Microbial Forensics

__Microbial Forensics, Third Edition,__ serves as a complete reference on the discipline, describing the advances, challenges and opportunities that are integral in applying science to help solve future biocrimes. New chapters include: Microbial Source Tracking, Clinical Recognition, Bioinformatics, and Quality Assurance. This book is intended for a wide audience, but will be indispensable to forensic scientists and researchers interested in contributing to the growing field of microbial forensics. Biologists and microbiologists, the legal and judicial system, and the international community involved with Biological Weapons Treaties will also find this volume invaluable. * Presents new and expanded content that includes a statistical analysis of forensic data, legal admissibility and standards of evidence * Discusses actual cases of forensic bioterrorism * Includes contributions from editors and authors who are leading experts in the field, with primary experience in the application of this fast-growing discipline 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 "Microbial Forensics, Third Edition serves as a complete reference on the discipline, describing the advances, challenges and opportunities that are integral in applying science to help solve future biocrimes. New chapters include: Microbial Source Tracking, Clinical Recognition, Bioinformatics, and Quality Assurance. This book is intended for a wide audience, but will be indispensable to forensic scientists and researchers interested in contributing to the growing field of microbial forensics. Biologists and microbiologists, the legal and judicial system, and the international community involved with Biological Weapons Treaties will also find this volume invaluable"-- Provided by publisher