Forensic Microbiology

 
 
Standards Information Network (Verlag)
  • erschienen am 21. März 2017
  • |
  • 424 Seiten
 
E-Book | PDF mit Adobe-DRM | Systemvoraussetzungen
978-1-119-06256-1 (ISBN)
 
Forensic Microbiology focuses on newly emerging areas of microbiology relevant to medicolegal and criminal investigations: postmortem changes, establishing cause of death, estimating postmortem interval, and trace evidence analysis. Recent developments in sequencing technology allow researchers, and potentially practitioners, to examine microbial communities at unprecedented resolution and in multidisciplinary contexts. This detailed study of microbes facilitates the development of new forensic tools that use the structure and function of microbial communities as physical evidence.
Chapters cover:
* Experiment design
* Data analysis
* Sample preservation
* The influence of microbes on results from autopsy, toxicology, and histology
* Decomposition ecology
* Trace evidence
This diverse, rapidly evolving field of study has the potential to provide high quality microbial evidence which can be replicated across laboratories, providing spatial and temporal evidence which could be crucial in a broad range of investigative contexts. This book is intended as a resource for students, microbiologists, investigators, pathologists, and other forensic science professionals.
1. Auflage
  • Englisch
  • New York
  • |
  • Großbritannien
John Wiley & Sons Inc
  • Für Beruf und Forschung
  • 13,36 MB
978-1-119-06256-1 (9781119062561)
weitere Ausgaben werden ermittelt
Edited by
David O. Carter
Forensic Sciences Unit, Chaminade University of Honolulu, USA
Jeffery K. Tomberlin
Department of Entomology, Texas A&M University, USA
M. Eric Benbow
Department of Entomology, Michigan State University, USA
Jessica L. Metcalf
Department of Animal Sciences, Colorado State University, USA
1 - Title Page [Seite 5]
2 - Copyright Page [Seite 6]
3 - Contents [Seite 9]
4 - About the editors [Seite 18]
5 - List of contributors [Seite 21]
6 - Foreword [Seite 24]
7 - Series preface [Seite 26]
8 - Preface [Seite 27]
9 - Chapter 1 A primer on microbiology [Seite 29]
9.1 - 1.1 Introduction [Seite 29]
9.2 - 1.2 Microbial characteristics [Seite 30]
9.2.1 - 1.2.1 Microbial taxonomy and function [Seite 30]
9.2.2 - 1.2.2 Enzyme activity [Seite 33]
9.3 - 1.3 Microorganisms and their habitats [Seite 35]
9.3.1 - 1.3.1 Oxygen and moisture [Seite 36]
9.3.2 - 1.3.2 Temperature [Seite 37]
9.4 - 1.4 Competition for resources [Seite 38]
9.5 - 1.5 The ecology of some forensically relevant bacteria [Seite 39]
9.5.1 - 1.5.1 Actinobacteria [Seite 39]
9.5.2 - 1.5.2 Firmicutes [Seite 41]
9.5.3 - 1.5.3 Proteobacteria [Seite 44]
9.6 - 1.6 Archaea and microbial eukaryotes [Seite 48]
9.7 - 1.7 Conclusions [Seite 49]
9.8 - Acknowledgments [Seite 49]
9.9 - References [Seite 49]
10 - Chapter 2 History, current, and future use of microorganisms as physical evidence [Seite 53]
10.1 - 2.1 Introduction [Seite 53]
10.1.1 - 2.1.1 Why and how are microorganisms used in forensic science? [Seite 53]
10.2 - 2.2 Methods for identification [Seite 54]
10.2.1 - 2.2.1 Classical microbiology [Seite 54]
10.2.2 - 2.2.2 Genomics and strain typing [Seite 55]
10.3 - 2.3 Estimating PMI [Seite 58]
10.3.1 - 2.3.1 Microbial succession [Seite 60]
10.4 - 2.4 Cause of death [Seite 64]
10.4.1 - 2.4.1 Natural causes [Seite 64]
10.4.2 - 2.4.2 Biocrimes [Seite 66]
10.5 - 2.5 Trace evidence [Seite 68]
10.5.1 - 2.5.1 Human [Seite 68]
10.5.2 - 2.5.2 Nonhuman animals and food [Seite 70]
10.6 - 2.6 Other medicolegal aspects [Seite 71]
10.6.1 - 2.6.1 Sexual assault [Seite 71]
10.6.2 - 2.6.2 Medical malpractice [Seite 71]
10.6.3 - 2.6.3 Nosocomial infections and antibiotic resistance [Seite 72]
10.6.4 - 2.6.4 Food safety and environmental contamination [Seite 72]
10.7 - 2.7 Needs that must be met for use in chain of custody [Seite 76]
10.8 - 2.8 Summary [Seite 77]
10.9 - Acknowledgments [Seite 78]
10.10 - References [Seite 78]
11 - Chapter 3 Approaches and considerations for forensic microbiology decomposition research [Seite 84]
11.1 - 3.1 Introduction [Seite 84]
11.2 - 3.2 Challenges of human remains research [Seite 85]
11.3 - 3.3 Human remains research during death investigations [Seite 86]
11.4 - 3.4 Human surrogates in research [Seite 88]
11.5 - 3.5 Considerations for field studies [Seite 89]
11.6 - 3.6 Descriptive and hypothesis?driven research [Seite 90]
11.7 - 3.7 Experiment design [Seite 93]
11.8 - 3.8 Validation studies [Seite 97]
11.9 - Acknowledgments [Seite 98]
11.10 - References [Seite 98]
12 - Chapter 4 Sampling methods and data generation [Seite 100]
12.1 - 4.1 Introduction [Seite 100]
12.2 - 4.2 Materials [Seite 101]
12.2.1 - 4.2.1 Financial considerations [Seite 101]
12.2.2 - 4.2.2 Terrestrial settings [Seite 102]
12.2.3 - 4.2.3 Aquatic settings [Seite 105]
12.3 - 4.3 Sample collection techniques [Seite 107]
12.4 - 4.4 Sample preservation, storage, and handling techniques [Seite 108]
12.5 - 4.5 Data considerations [Seite 114]
12.6 - 4.6 Conclusions [Seite 118]
12.7 - Acknowledgments [Seite 118]
12.8 - References [Seite 119]
13 - Chapter 5 An introduction to metagenomic data generation, analysis, visualization, and interpretation [Seite 122]
13.1 - 5.1 Introduction [Seite 122]
13.2 - 5.2 DNA extraction [Seite 124]
13.2.1 - 5.2.1 Sample collection and storage [Seite 124]
13.2.2 - 5.2.2 Extraction methods [Seite 125]
13.3 - 5.3 DNA sequencing [Seite 127]
13.3.1 - 5.3.1 Amplicon sequencing of marker (16S rDNA/18S rDNA/ITS) loci [Seite 127]
13.3.2 - 5.3.2 Multi-omics sequencing: metagenomic, metatranscriptomic, metaproteomic, and metametabolomic approaches [Seite 130]
13.3.3 - 5.3.3 Next-generation sequencing platforms [Seite 133]
13.4 - 5.4 Marker gene data analysis, visualization, and interpretation [Seite 135]
13.4.1 - 5.4.1 Data analysis pipelines [Seite 135]
13.4.2 - 5.4.2 Preprocessing of sequence data [Seite 136]
13.4.3 - 5.4.3 Sequence clustering approaches [Seite 139]
13.4.4 - 5.4.4 Microbial diversity estimations [Seite 140]
13.5 - 5.5 Multi-omics data analysis, visualization, and interpretation [Seite 142]
13.5.1 - 5.5.1 Sequence preprocessing [Seite 143]
13.5.2 - 5.5.2 Sequence assembly [Seite 143]
13.5.3 - 5.5.3 Taxonomic profiling [Seite 144]
13.5.4 - 5.5.4 Gene prediction and metabolic profiling [Seite 144]
13.6 - 5.6 Statistical analysis [Seite 145]
13.7 - 5.7 Major challenges and future directions [Seite 146]
13.8 - References [Seite 147]
14 - Chapter 6 Culture and long-term storage of microorganisms for forensic science [Seite 155]
14.1 - 6.1 Introduction [Seite 155]
14.2 - 6.2 The value of culturing microorganisms [Seite 156]
14.3 - 6.3 Collection and handling of samples [Seite 160]
14.4 - 6.4 Protocols [Seite 162]
14.4.1 - 6.4.1 Aerobic culture [Seite 162]
14.4.2 - 6.4.2 Sterile technique [Seite 162]
14.4.3 - 6.4.3 Sample collection, transport, and culture [Seite 162]
14.4.4 - 6.4.4 Anaerobic culture [Seite 166]
14.4.5 - 6.4.5 Preparing freezer stocks of pure culture [Seite 170]
14.4.6 - 6.4.6 Reculturing stored microorganisms [Seite 171]
14.5 - 6.5 Conclusions [Seite 171]
14.6 - Acknowledgments [Seite 171]
14.7 - References [Seite 171]
15 - Chapter 7 Clinical microbiology and virology in the context of the autopsy [Seite 174]
15.1 - 7.1 Introduction [Seite 174]
15.2 - 7.2 The historical view of autopsy microbiology [Seite 175]
15.3 - 7.3 Which samples should you collect and how? [Seite 177]
15.3.1 - 7.3.1 Blood [Seite 179]
15.3.2 - 7.3.2 Cerebrospinal fluid [Seite 180]
15.3.3 - 7.3.3 Tissue, pus, and fluids [Seite 181]
15.3.4 - 7.3.4 Urine and bowel contents/feces [Seite 182]
15.4 - 7.4 Which methods are available for the diagnosis of infection? [Seite 182]
15.5 - 7.5 How do you put the results into context? [Seite 184]
15.5.1 - 7.5.1 Culture [Seite 184]
15.5.2 - 7.5.2 Serology and molecular tests [Seite 188]
15.5.3 - 7.5.3 Biochemical markers [Seite 189]
15.6 - 7.6 What are the risks of transmission of infection in the postmortem room? [Seite 191]
15.7 - 7.7 How does autopsy microbiology contribute to the diagnosis of specific conditions? [Seite 192]
15.7.1 - 7.7.1 Pneumonia [Seite 192]
15.7.2 - 7.7.2 Mycobacterial infection [Seite 196]
15.7.3 - 7.7.3 Fungal infections [Seite 198]
15.7.4 - 7.7.4 Infective endocarditis [Seite 199]
15.7.5 - 7.7.5 Gastrointestinal infection [Seite 200]
15.7.6 - 7.7.6 Meningitis and central nervous system infections [Seite 201]
15.7.7 - 7.7.7 Septicemia [Seite 202]
15.7.8 - 7.7.8 Neonates and sudden unexplained death in infancy [Seite 203]
15.7.9 - 7.7.9 Emerging infectious diseases and bioterrorism agents [Seite 206]
15.8 - 7.8 Conclusion [Seite 210]
15.9 - References [Seite 210]
16 - Chapter 8 Postmortem bacterial translocation [Seite 220]
16.1 - 8.1 Introduction [Seite 220]
16.1.1 - 8.1.1 The intestinal microbiota in health [Seite 220]
16.2 - 8.2 Bacterial translocation in health and disease [Seite 223]
16.2.1 - 8.2.1 Pathophysiological mechanisms [Seite 224]
16.2.2 - 8.2.2 Factors responsible for an increase in the bacterial translocation [Seite 225]
16.3 - 8.3 Bacterial translocation in humans [Seite 226]
16.3.1 - 8.3.1 Bacterial translocation after death [Seite 227]
16.3.2 - 8.3.2 Identification of bacterial metabolites around the corpse [Seite 228]
16.4 - 8.4 Physiological changes after death influencing the selection of commensal bacteria [Seite 228]
16.4.1 - 8.4.1 Variations of available substrates for bacterial proliferation [Seite 228]
16.4.2 - 8.4.2 Temperature [Seite 229]
16.4.3 - 8.4.3 Anaerobic conditions [Seite 230]
16.5 - 8.5 Consequences of bacterial translocation [Seite 232]
16.5.1 - 8.5.1 Clinical interest [Seite 232]
16.5.2 - 8.5.2 Identification of infectious agents at autopsy [Seite 232]
16.5.3 - 8.5.3 Postmortem interval estimation [Seite 232]
16.5.4 - 8.5.4 Infectious risk for postmortem organ transplantation [Seite 233]
16.5.5 - 8.5.5 Postmortem toxicological analysis [Seite 233]
16.5.6 - 8.5.6 Prevention of biological risk at autopsy [Seite 234]
16.5.7 - 8.5.7 Environmental consequences [Seite 234]
16.6 - 8.6 Conclusion [Seite 234]
16.7 - References [Seite 235]
17 - Chapter 9 Microbial impacts in postmortem toxicology [Seite 240]
17.1 - 9.1 Introduction [Seite 240]
17.2 - 9.2 Microbial factors complicating postmortem toxicological analyses [Seite 241]
17.2.1 - 9.2.1 Cadaver decomposition and specimen contamination [Seite 241]
17.2.2 - 9.2.2 Postmortem drug and metabolite degradation [Seite 242]
17.3 - 9.3 Precautions taken to limit microbial impacts [Seite 242]
17.4 - 9.4 Experimental protocols used to investigate postmortem drug and metabolite degradation due to microbial activity [Seite 246]
17.5 - 9.5 Examples of microbially mediated drug degradation [Seite 247]
17.5.1 - 9.5.1 Drugs [Seite 248]
17.5.2 - 9.5.2 Poisons [Seite 261]
17.6 - 9.6 Concluding remarks [Seite 262]
17.7 - References [Seite 263]
18 - Chapter 10 Microbial communities associated with decomposing corpses [Seite 273]
18.1 - 10.1 Introduction [Seite 273]
18.1.1 - 10.1.1 Overview of the importance of bacteria in decomposition and Arpad Vass' original efforts to catalogue this diversity [Seite 274]
18.1.2 - 10.1.2 Marker gene and metagenomics methods for facilitating studies of the microbial ecology of decomposition [Seite 275]
18.2 - 10.2 The soil microbiology of decomposition [Seite 276]
18.2.1 - 10.2.1 Microbial diversity of gravesoil and the rate of decomposition [Seite 276]
18.2.2 - 10.2.2 Detecting decomposition signatures in soil and clandestine graves [Seite 278]
18.2.3 - 10.2.3 Plant litter [Seite 279]
18.3 - 10.3 Freshwater and marine decomposition [Seite 280]
18.3.1 - 10.3.1 Freshwater decomposition: Fish [Seite 280]
18.3.2 - 10.3.2 Freshwater decomposition: Swine [Seite 281]
18.3.3 - 10.3.3 Marine decomposition: Whale falls [Seite 281]
18.3.4 - 10.3.4 Marine decomposition: Swine [Seite 282]
18.4 - 10.4 The microbiology of nonhuman models of terrestrial decomposition [Seite 283]
18.4.1 - 10.4.1 Terrestrial decomposition: Rats [Seite 283]
18.4.2 - 10.4.2 Terrestrial decomposition: Mice [Seite 284]
18.4.3 - 10.4.3 Terrestrial decomposition: Swine [Seite 285]
18.5 - 10.5 The microbiology of terrestrial human decomposition [Seite 286]
18.5.1 - 10.5.1 Initial insights into the microbial ecology of human decomposition [Seite 287]
18.5.2 - 10.5.2 Identification of microbial signatures associated with decomposition [Seite 288]
18.5.3 - 10.5.3 Microbial eukaryotic decomposers [Seite 289]
18.5.4 - 10.5.4 Linking cadaver and soil microbial communities [Seite 289]
18.5.5 - 10.5.5 Linking cadaver and insect microbial communities [Seite 290]
18.6 - 10.6 Is there a universal decomposition signature? [Seite 291]
18.7 - 10.7 Using microbial signatures to estimate PMI [Seite 292]
18.7.1 - 10.7.1 Estimating PMI in terrestrial systems using gene marker data in nonhuman models of decomposition [Seite 294]
18.7.2 - 10.7.2 Estimating PMI in terrestrial systems using gene marker data in human models [Seite 295]
18.8 - 10.8 Conclusions [Seite 296]
18.9 - Acknowledgments [Seite 296]
18.10 - References [Seite 297]
19 - Chapter 11 Arthropod-microbe interactions on vertebrate remains: Potential applications in the forensic sciences [Seite 302]
19.1 - 11.1 Introduction [Seite 302]
19.1.1 - 11.1.1 Decomposition and applications in forensic entomology [Seite 303]
19.1.2 - 11.1.2 Microbe-arthropod interactions [Seite 306]
19.2 - 11.2 Framework for understanding microbe-arthropod interactions on vertebrate remains [Seite 310]
19.2.1 - 11.2.1 Precolonization interval [Seite 310]
19.3 - 11.3 Postcolonization interval [Seite 315]
19.3.1 - 11.3.1 Colonization [Seite 316]
19.3.2 - 11.3.2 Development [Seite 318]
19.3.3 - 11.3.3 Succession [Seite 320]
19.3.4 - 11.3.4 Dispersal [Seite 323]
19.4 - 11.4 Future directions and conclusion [Seite 325]
19.4.1 - 11.4.1 Forensic sciences [Seite 325]
19.4.2 - 11.4.2 Environmental sciences [Seite 326]
19.4.3 - 11.4.3 Medical research [Seite 326]
19.5 - Acknowledgments [Seite 326]
19.6 - References [Seite 326]
20 - Chapter 12 Microbes, anthropology, and bones [Seite 340]
20.1 - 12.1 Introduction [Seite 340]
20.2 - 12.2 Bone microstructure [Seite 341]
20.3 - 12.3 Microbially mediated decomposition [Seite 343]
20.4 - 12.4 Bone bioerosion [Seite 345]
20.4.1 - 12.4.1 Mechanisms, timing, and source of microbial interaction [Seite 347]
20.4.2 - 12.4.2 Exploration of bioerosion and bacterial community analysis [Seite 348]
20.5 - 12.5 Reconstructing postmortem histories [Seite 350]
20.6 - 12.6 Conclusions [Seite 352]
20.7 - References [Seite 352]
21 - Chapter 13 Forensic microbiology in built environments [Seite 356]
21.1 - 13.1 Introduction [Seite 356]
21.2 - 13.2 The human skin microbiome [Seite 356]
21.3 - 13.3 The microbiota of the built environment [Seite 357]
21.3.1 - 13.3.1 Human-home microbial dynamics [Seite 358]
21.3.2 - 13.3.2 Influence of pets [Seite 360]
21.3.3 - 13.3.3 Influence of interpersonal relationships [Seite 360]
21.4 - 13.4 Tools for the forensic classification of the built environment microbiome [Seite 360]
21.4.1 - 13.4.1 Sampling and sequencing considerations [Seite 360]
21.4.2 - 13.4.2 Machine learning and statistical classification [Seite 362]
21.4.3 - 13.4.3 Sequence clustering [Seite 362]
21.5 - 13.5 Forensic microbiology of the built environment [Seite 363]
21.5.1 - 13.5.1 Tracking disease in hospital environments [Seite 363]
21.5.2 - 13.5.2 Tracking occupancy and activity in a built environment [Seite 364]
21.6 - 13.6 Conclusion [Seite 364]
21.7 - References [Seite 365]
22 - Chapter 14 Soil bacteria as trace evidence [Seite 367]
22.1 - 14.1 The forensic analysis of soil [Seite 367]
22.2 - 14.2 Assessing the biological components of soil [Seite 368]
22.3 - 14.3 Bacteria in soil [Seite 369]
22.4 - 14.4 Molecular techniques for the forensic analysis of soil [Seite 370]
22.4.1 - 14.4.1 Analysis of soil bacteria [Seite 370]
22.4.2 - 14.4.2 Denaturing gradient gel electrophoresis [Seite 371]
22.4.3 - 14.4.3 Assaying DNA size variability [Seite 371]
22.4.4 - 14.4.4 Next-generation DNA sequencing [Seite 372]
22.5 - 14.5 Soil microbial profile data analysis methods [Seite 373]
22.5.1 - 14.5.1 Qualities of ideal forensic data analysis techniques [Seite 373]
22.5.2 - 14.5.2 Objective microbial profiling analysis methods [Seite 374]
22.5.3 - 14.5.3 Demonstrative microbial profiling analysis methods [Seite 375]
22.5.4 - 14.5.4 Combinations of data analysis techniques [Seite 378]
22.6 - 14.6 Feasibility of next?generation sequencing for forensic soil analysis [Seite 378]
22.6.1 - 14.6.1 Differentiating diverse and similar habitats [Seite 378]
22.6.2 - 14.6.2 Temporal changes in soil microbial profiles [Seite 379]
22.6.3 - 14.6.3 Spatial differences in soil microbial profiles [Seite 379]
22.6.4 - 14.6.4 Soil sample collection strategies [Seite 380]
22.6.5 - 14.6.5 Evidence storage and changes in bacterial abundance over time [Seite 380]
22.6.6 - 14.6.6 Costs of next-generation sequencing of forensic soil samples [Seite 380]
22.6.7 - 14.6.7 Legal considerations for the implementation of microbial profiling [Seite 381]
22.7 - 14.7 Consensus on methodologies for soil collection and analysis [Seite 381]
22.8 - Acknowledgments [Seite 382]
22.9 - References [Seite 382]
23 - Chapter 15 DNA profiling of bacteria from human hair: Potential and pitfalls [Seite 386]
23.1 - 15.1 An introduction to human hair as a forensic substrate [Seite 386]
23.1.1 - 15.1.1 Relevance of hair in forensic science [Seite 386]
23.1.2 - 15.1.2 Historical and current forensic perspectives of hair examination and analysis [Seite 387]
23.2 - 15.2 Current research into hair microbiomes [Seite 389]
23.2.1 - 15.2.1 Studies conducted into the metagenomic potential of human hair as a forensic substrate [Seite 390]
23.3 - 15.3 Importance of hair sample collection, storage, and isolation of microbial DNA [Seite 393]
23.3.1 - 15.3.1 Hair sample collection, storage, and analysis [Seite 393]
23.4 - 15.4 DNA sequencing of hair microbiomes [Seite 395]
23.4.1 - 15.4.1 Bioinformatics considerations for analyzing microbial hair data [Seite 396]
23.5 - 15.5 Conclusions and future directions [Seite 397]
23.5.1 - 15.5.1 Major challenges and future directions of metagenomic analyses of hairs in forensic science [Seite 397]
23.5.2 - 15.5.2 Future metagenomic assessments of hair samples [Seite 398]
23.5.3 - 15.5.3 Development of more focused approaches to detect bacterial population level differences between bacteria inhabiting human hairs [Seite 398]
23.5.4 - 15.5.4 General requirements for quality management [Seite 399]
23.6 - Acknowledgments [Seite 400]
23.7 - References [Seite 400]
24 - Perspectives on the future of forensic microbiology [Seite 404]
25 - Index [Seite 407]
26 - EULA [Seite 420]

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