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Forensic Microbiology.

By: Contributor(s): Material type: TextTextSeries: Forensic Science in Focus SeriesPublisher: Newark : John Wiley & Sons, Incorporated, 2017Copyright date: ©2017Edition: 1st edDescription: 1 online resource (420 pages)Content type:
  • text
Media type:
  • computer
Carrier type:
  • online resource
ISBN:
  • 9781119062561
Subject(s): Genre/Form: Additional physical formats: Print version:: Forensic MicrobiologyDDC classification:
  • 363.25
LOC classification:
  • QR41.2.F674 2017
Online resources:
Contents:
Intro -- Title Page -- Copyright Page -- Contents -- About the editors -- List of contributors -- Foreword -- Series preface -- Preface -- Chapter 1 A primer on microbiology -- 1.1 Introduction -- 1.2 Microbial characteristics -- 1.2.1 Microbial taxonomy and function -- 1.2.2 Enzyme activity -- 1.3 Microorganisms and their habitats -- 1.3.1 Oxygen and moisture -- 1.3.2 Temperature -- 1.4 Competition for resources -- 1.5 The ecology of some forensically relevant bacteria -- 1.5.1 Actinobacteria -- 1.5.2 Firmicutes -- 1.5.3 Proteobacteria -- 1.6 Archaea and microbial eukaryotes -- 1.7 Conclusions -- Acknowledgments -- References -- Chapter 2 History, current, and future use of microorganisms as physical evidence -- 2.1 Introduction -- 2.1.1 Why and how are microorganisms used in forensic science? -- 2.2 Methods for identification -- 2.2.1 Classical microbiology -- 2.2.2 Genomics and strain typing -- 2.3 Estimating PMI -- 2.3.1 Microbial succession -- 2.4 Cause of death -- 2.4.1 Natural causes -- 2.4.2 Biocrimes -- 2.5 Trace evidence -- 2.5.1 Human -- 2.5.2 Nonhuman animals and food -- 2.6 Other medicolegal aspects -- 2.6.1 Sexual assault -- 2.6.2 Medical malpractice -- 2.6.3 Nosocomial infections and antibiotic resistance -- 2.6.4 Food safety and environmental contamination -- 2.7 Needs that must be met for use in chain of custody -- 2.8 Summary -- Acknowledgments -- References -- Chapter 3 Approaches and considerations for forensic microbiology decomposition research -- 3.1 Introduction -- 3.2 Challenges of human remains research -- 3.3 Human remains research during death investigations -- 3.4 Human surrogates in research -- 3.5 Considerations for field studies -- 3.6 Descriptive and hypothesis‐driven research -- 3.7 Experiment design -- 3.8 Validation studies -- Acknowledgments -- References -- Chapter 4 Sampling methods and data generation.
4.1 Introduction -- 4.2 Materials -- 4.2.1 Financial considerations -- 4.2.2 Terrestrial settings -- 4.2.3 Aquatic settings -- 4.3 Sample collection techniques -- 4.4 Sample preservation, storage, and handling techniques -- 4.5 Data considerations -- 4.6 Conclusions -- Acknowledgments -- References -- Chapter 5 An introduction to metagenomic data generation, analysis, visualization, and interpretation -- 5.1 Introduction -- 5.2 DNA extraction -- 5.2.1 Sample collection and storage -- 5.2.2 Extraction methods -- 5.3 DNA sequencing -- 5.3.1 Amplicon sequencing of marker (16S rDNA/18S rDNA/ITS) loci -- 5.3.2 Multi-omics sequencing: metagenomic, metatranscriptomic, metaproteomic, and metametabolomic approaches -- 5.3.3 Next-generation sequencing platforms -- 5.4 Marker gene data analysis, visualization, and interpretation -- 5.4.1 Data analysis pipelines -- 5.4.2 Preprocessing of sequence data -- 5.4.3 Sequence clustering approaches -- 5.4.4 Microbial diversity estimations -- 5.5 Multi-omics data analysis, visualization, and interpretation -- 5.5.1 Sequence preprocessing -- 5.5.2 Sequence assembly -- 5.5.3 Taxonomic profiling -- 5.5.4 Gene prediction and metabolic profiling -- 5.6 Statistical analysis -- 5.7 Major challenges and future directions -- References -- Chapter 6 Culture and long-term storage of microorganisms for forensic science -- 6.1 Introduction -- 6.2 The value of culturing microorganisms -- 6.3 Collection and handling of samples -- 6.4 Protocols -- 6.4.1 Aerobic culture -- 6.4.2 Sterile technique -- 6.4.3 Sample collection, transport, and culture -- 6.4.4 Anaerobic culture -- 6.4.5 Preparing freezer stocks of pure culture -- 6.4.6 Reculturing stored microorganisms -- 6.5 Conclusions -- Acknowledgments -- References -- Chapter 7 Clinical microbiology and virology in the context of the autopsy -- 7.1 Introduction.
7.2 The historical view of autopsy microbiology -- 7.3 Which samples should you collect and how? -- 7.3.1 Blood -- 7.3.2 Cerebrospinal fluid -- 7.3.3 Tissue, pus, and fluids -- 7.3.4 Urine and bowel contents/feces -- 7.4 Which methods are available for the diagnosis of infection? -- 7.5 How do you put the results into context? -- 7.5.1 Culture -- 7.5.2 Serology and molecular tests -- 7.5.3 Biochemical markers -- 7.6 What are the risks of transmission of infection in the postmortem room? -- 7.7 How does autopsy microbiology contribute to the diagnosis of specific conditions? -- 7.7.1 Pneumonia -- 7.7.2 Mycobacterial infection -- 7.7.3 Fungal infections -- 7.7.4 Infective endocarditis -- 7.7.5 Gastrointestinal infection -- 7.7.6 Meningitis and central nervous system infections -- 7.7.7 Septicemia -- 7.7.8 Neonates and sudden unexplained death in infancy -- 7.7.9 Emerging infectious diseases and bioterrorism agents -- 7.8 Conclusion -- References -- Chapter 8 Postmortem bacterial translocation -- 8.1 Introduction -- 8.1.1 The intestinal microbiota in health -- 8.2 Bacterial translocation in health and disease -- 8.2.1 Pathophysiological mechanisms -- 8.2.2 Factors responsible for an increase in the bacterial translocation -- 8.3 Bacterial translocation in humans -- 8.3.1 Bacterial translocation after death -- 8.3.2 Identification of bacterial metabolites around the corpse -- 8.4 Physiological changes after death influencing the selection of commensal bacteria -- 8.4.1 Variations of available substrates for bacterial proliferation -- 8.4.2 Temperature -- 8.4.3 Anaerobic conditions -- 8.5 Consequences of bacterial translocation -- 8.5.1 Clinical interest -- 8.5.2 Identification of infectious agents at autopsy -- 8.5.3 Postmortem interval estimation -- 8.5.4 Infectious risk for postmortem organ transplantation -- 8.5.5 Postmortem toxicological analysis.
8.5.6 Prevention of biological risk at autopsy -- 8.5.7 Environmental consequences -- 8.6 Conclusion -- References -- Chapter 9 Microbial impacts in postmortem toxicology -- 9.1 Introduction -- 9.2 Microbial factors complicating postmortem toxicological analyses -- 9.2.1 Cadaver decomposition and specimen contamination -- 9.2.2 Postmortem drug and metabolite degradation -- 9.3 Precautions taken to limit microbial impacts -- 9.4 Experimental protocols used to investigate postmortem drug and metabolite degradation due to microbial activity -- 9.5 Examples of microbially mediated drug degradation -- 9.5.1 Drugs -- 9.5.2 Poisons -- 9.6 Concluding remarks -- References -- Chapter 10 Microbial communities associated with decomposing corpses -- 10.1 Introduction -- 10.1.1 Overview of the importance of bacteria in decomposition and Arpad Vass' original efforts to catalogue this diversity -- 10.1.2 Marker gene and metagenomics methods for facilitating studies of the microbial ecology of decomposition -- 10.2 The soil microbiology of decomposition -- 10.2.1 Microbial diversity of gravesoil and the rate of decomposition -- 10.2.2 Detecting decomposition signatures in soil and clandestine graves -- 10.2.3 Plant litter -- 10.3 Freshwater and marine decomposition -- 10.3.1 Freshwater decomposition: Fish -- 10.3.2 Freshwater decomposition: Swine -- 10.3.3 Marine decomposition: Whale falls -- 10.3.4 Marine decomposition: Swine -- 10.4 The microbiology of nonhuman models of terrestrial decomposition -- 10.4.1 Terrestrial decomposition: Rats -- 10.4.2 Terrestrial decomposition: Mice -- 10.4.3 Terrestrial decomposition: Swine -- 10.5 The microbiology of terrestrial human decomposition -- 10.5.1 Initial insights into the microbial ecology of human decomposition -- 10.5.2 Identification of microbial signatures associated with decomposition.
10.5.3 Microbial eukaryotic decomposers -- 10.5.4 Linking cadaver and soil microbial communities -- 10.5.5 Linking cadaver and insect microbial communities -- 10.6 Is there a universal decomposition signature? -- 10.7 Using microbial signatures to estimate PMI -- 10.7.1 Estimating PMI in terrestrial systems using gene marker data in nonhuman models of decomposition -- 10.7.2 Estimating PMI in terrestrial systems using gene marker data in human models -- 10.8 Conclusions -- Acknowledgments -- References -- Chapter 11 Arthropod-microbe interactions on vertebrate remains: Potential applications in the forensic sciences -- 11.1 Introduction -- 11.1.1 Decomposition and applications in forensic entomology -- 11.1.2 Microbe-arthropod interactions -- 11.2 Framework for understanding microbe-arthropod interactions on vertebrate remains -- 11.2.1 Precolonization interval -- 11.3 Postcolonization interval -- 11.3.1 Colonization -- 11.3.2 Development -- 11.3.3 Succession -- 11.3.4 Dispersal -- 11.4 Future directions and conclusion -- 11.4.1 Forensic sciences -- 11.4.2 Environmental sciences -- 11.4.3 Medical research -- Acknowledgments -- References -- Chapter 12 Microbes, anthropology, and bones -- 12.1 Introduction -- 12.2 Bone microstructure -- 12.3 Microbially mediated decomposition -- 12.4 Bone bioerosion -- 12.4.1 Mechanisms, timing, and source of microbial interaction -- 12.4.2 Exploration of bioerosion and bacterial community analysis -- 12.5 Reconstructing postmortem histories -- 12.6 Conclusions -- References -- Chapter 13 Forensic microbiology in built environments -- 13.1 Introduction -- 13.2 The human skin microbiome -- 13.3 The microbiota of the built environment -- 13.3.1 Human-home microbial dynamics -- 13.3.2 Influence of pets -- 13.3.3 Influence of interpersonal relationships.
13.4 Tools for the forensic classification of the built environment microbiome.
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Intro -- Title Page -- Copyright Page -- Contents -- About the editors -- List of contributors -- Foreword -- Series preface -- Preface -- Chapter 1 A primer on microbiology -- 1.1 Introduction -- 1.2 Microbial characteristics -- 1.2.1 Microbial taxonomy and function -- 1.2.2 Enzyme activity -- 1.3 Microorganisms and their habitats -- 1.3.1 Oxygen and moisture -- 1.3.2 Temperature -- 1.4 Competition for resources -- 1.5 The ecology of some forensically relevant bacteria -- 1.5.1 Actinobacteria -- 1.5.2 Firmicutes -- 1.5.3 Proteobacteria -- 1.6 Archaea and microbial eukaryotes -- 1.7 Conclusions -- Acknowledgments -- References -- Chapter 2 History, current, and future use of microorganisms as physical evidence -- 2.1 Introduction -- 2.1.1 Why and how are microorganisms used in forensic science? -- 2.2 Methods for identification -- 2.2.1 Classical microbiology -- 2.2.2 Genomics and strain typing -- 2.3 Estimating PMI -- 2.3.1 Microbial succession -- 2.4 Cause of death -- 2.4.1 Natural causes -- 2.4.2 Biocrimes -- 2.5 Trace evidence -- 2.5.1 Human -- 2.5.2 Nonhuman animals and food -- 2.6 Other medicolegal aspects -- 2.6.1 Sexual assault -- 2.6.2 Medical malpractice -- 2.6.3 Nosocomial infections and antibiotic resistance -- 2.6.4 Food safety and environmental contamination -- 2.7 Needs that must be met for use in chain of custody -- 2.8 Summary -- Acknowledgments -- References -- Chapter 3 Approaches and considerations for forensic microbiology decomposition research -- 3.1 Introduction -- 3.2 Challenges of human remains research -- 3.3 Human remains research during death investigations -- 3.4 Human surrogates in research -- 3.5 Considerations for field studies -- 3.6 Descriptive and hypothesis‐driven research -- 3.7 Experiment design -- 3.8 Validation studies -- Acknowledgments -- References -- Chapter 4 Sampling methods and data generation.

4.1 Introduction -- 4.2 Materials -- 4.2.1 Financial considerations -- 4.2.2 Terrestrial settings -- 4.2.3 Aquatic settings -- 4.3 Sample collection techniques -- 4.4 Sample preservation, storage, and handling techniques -- 4.5 Data considerations -- 4.6 Conclusions -- Acknowledgments -- References -- Chapter 5 An introduction to metagenomic data generation, analysis, visualization, and interpretation -- 5.1 Introduction -- 5.2 DNA extraction -- 5.2.1 Sample collection and storage -- 5.2.2 Extraction methods -- 5.3 DNA sequencing -- 5.3.1 Amplicon sequencing of marker (16S rDNA/18S rDNA/ITS) loci -- 5.3.2 Multi-omics sequencing: metagenomic, metatranscriptomic, metaproteomic, and metametabolomic approaches -- 5.3.3 Next-generation sequencing platforms -- 5.4 Marker gene data analysis, visualization, and interpretation -- 5.4.1 Data analysis pipelines -- 5.4.2 Preprocessing of sequence data -- 5.4.3 Sequence clustering approaches -- 5.4.4 Microbial diversity estimations -- 5.5 Multi-omics data analysis, visualization, and interpretation -- 5.5.1 Sequence preprocessing -- 5.5.2 Sequence assembly -- 5.5.3 Taxonomic profiling -- 5.5.4 Gene prediction and metabolic profiling -- 5.6 Statistical analysis -- 5.7 Major challenges and future directions -- References -- Chapter 6 Culture and long-term storage of microorganisms for forensic science -- 6.1 Introduction -- 6.2 The value of culturing microorganisms -- 6.3 Collection and handling of samples -- 6.4 Protocols -- 6.4.1 Aerobic culture -- 6.4.2 Sterile technique -- 6.4.3 Sample collection, transport, and culture -- 6.4.4 Anaerobic culture -- 6.4.5 Preparing freezer stocks of pure culture -- 6.4.6 Reculturing stored microorganisms -- 6.5 Conclusions -- Acknowledgments -- References -- Chapter 7 Clinical microbiology and virology in the context of the autopsy -- 7.1 Introduction.

7.2 The historical view of autopsy microbiology -- 7.3 Which samples should you collect and how? -- 7.3.1 Blood -- 7.3.2 Cerebrospinal fluid -- 7.3.3 Tissue, pus, and fluids -- 7.3.4 Urine and bowel contents/feces -- 7.4 Which methods are available for the diagnosis of infection? -- 7.5 How do you put the results into context? -- 7.5.1 Culture -- 7.5.2 Serology and molecular tests -- 7.5.3 Biochemical markers -- 7.6 What are the risks of transmission of infection in the postmortem room? -- 7.7 How does autopsy microbiology contribute to the diagnosis of specific conditions? -- 7.7.1 Pneumonia -- 7.7.2 Mycobacterial infection -- 7.7.3 Fungal infections -- 7.7.4 Infective endocarditis -- 7.7.5 Gastrointestinal infection -- 7.7.6 Meningitis and central nervous system infections -- 7.7.7 Septicemia -- 7.7.8 Neonates and sudden unexplained death in infancy -- 7.7.9 Emerging infectious diseases and bioterrorism agents -- 7.8 Conclusion -- References -- Chapter 8 Postmortem bacterial translocation -- 8.1 Introduction -- 8.1.1 The intestinal microbiota in health -- 8.2 Bacterial translocation in health and disease -- 8.2.1 Pathophysiological mechanisms -- 8.2.2 Factors responsible for an increase in the bacterial translocation -- 8.3 Bacterial translocation in humans -- 8.3.1 Bacterial translocation after death -- 8.3.2 Identification of bacterial metabolites around the corpse -- 8.4 Physiological changes after death influencing the selection of commensal bacteria -- 8.4.1 Variations of available substrates for bacterial proliferation -- 8.4.2 Temperature -- 8.4.3 Anaerobic conditions -- 8.5 Consequences of bacterial translocation -- 8.5.1 Clinical interest -- 8.5.2 Identification of infectious agents at autopsy -- 8.5.3 Postmortem interval estimation -- 8.5.4 Infectious risk for postmortem organ transplantation -- 8.5.5 Postmortem toxicological analysis.

8.5.6 Prevention of biological risk at autopsy -- 8.5.7 Environmental consequences -- 8.6 Conclusion -- References -- Chapter 9 Microbial impacts in postmortem toxicology -- 9.1 Introduction -- 9.2 Microbial factors complicating postmortem toxicological analyses -- 9.2.1 Cadaver decomposition and specimen contamination -- 9.2.2 Postmortem drug and metabolite degradation -- 9.3 Precautions taken to limit microbial impacts -- 9.4 Experimental protocols used to investigate postmortem drug and metabolite degradation due to microbial activity -- 9.5 Examples of microbially mediated drug degradation -- 9.5.1 Drugs -- 9.5.2 Poisons -- 9.6 Concluding remarks -- References -- Chapter 10 Microbial communities associated with decomposing corpses -- 10.1 Introduction -- 10.1.1 Overview of the importance of bacteria in decomposition and Arpad Vass' original efforts to catalogue this diversity -- 10.1.2 Marker gene and metagenomics methods for facilitating studies of the microbial ecology of decomposition -- 10.2 The soil microbiology of decomposition -- 10.2.1 Microbial diversity of gravesoil and the rate of decomposition -- 10.2.2 Detecting decomposition signatures in soil and clandestine graves -- 10.2.3 Plant litter -- 10.3 Freshwater and marine decomposition -- 10.3.1 Freshwater decomposition: Fish -- 10.3.2 Freshwater decomposition: Swine -- 10.3.3 Marine decomposition: Whale falls -- 10.3.4 Marine decomposition: Swine -- 10.4 The microbiology of nonhuman models of terrestrial decomposition -- 10.4.1 Terrestrial decomposition: Rats -- 10.4.2 Terrestrial decomposition: Mice -- 10.4.3 Terrestrial decomposition: Swine -- 10.5 The microbiology of terrestrial human decomposition -- 10.5.1 Initial insights into the microbial ecology of human decomposition -- 10.5.2 Identification of microbial signatures associated with decomposition.

10.5.3 Microbial eukaryotic decomposers -- 10.5.4 Linking cadaver and soil microbial communities -- 10.5.5 Linking cadaver and insect microbial communities -- 10.6 Is there a universal decomposition signature? -- 10.7 Using microbial signatures to estimate PMI -- 10.7.1 Estimating PMI in terrestrial systems using gene marker data in nonhuman models of decomposition -- 10.7.2 Estimating PMI in terrestrial systems using gene marker data in human models -- 10.8 Conclusions -- Acknowledgments -- References -- Chapter 11 Arthropod-microbe interactions on vertebrate remains: Potential applications in the forensic sciences -- 11.1 Introduction -- 11.1.1 Decomposition and applications in forensic entomology -- 11.1.2 Microbe-arthropod interactions -- 11.2 Framework for understanding microbe-arthropod interactions on vertebrate remains -- 11.2.1 Precolonization interval -- 11.3 Postcolonization interval -- 11.3.1 Colonization -- 11.3.2 Development -- 11.3.3 Succession -- 11.3.4 Dispersal -- 11.4 Future directions and conclusion -- 11.4.1 Forensic sciences -- 11.4.2 Environmental sciences -- 11.4.3 Medical research -- Acknowledgments -- References -- Chapter 12 Microbes, anthropology, and bones -- 12.1 Introduction -- 12.2 Bone microstructure -- 12.3 Microbially mediated decomposition -- 12.4 Bone bioerosion -- 12.4.1 Mechanisms, timing, and source of microbial interaction -- 12.4.2 Exploration of bioerosion and bacterial community analysis -- 12.5 Reconstructing postmortem histories -- 12.6 Conclusions -- References -- Chapter 13 Forensic microbiology in built environments -- 13.1 Introduction -- 13.2 The human skin microbiome -- 13.3 The microbiota of the built environment -- 13.3.1 Human-home microbial dynamics -- 13.3.2 Influence of pets -- 13.3.3 Influence of interpersonal relationships.

13.4 Tools for the forensic classification of the built environment microbiome.

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Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2024. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.

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