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 Microbial Forensics Copyright Contributors Foreword Introduction References Section I: Anthrax 1 - The Kameido anthrax incident: a microbial forensic case study Introduction The Aum Shinrikyo: a brief history The Kameido anthrax incident Microbial forensic investigation Epidemiologic investigation Discussion Challenges References 2 - The FBI's Amerithrax Task Force and the advent of microbial forensics Concern for the future Laboratory Response Network Post-9/11: the second wave of attack Quality of spore material—behavioral assessment Amerithrax Task Force Colony morphology and DNA sequencing Carbon-14 dating Flexographic print defects Bacterial contamination Operational concerns—collection and preservation of microbial evidence References 3 - Microbial forensic investigation of the anthrax letter attacks: how the investigation would differ using today's technologies Methods used to analyze the attack isolate Bacillus anthracis strain archives Analysis using today's advanced forensic methods Limits to sample analysis and other issues Conclusion References Section II: Applications of microbial forensics 4 - Foodborne outbreaks Whole genome sequencing for foodborne outbreaks 'Omics and global scientific and regulatory trends Drivers for scientific development Regulatory framework and trends in standard setting Implications for developing and transitioning countries Key roles for international organizations Summary References Further reading 5 - Forensic plant pathology Introduction Naturally caused versus intentional introduction History of agricultural bioweapons The need for forensic plant pathology Pathogen detection and diagnostics Epidemiology in forensic investigation Vulnerability assessment Source attribution Natural versus deliberate introduction Sampling considerations Mutation, evolution, and forensic plant pathology Investigation Roles and responsibilities Education and outreach Resources and infrastructure Prevention Detection and diagnostics Response Gaps Summary References 6 - Microbial source tracking: characterization of human fecal pollution in environmental waters with HF183 quantitative real-t ... The burden of human fecal pollution on public health and the economy A human fecal source identification solution Identification of nonpoint pollution sources Municipal stormwater discharge characterization Water quality best management practice evaluation Waterborne disease outbreak response Hazardous event response Development of the human-associated HF183 qPCR method Validation of the HF183 qPCR method HF183 qPCR analytical performance HF183 target survival in environmental settings Interlaboratory performance Application-specific field demonstration HF183 concentration link to public health risk Implementation of nonfully validated HF183 qPCR method Define the water quality challenge Identify key factors that could influence human fecal pollution occurrence Assemble team to generate experimental design and interpret results Include appropriate quality controls Document performed procedures in detail Employ a standardized procedure Conduct proficiency testing before working with environmental samples Conclusions Disclaimer References 7 - Influenza forensics Introduction Influenza virus Influenza A virus genome Influenza nomenclature Influenza A virus subtypes Influenza A virus isolate names Antigenic drift and shift Brief history of influenza pandemics and epidemics 1918 H1N1 “Spanish Flu” pandemic 1957 H2N2 “Asian Flu” and 1968 H3N2 “Hong Kong flu” pandemics 2009 H1N1 “Swine Flu” pandemic H5N1 and H7N9 epidemics Outbreak detection Surveillance Antigenic and genetic characterization Diagnostics Protection against influenza Influenza virus vaccines Antiviral drugs Influenza virus as a biological weapon? Dual-use research The 1977 H1N1 “Russian Flu” outbreak: A laboratory escape? The reconstruction of the 1918 influenza virus Highly pathogenic avian influenza H5N1 virus Conclusions References 8 - Forensic public health: epidemiological and microbiological investigations for biosecurity Introduction Dynamics of disease transmission Outbreak investigation Deliberate introduction of a biological agent Molecular strain typing Challenges Summary Acknowledgments References 9 - Forensic analysis in bacterial pathogens Introduction 16S sequences and rapid ID of microbes Forensic signatures: human versus bacterial pathogens Bacillus anthracis: a model system The pan-genome of Bacillus cereus sensu lato The Sverdlovsk genome Mutation rates in bacteria Yersinia pestis and plague: another recently emerged pathogen Francisella tularensis and tularemia Brucella spp. and brucellosis Burkholderia pseudomallei and melioidosis Botulinum neurotoxin–producing clostridium species Conclusions References 10 - Genomic epidemiology and forensics of fungal pathogens Introduction The kingdom fungi Pathogenic fungi Coccidioides and coccidioidomycosis Background and epidemiology Detection and identification Genetics and genomics of Coccidioides Molecular genotyping and forensics of Coccidioides Whole genome sequence typing Genomic epidemiology case study Other pathogenic fungi Genomic epidemiology in action Molecular epidemiology guides outbreak investigations: Fusarium and Bipolaris Whole genome sequencing helps to link fungal outbreaks to contaminated products: Exserohilum, Sarocladium, and Exophiala Federal murder trial Sarocladium deaths in pediatric cancer patients Exophiala in an NYC oncology clinic Conclusions Disclaimer References 11 - Forensic human identification using skin microbiome genetic signatures Introduction Human microbiome Human identity testing Human host attribution Methodologies Targeted multiplex panel of clade-specific markers Conclusions References Further reading 12 - Using microbiome tools for estimating the postmortem interval Introduction Decomposition and estimation of the postmortem interval Stages of decomposition Estimating the postmortem interval The microbial clock Using decomposition studies to build regression models for predicting postmortem interval Early studies of microbial ecosystems The use of mammalian model systems to develop a microbial clock Human decomposition studies The microbial clock of different sampling environments Human body: externally accessible locations Human body: internally accessible locations Bone Soil The effect of environmental variables on the microbial clock Knowledge gaps and areas of investigation Adoption of technology Conclusions References Section III: Methodology 13 - Select methods for microbial forensic nucleic acid analysis of trace and uncultivable specimens References 14 - The use of host factors in microbial forensics Introduction and background General concepts Illustrative concepts Utility of serologic analysis of people exposed to anthrax: strengths and limitations Considerations and concerns raised by analysis of other infections Possible scenarios of bioterrorism attacks: distinguishing victims from perpetrators References 15 - Toxin analysis using mass spectrometry Introduction Toxins Sample preparation Mass spectrometry Specific toxin analysis methods Saxitoxin analysis α-Amanitin analysis Botulinum neurotoxin analysis Ricin analysis Validation of toxin methods Current limitations to toxin analysis References 16 - Ricin forensics: comparisons to microbial forensics Introduction Background History of castor beans Ricin poisoning Ricin toxin detection Castor bean genotyping Amplified fragment length polymorphisms Simple sequence repeats Chloroplast DNA Nuclear SNPs Challenges References 17 - Proteomics for bioforensics Introduction Why proteomics? Proteomic analysis workflow Protein extraction Protease digestion Separation by liquid chromatography Mass spectrometry Data analysis Applications of proteomic methods in microbial forensics Distinguishing wild isolates from laboratory-adapted strains Elucidating methods of production: impacts of growth environment on endogenous protein expression Elucidating methods of production: exogenous proteomic signatures of production methods Protein toxin identification Distinctive aspects of forensic proteomics Complex and diverse samples Single sample analysis Rigor and confidence measures Selection of search database Conclusions References 18 - Bioinformatics Molecular epidemiology and typing Multilocus sequence typing Impact of NGS on bacterial typing schemes Alignment-based computational methods Alignment-free computational methods Genome-enabled bacterial typing schemes Computational approaches to large-scale typing schemes Community adoption of genome-based bacterial typing References 19 - Genomics Sequencing technologies Sanger sequencing: historic context Next-generation sequencing by synthesis, pH mediation, single molecules, and nanopores Next-generation sequencing by synthesis Next-generation sequencing using pH mediation Next-generation sequencing using single molecules Next-generation sequencing using nanopores Future developments in microbial sequencing Bioinformatics sequence analysis The pregenomic era Comparative genomics High-throughput screening assays Metagenomics Genome architecture and evolution Future challenges Genomics and microbial forensics Acknowledgments References 20 - Design of genomic signatures for pathogen identification and characterization Genomic signatures Different types and resolutions of genomic signatures Potential target organisms Signature resolution Genomic sequence data: what to use and where to get it Identifying conserved sequence among targets Identifying sequences unique to targets Mining for signatures RNA viruses present additional challenges Signatures of potential bacterial genetic engineering Viral and bacterial detection array signatures The future of genomic signatures Protein signatures: a new forensic approach? Acknowledgments References 21 - Collection and preservation of microbial forensic samples General best practices of collection of forensic evidence Collection strategies and methods for microbial forensic sampling Looking to the future References Section IV: Legal aspects and interpretation of data 22 - Assessment of the threat National threat assessment: role of the Intelligence Community Threat credibility assessments: role of law enforcement and public health officials Validation of biological agent detection assays Admission of scientific evidence Conclusion References 23 - Scientific testimonial standards for microbial forensic evidence Introduction Considerations based on recent criticism of forensic science testimony Common practices in science communication may cause problems in testimony When can statistical language be justified? Some examples of certainty expression in microbial forensics Microbial identification: asserting that an organism is a pathogenic strain Statements regarding identification Statements regarding uncertainty in identification Statements regarding the presumption of pathogenicity Morph statistics—responding to criticisms of imperfect tests Genetic inference—avoiding the need for hedging or “inclusion” type testimony Trace DNA detection: discounting questions of background and contamination Can more liberal standards for expressing uncertainty in scientific testimony be justified? References Further reading 24 - Inferential validation and evidence interpretation Introduction Formalization of the idea of a “forensic test” Requirements for inferential validation of a forensic test Defining the hypotheses to be tested Choosing a set of signatures Formulating a comparison metric Defining the population Randomly sampling from the population to form the “learning set” Verifying the oracle Optimizing the decision rule (minimizing the empirical error rate) Constructing estimators for error rate, probability, and likelihood ratio characterizations of degree of certainty More subtle issues with inferential validation Validation issues with “expanded” forensic microbiology applications Postmortem interval estimation Body fluid identification Human source attribution Inferences about geolocation Concluding remarks References Further reading 25 - Microbial forensic investigations in the context of bacterial population genetics Introduction and background A microbial forensic paradigm Step 1—availability of population genetic data Step 2—population genetic database development Step 3—definition of specific hypotheses Step 4—hypothesis testing needs to be done in the context of a relevant reference population Step 5—define the replication mode Step 6—inheritance mode: clonal replication Step 7—inheritance mode: recombining or nonclonal replication Step 8—likelihood ratios Step 9—evaluation of analyses Step 10—improve understanding of population structure Calculating match probabilities Reference database Discussion References 26 - Use of microbial forensics data in scientific, legal, and policy contexts Introduction Microbial forensics in a policy context Historical drivers Current U.S. Strategy International considerations Microbial forensics in an international decision-making process Competing timelines Microbial forensics in a legal context Admissibility Case precedent Microbial forensics evidence in comparison to other forensic disciplines (Bidwell and Bhatt, 2016) Basis for challenges The CSI effect Chain of custody issues Conclusion References 27 - Lessons for expert witnesses Introduction The legal standard An unusual process: lay judges rule on the reliability of expert work The ultimate error Expert exaggeration: a particular example of the ultimate error An example of careful science and the lessons it teaches Judicial skepticism Judicial findings of reliability State cases Expert credibility The importance of discovery Anticipating impeachment and attack Some tips for expert witnesses Cross-examination of government tanker expert Rule 706. Court-appointed expert witnesses Conclusion Section V: Miscellaneous 28 - Select agent regulations Introduction The select agent regulations Select agents and toxins Tier 1 select agents Restricted experiments Exemptions Exclusions Transfers Records Security Biosafety/biocontainment Incident response Training Summary References 29 - Biorepositories and their foundation Managing microbial forensics biological resources Biological Resource Centers Creating value Sustainability Building a biological resource Long-term maintenance Assuring quality and standardization Data management and integration Acquisition Equitable access Safety and security Regulatory compliance Ideal microbial forensics biological resource References Further reading 30 - The National Bioforensic Analysis Center History of the NBFAC NBFAC operations NBFAC science NBFAC and the future of bioforensics Conclusion Standard Acknowledgment References 31. An international microbial forensics research strategy and its collaborative pursuit is needed Introduction and background The strategic path to Zagreb Developing international microbial forensics research Priorities, Zagreb 2013 Additional perspectives An international research strategy matters to the United Nations office of disarmament affairs, the SGM, and beyond References 32 - Education and training in microbial forensics Microbial forensic curricula and training Curricular guidelines from the American Society of Microbiology and American Academy of Forensic Sciences Basic epidemiology Molecular epidemiology Microbes and their products as biological weapons Host factors including immune responses Processes and technology Crime scenes and chain of custody Sample collection and preservation of forensic evidence Extraction Advanced microscopy Proteomics Genomics Interpretation, statistical analysis, and confidence Bioinformatics Indicators of engineering Population genetics Nonbiological tools Forensic science Case histories Legal issues Operational and intelligence issues National-level capabilities and resources Conclusion References 33 - Microbial forensics: what next? References Index A B C D E F G H I K L M N O P R S T U V W Y Z Back Cover "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