
Safety and security......Page 442
Regulatory compliance......Page 443
Ideal microbial forensics biological resource......Page 444
Further reading......Page 445
History of the NBFAC......Page 446
NBFAC operations......Page 447
NBFAC science......Page 448
NBFAC and the future of bioforensics......Page 449
References......Page 450
Introduction and background......Page 451
The strategic path to Zagreb......Page 452
Developing international microbial forensics research Priorities, Zagreb 2013......Page 455
Additional perspectives......Page 457
An international research strategy matters to the United Nations office of disarmament affairs, the SGM, and beyond......Page 459
References......Page 460
32 - Education and training in microbial forensics......Page 461
Microbial forensic curricula and training......Page 463
Curricular guidelines from the American Society of Microbiology and American Academy of Forensic Sciences......Page 466
Basic epidemiology......Page 472
Host factors including immune responses......Page 473
Crime scenes and chain of custody......Page 474
Extraction......Page 475
Interpretation, statistical analysis, and confidence......Page 476
Indicators of engineering......Page 477
Forensic science......Page 478
Legal issues......Page 479
Conclusion......Page 480
References......Page 481
33 - Microbial forensics: what next?......Page 484
References......Page 487
C......Page 488
G......Page 489
M......Page 490
N......Page 491
S......Page 492
Z......Page 493