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E-raamat: Forensic Microbiology

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  • Sari: Forensic Science in Focus
  • Ilmumisaeg: 21-Mar-2017
  • Kirjastus: John Wiley & Sons Inc
  • Keel: eng
  • ISBN-13: 9781119062561
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Forensic MicrobiologySuurem pilt
  • Formaat: PDF+DRM
  • Sari: Forensic Science in Focus
  • Ilmumisaeg: 21-Mar-2017
  • Kirjastus: John Wiley & Sons Inc
  • Keel: eng
  • ISBN-13: 9781119062561
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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. 

About the editors xvi
List of contributors
xix
Foreword xxii
Series preface xxiv
Preface xxv
1 A Primer On Microbiology
1(24)
David O. Carter
Emily N. Junkins
Whitney A. Kodama
1.1 Introduction
1(1)
1.2 Microbial characteristics
2(5)
1.2.1 Microbial taxonomy and function
2(3)
1.2.2 Enzyme activity
5(2)
1.3 Microorganisms and their habitats
7(3)
1.3.1 Oxygen and moisture
8(1)
1.3.2 Temperature
9(1)
1.4 Competition for resources
10(1)
1.5 The ecology of some forensically relevant bacteria
11(9)
1.5.1 Actinobacteria
11(2)
1.5.2 Firmicutes
13(3)
1.5.3 Proteobacteria
16(4)
1.6 Archaea and microbial eukaryotes
20(1)
1.7 Conclusions
21(4)
Acknowledgments
21(1)
References
21(4)
2 History, current, and future use of microorganisms as physical evidence
25(31)
Zachary M. Burcham
Heather R. Jordan
2.1 Introduction
25(1)
2.1.1 Why and how are microorganisms used in forensic science?
25(1)
2.2 Methods for identification
26(4)
2.2.1 Classical microbiology
26(1)
2.2.2 Genomics and strain typing
27(3)
2.3 Estimating PMI
30(6)
2.3.1 Microbial succession
32(4)
2.4 Cause of death
36(4)
2.4.1 Natural causes
36(2)
2.4.2 Biocrimes
38(2)
2.5 Trace evidence
40(3)
2.5.1 Human
40(2)
2.5.2 Nonhuman animals and food
42(1)
2.6 Other medicolegal aspects
43(5)
2.6.1 Sexual assault
43(1)
2.6.2 Medical malpractice
43(1)
2.6.3 Nosocomial infections and antibiotic resistance
44(1)
2.6.4 Food safety and environmental contamination
44(4)
2.7 Needs that must be met for use in chain of custody
48(1)
2.8 Summary
49(7)
Acknowledgments
50(1)
References
50(6)
3 Approaches and considerations for forensic microbiology decomposition research
56(16)
M. Eric Benbow
Jennifer L. Pechal
3.1 Introduction
56(1)
3.2 Challenges of human remains research
57(1)
3.3 Human remains research during death investigations
58(2)
3.4 Human surrogates in research
60(1)
3.5 Considerations for field studies
61(1)
3.6 Descriptive and hypothesis-driven research
62(3)
3.7 Experiment design
65(4)
3.8 Validation studies
69(3)
Acknowledgments
70(1)
References
70(2)
4 Sampling methods and data generation
72(22)
Jennifer L. Pechal
M. Eric Benbow
Tawni L. Crippen
4.1 Introduction
72(1)
4.2 Materials
73(6)
4.2.1 Financial considerations
73(1)
4.2.2 Terrestrial settings
74(3)
4.2.3 Aquatic settings
77(2)
4.3 Sample collection techniques
79(1)
4.4 Sample preservation, storage, and handling techniques
80(6)
4.5 Data considerations
86(4)
4.6 Conclusions
90(4)
Acknowledgments
90(1)
References
91(3)
5 An introduction to metagenomic data generation, analysis, visualization, and interpretation
94(33)
Baneshwar Singh
Tawni L. Crippen
Jeffery K. Tomberlin
5.1 Introduction
94(2)
5.2 DNA extraction
96(3)
5.2.1 Sample collection and storage
96(1)
5.2.2 Extraction methods
97(2)
5.3 DNA sequencing
99(8)
5.3.1 Amplicon sequencing of marker (16S rDNA/18S rDNA/ITS) loci
99(3)
5.3.2 Multi-omics sequencing: metagenomic, metatranscriptomic, metaproteomic, and metametabolomic approaches
102(3)
5.3.3 Next-generation sequencing platforms
105(2)
5.4 Marker gene data analysis, visualization, and interpretation
107(7)
5.4.1 Data analysis pipelines
107(1)
5.4.2 Preprocessing of sequence data
108(3)
5.4.3 Sequence clustering approaches
111(1)
5.4.4 Microbial diversity estimations
112(2)
5.5 Multi-omics data analysis, visualization, and interpretation
114(3)
5.5.1 Sequence preprocessing
115(1)
5.5.2 Sequence assembly
115(1)
5.5.3 Taxonomic profiling
116(1)
5.5.4 Gene prediction and metabolic profiling
116(1)
5.6 Statistical analysis
117(1)
5.7 Major challenges and future directions
118(9)
References
119(8)
6 Culture and long-term storage of microorganisms for forensic science
127(19)
Emily N. Junkins
Embriette R. Hyde
David O. Carter
6.1 Introduction
127(1)
6.2 The value of culturing microorganisms
128(4)
6.3 Collection and handling of samples
132(2)
6.4 Protocols
134(9)
6.4.1 Aerobic culture
134(1)
6.4.2 Sterile technique
134(1)
6.4.3 Sample collection, transport, and culture
134(4)
6.4.4 Anaerobic culture
138(4)
6.4.5 Preparing freezer stocks of pure culture
142(1)
6.4.6 Reculturing stored microorganisms
143(1)
6.5 Conclusions
143(3)
Acknowledgments
143(1)
References
143(3)
7 Clinical microbiology and virology in the context of the autopsy
146(46)
Elisabeth J. Ridgway
Bala M. Subramanian
Mohammad Raza
7.1 Introduction
146(1)
7.2 The historical view of autopsy microbiology
147(2)
7.3 Which samples should you collect and how?
149(5)
7.3.1 Blood
151(1)
7.3.2 Cerebrospinal fluid
152(1)
7.3.3 Tissue, pus, and fluids
153(1)
7.3.4 Urine and bowel contents/feces
154(1)
7.4 Which methods are available for the diagnosis of infection?
154(2)
7.5 How do you put the results into context?
156(7)
7.5.1 Culture
156(4)
7.5.2 Serology and molecular tests
160(1)
7.5.3 Biochemical markers
161(2)
7.6 What are the risks of transmission of infection in the postmortem room?
163(1)
7.7 How does autopsy microbiology contribute to the diagnosis of specific conditions?
164(18)
7.7.1 Pneumonia
164(4)
7.7.2 Mycobacterial infection
168(2)
7.7.3 Fungal infections
170(1)
7.7.4 Infective endocarditis
171(1)
7.7.5 Gastrointestinal infection
172(1)
7.7.6 Meningitis and central nervous system infections
173(1)
7.7.7 Septicemia
174(1)
7.7.8 Neonates and sudden unexplained death in infancy
175(3)
7.7.9 Emerging infectious diseases and bioterrorism agents
178(4)
7.8 Conclusion
182(10)
References
182(10)
8 Postmortem bacterial translocation
192(20)
Vadim Mesli
Christel Neut
Valery Hedouin
8.1 Introduction
192(3)
8.1.1 The intestinal microbiota in health
192(3)
8.2 Bacterial translocation in health and disease
195(3)
8.2.1 Pathophysiological mechanisms
196(1)
8.2.2 Factors responsible for an increase in the bacterial translocation
197(1)
8.3 Bacterial translocation in humans
198(2)
8.3.1 Bacterial translocation after death
199(1)
8.3.2 Identification of bacterial metabolites around the corpse
200(1)
8.4 Physiological changes alter death influencing the selection of commensal bacteria
200(4)
8.4.1 Variations of available substrates for bacterial proliferation
200(1)
8.4.2 Temperature
201(1)
8.4.3 Anaerobic conditions
202(2)
8.5 Consequences of bacterial translocation
204(2)
8.5.1 Clinical interest
204(1)
8.5.2 Identification of infectious agents at autopsy
204(1)
8.5.3 Postmortem interval estimation
204(1)
8.5.4 Infectious risk for postmortem organ transplantation
205(1)
8.5.5 Postmortem toxicological analysis
205(1)
8.5.6 Prevention of biological risk at autopsy
206(1)
8.5.7 Environmental consequences
206(1)
8.6 Conclusion
206(6)
References
207(5)
9 Microbial impacts in postmortem toxicology
212(33)
Jared W. Castle
Danielle M. Butzbach
G. Stewart Walker
Claire E. Lenehan
Frank Reith
K. Paul Kirkbride
9.1 Introduction
212(1)
9.2 Microbial factors complicating postmortem toxicological analyses
213(1)
9.2.1 Cadaver decomposition and specimen contamination
213(1)
9.2.2 Postmortem drug and metabolite degradation
214(1)
9.3 Precautions taken to limit microbial impacts
214(4)
9.4 Experimental protocols used to investigate postmortem drug and metabolite degradation due to microbial activity
218(1)
9.5 Examples of microbially mediated drug degradation
219(15)
9.5.1 Drugs
220(13)
9.5.2 Poisons
233(1)
9.6 Concluding remarks
234(11)
References
235(10)
10 Microbial communities associated with decomposing corpses
245(29)
Embriette R. Hyde
Jessica L. Metcalf
Sibyl R. Bucheli
Aaron M. Lynne
Rob Knight
10.1 Introduction
245(3)
10.1.1 Overview of the importance of bacteria in decomposition and Arpad Vass' original efforts to catalogue this diversity
246(1)
10.1.2 Marker gene and metagenomics methods for facilitating studies of the microbial ecology of decomposition
247(1)
10.2 The soil microbiology of decomposition
248(4)
10.2.1 Microbial diversity of gravesoil and the rate of decomposition
248(2)
10.2.2 Detecting decomposition signatures in soil and clandestine graves
250(1)
10.2.3 Plant litter
251(1)
10.3 Freshwater and marine decomposition
252(3)
10.3.1 Freshwater decomposition: Fish
252(1)
10.3.2 Freshwater decomposition: Swine
253(1)
10.3.3 Marine decomposition: Whale falls
253(1)
10.3.4 Marine decomposition: Swine
254(1)
10.4 The microbiology of nonhuman models of terrestrial decomposition
255(3)
10.4.1 Terrestrial decomposition: Rats
255(1)
10.4.2 Terrestrial decomposition: Mice
256(1)
10.4.3 Terrestrial decomposition: Swine
257(1)
10.5 The microbiology of terrestrial human decomposition
258(5)
10.5.1 Initial insights into the microbial ecology of human decomposition
259(1)
10.5.2 Identification of microbial signatures associated with decomposition
260(1)
10.5.3 Microbial eukaryotic decomposers
261(1)
10.5.4 Linking cadaver and soil microbial communities
261(1)
10.5.5 Linking cadaver and insect microbial communities
262(1)
10.6 Is there a universal decomposition signature?
263(1)
10.7 Using microbial signatures to estimate PMI
264(4)
10.7.1 Estimating PMI in terrestrial systems using gene marker data in nonhuman models of decomposition
266(1)
10.7.2 Estimating PMI in terrestrial systems using gene marker data in human models
267(1)
10.8 Conclusions
268(6)
Acknowledgments
268(1)
References
269(5)
11 Arthropod-microbe interactions on vertebrate remains: Potential applications in the forensic sciences
274(38)
Jeffery K. Tomberlin
M. Eric Benbow
Kate M. Barnes
Heather R. Jordan
11.1 Introduction
274(8)
11.1.1 Decomposition and applications in forensic entomology
275(3)
11.1.2 Microbe-arthropod interactions
278(4)
11.2 Framework for understanding microbe-arthropod interactions on vertebrate remains
282(5)
11.2.1 Precolonization interval
282(5)
11.3 Postcolonization interval
287(10)
11.3.1 Colonization
288(2)
11.3.2 Development
290(2)
11.3.3 Succession
292(3)
11.3.4 Dispersal
295(2)
11.4 Future directions and conclusion
297(1)
11.4.1 Forensic sciences
297(1)
11.4.2 Environmental sciences
298(1)
11.4.3 Medical research
298(1)
11.5 Acknowledgments
298(1)
References
298(14)
12 Microbes, anthropology, and bones
312(16)
Franklin E. Damann
Miranda M.E. Jans
12.1 Introduction
312(1)
12.2 Bone microstructure
313(2)
12.3 Microbially mediated decomposition
315(2)
12.4 Bone bioerosion
317(5)
12.4.1 Mechanisms, timing, and source of microbial interaction
319(1)
12.4.2 Exploration of bioerosion and bacterial community analysis
320(2)
12.5 Reconstructing postmortem histories
322(2)
12.6 Conclusions
324(4)
References
324(4)
13 Forensic microbiology in built environments
328(11)
Simon Lax
Jack A. Gilbert
13.1 Introduction
328(1)
13.2 The human skin microbiome
328(1)
13.3 The microbiota of the built environment
329(3)
13.3.1 Human-home microbial dynamics
330(2)
13.3.2 Influence of pets
332(1)
13.3.3 Influence of interpersonal relationships
332(1)
13.4 Tools for the forensic classification of the built environment microbiome
332(3)
13.4.1 Sampling and sequencing considerations
332(2)
13.4.2 Machine learning and statistical classification
334(1)
13.4.3 Sequence clustering
334(1)
13.5 Forensic microbiology of the built environment
335(1)
13.5.1 Tracking disease in hospital environments
335(1)
13.5.2 Tracking occupancy and activity in a built environment
336(1)
13.6 Conclusion
336(3)
References
337(2)
14 Soil bacteria as trace evidence
339(19)
David R. Foran
Ellen M. Jesmok
James M. Hopkins
14.1 The forensic analysis of soil
339(1)
14.2 Assessing the biological components of soil
340(1)
14.3 Bacteria in soil
341(1)
14.4 Molecular techniques for the forensic analysis of soil
342(3)
14.4.1 Analysis of soil bacteria
342(1)
14.4.2 Denaturing gradient gel electrophoresis
343(1)
14.4.3 Assaying DNA size variability
343(1)
14.4.4 Next-generation sequencing
344(1)
14.5 Soil microbial profile data analysis methods
345(5)
14.5.1 Qualities of ideal forensic data analysis techniques
345(1)
14.5.2 Objective microbial profiling analysis methods
346(1)
14.5.3 Demonstrative microbial profiling analysis methods
347(3)
14.5.4 Combinations of data analysis techniques
350(1)
14.6 Feasibility of next-generation sequencing for forensic soil analysis
350(3)
14.6.1 Differentiating diverse and similar habitats
350(1)
14.6.2 Temporal changes in soil microbial profiles
351(1)
14.6.3 Spatial differences in soil microbial profiles
351(1)
14.6.4 Soil sample collection strategies
352(1)
14.6.5 Evidence storage and changes in bacterial abundance over time
352(1)
14.6.6 Costs of next-generation sequencing of forensic soil samples
352(1)
14.6.7 Legal considerations for the implementation of microbial profiling
353(1)
14.7 Consensus on methodologies for soil collection and analysis
353(5)
Acknowledgments
354(1)
References
354(4)
15 DNA profiling of bacteria from human hair: Potential and pitfalls
358(21)
Silvana R. Tridico
Daithi C. Murray
Michael Bunce
K. Paul Kirkbride
15.1 An introduction to human hair as a forensic substrate
358(3)
15.1.1 Relevance of hair in forensic science
358(1)
15.1.2 Historical and current forensic perspectives of hair examination and analysis
359(2)
15.2 Current research into hair microbiomes
361(4)
15.2.1 Studies conducted into the metagenomic potential of human hair as a forensic substrate
362(3)
15.3 Importance of hair sample collection, storage, and isolation of microbial DNA
365(2)
15.3.1 Hair sample collection, storage, and analysis
365(2)
15.4 DNA sequencing of hair microbiomes
367(2)
15.4.1 Bio informatics considerations for analyzing microbial hair data
368(1)
15.5 Conclusions and future directions
369(10)
15.5.1 Major challenges and future directions of metagenomic analyses of hairs in forensic science
369(1)
15.5.2 Future metagenomic assessments of hair samples
370(1)
15.5.3 Development of more focused approaches to detect bacterial population level differences between bacteria inhabiting human hairs
370(1)
15.5.4 General requirements for quality management
371(1)
Acknowledgments
372(1)
References
372(4)
Perspectives on the future of forensic microbiology
376(3)
David O. Carter
Jeffery K. Tomberlin
M. Eric Benbow
Jessica L. Metcalf
Index 379
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
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