Bacterial Pathogenesis: A Molecular Approach

Cover
Dedication
Contents
Preface
In Memoriam
About the Authors
Chapter 1: The Power of Bacteria
	Why Are Bacteria So Much in the Public Health Spotlight Nowadays?
	Bacteria, a Formidable Ancient Life Form
	Pressing Current Infectious Disease Issues
		Emerging and Reemerging Infectious Diseases
		Foodborne and Waterborne Infections
		Modern Medicine as a Source of New Diseases
		Postsurgical and Other Wound Infections
		Bioterrorism
	A New Respect for Prevention
		Surveillance: An Early Warning System
		Making Hospitals Safe for Patients
	And Now for Some Good News: You’ve Got a Bacterial Infection
		The Helicobacter pylori Revolution
		The Aftermath
		Microbiota Shift Diseases
	A Brave New World of Pathogenesis Research
		The New Age of Genomics
		Insights into Pathogen Evolution
		Modeling the Host-Pathogen Interaction in Experimental Animals
		Correlation Studies
	Selected Readings
	Questions
Chapter 2: Skin and Mucosa: The First Lines of Defense against Bacterial Infections
	The Best Defense: Avoid, Reduce, and Prevent Exposure!
	Barriers: Skin and Mucosal Membranes
		The Layers of Cells That Protect the Body
		Normal Microbiota of the Skin and Mucosa
		Defenses of the Skin
		Defenses of Mucosal Surfaces
		Special Defenses of the Gastrointestinal Tract
		Special Defenses of the Urogenital Tract
		Special Defenses of the Respiratory Tract
	Immune Defenses of the Skin and Mucosa
	Models for Studying Breaches of Barrier Defenses
	Selected Readings
	Questions
Chapter 3: The Innate Immune System: Always on Guard
	Triggering Innate Immune Defenses
	Innate Immune Cells That Defend Blood and Tissue
		Neutrophils (PMNs)
		Monocytes, Macrophages, and Dendritic Cells (DCs
		Granulocytes: Basophils, Mast Cells, and Eosinophils
		Transmigration—How Do Phagocytes Know When and Where to Go
		Natural Killer (NK) Cells
	The Lymphatic System
	How Phagocytes Recognize and Respond to Bacteria
	How Phagocytes Kill Bacteria
		Oxidative Burst in Phagolysosomes
		Autophagy—Another Pathway for the Killing of Intracellular Pathogens
	The Complement Cascade
		Complement Proteins
		Overview of Complement Pathways and Their Function
		Steps in Complement Activation
		Controlling Complement Activation
	Cytokines and Chemokines—Mediators of Immune Responses
		Roles of Cytokines and Chemokines in Directing Innate Immune Responses
		Inflammation and Collateral Damage
	Septic Shock: The Dark Side of the Innate Defenses
	Other Innate Defenses of the Body—Nutritional Immunity
	Selected Readings
	Questions
Chapter 4: The Adaptive Defenses: Antibodies and Cytotoxic T Cells
	The Specialists: Adapting to a Particular Pathogen Challenge
	B Cells: Producers of Antibodies
		The Humoral (Antibody) Immune Response
		Characteristics of Antibodies and Their Diverse Roles in Preventing Infection
		Serum Antibodies
		Secretory Antibodies: Antibodies That Protect Mucosal Surfaces
		Pathogen and Toxin Neutralization by Antibodies
		Affinity and Avidity
	Cytotoxic T Cells, Also Known as Cytotoxic T Lymphocytes (CTLs)
		Cytotoxic T Lymphocytes: Critical Defense against Intracellular Pathogens
	Antigen Presentation to the Immune System
		Processing of Protein Antigens by Dendritic Cells
		Interaction between APCs and T Cells: The T-Cell-Dependent Response
		Th-(Th1/Th2/Th17)-Cell-Mediated Immunity
		Production of Antibodies by B Cells
	Links between the Innate and Adaptive Defense Systems
	T-Cell-Independent Antibody Responses
	Mucosal Immunity: IgA/sIgA Antibodies
	Development of the Adaptive Immune System from Infancy to Adulthood
	Adaptive Defense Systems in Nonmammals
	The Dark Side of the Adaptive Defenses: Autoimmune Disease
	Selected Readings
	Questions
	Solving Problems in Bacterial Pathogenesis
Chapter 5: The Microbiota of the Human Body: Microbiomes and Beyond
	Importance of the Normal Resident Microbial Populations (Microbiota) of the Human Body
	Characterization of the Body’s Microbiota
		Taking a Microbial Census by Using Microbial rRNA Gene Sequence Analysis
		Characterizing Microbiomes by Using Metagenomic Analysis
		Beyond the Metagenome
	Overview of the Human Microbiota
		Skin Microbiota
		Oropharyngeal Microbiota
		Microbiota of the Small Intestine and Colon
		Microbiota of the Vaginal Tract
	The Other Microbiota: The Forgotten Eukaryotes
	Selected Readings
	Questions
	Solving Problems in Bacterial Pathogenesis
Chapter 6: Microbes and Disease: Establishing a Connection
	History and Relevance of Koch’s Postulates
		Early Germ Theory
		Koch’s Postulates: A Set of Criteria Used To Establish a Microbe-Disease Connection
	Challenges to Satisfying Koch’s Postulates
		Easier Said than Done. . .
		The First Postulate: Association of the Microbe with Lesions of the Disease
		The Second Postulate: Isolating the Bacterium in Pure Culture
		The Third Postulate: Showing that the Isolated Bacterium Causes Disease Experimentally in Humans or Animals
		The Fourth Postulate: Reisolating the Bacterium from the Intentionally Infected Animal
	Modern Alternatives To Satisfy Koch’s Postulates
		Detecting the Presence of the Pathogen Only in Diseased Tissues
		Eliminate the Pathogen and Prevent or Cure the Disease
		Comparative Infectious Disease Causation
	The Microbiota Shift Disease Problem
		Koch’s Postulates and Pathogenic Microbial Communities
		Keystone Pathogens and Microbial Shift Diseases
	Molecular Koch’s Postulates
	Concepts of Disease
		Varieties of Human-Microbe Interactions
		Views of the Human-Microbe Interaction
		Virulence as a Complex Phenomenon
	Selected Readings
	Questions
	Solving Problemsin Bacterial Pathogenesis
Chapter 7: Mechanisms of Genetic Modification and Exchange: Role in Pathogen Evolution
	Adapt or Perish
		Acquiring New Virulence Traits by Horizontal Gene Transfer
	Mechanisms of Genetic Change and Diversification
		Spontaneous Mutation
		Phase Variation
		Antigenic Variation
	Horizontal Gene Transfer: Mobile Genetic Elements
		Natural Transformation
		Conjugation: Plasmids and Transposons
		Phage Transduction
	Control of Horizontal Gene Transfer
		Toxin-Antitoxin Systems—Retaining the Goods
		Restriction-Modification Systems—Bacterial Innate Immunity from Foreign DNA
		CRISPR-Cas Systems—Bacterial Adaptive Immunity from Foreign DNA
		Type 6 Secretion Systems—Bacterial Defense Against Conjugation
	Pathogenicity Islands and Pathogen Evolution
		Properties of Pathogenicity Islands
		Pathogen Evolution in Quantum Leaps
	Selected Readings
	Questions
	Solving Problems in Bacterial Pathogenesis
Chapter 8: Identification of Virulence Factors: Measuring Infectivity and Virulence
	How Does One Experimentally Measure Virulence and Satisfy Koch’s Postulates
	Animal Models of Infection
		Human Volunteers
		Nonhuman Animal Models
	Measuring Bacterial Infection in Animal Models
		Ethical Considerations
		Animal Model Basics
		Survival Curve Analysis and Biophotonic Imaging
		ID50 and LD50 Values
		Competition Assays
	Tissue Culture and Organ Culture Models
		Tissue Culture Models
		Gentamicin Protection Assay for Cell Adhesion and Invasion
		Plaque Assay for Intracellular Survival and Cell-to-Cell  Spread
		Fluorescence Microscopy Techniques for Assessing Effects of Pathogens on Host Cells
		Organ Culture Models
	The Continuing Need for Reliable and Plentiful Information about Disease Pathology
	Selected Readings
	Questions
	Solving Problems in Bacterial Pathogenesis
Chapter 9: Identification of Virulence Factors: Molecular Approaches for Bacterial Factors
	Finding a Needle in a Haystack
	Biochemical Approaches
		Isolation and Purification of Toxic Factors
	Molecular Genetic Approaches
		Screening Using Recombinant Genes
		Reporter Fusions
		Mutagenesis Screening
	Genome-wide Sequencing Approaches for Identifying Virulence Genes
		Tn-Seq Technology to Identify In Vivo-Expressed Genes
		RNA-Seq Technology to Identify In Vivo-Expressed Genes
		Comparative Genomic Sequence Analysis for Identifying Virulence Genes
	Proteomics Approaches for Identifying Virulence Factors
		Protein Microarrays (Proteoarrays)
		In Vivo-Induced Antigen Technology (IVIAT)
	The Importance of Understanding Bacterial Physiology
	Selected Readings
	Questions
	Solving Problems in Bacterial Pathogenesis
Chapter 10: Identification of Virulence Factors: Molecular Approaches for Host Factors
	Comparative Approaches to Identify Host Factors  Required for Infection
		Transgenic Animal Models
		In vivo Imaging of Animals during Infection
		Systems Genetics: Comparative Genomics of the Host Response
	Screening Approaches to Identify Host Factors Required for Infection
		Genome-Wide Screening
	Host Response Profiling to Identify Host Factors Required for Infection
		Transcriptomics
		Proteomics
		Metabolomics
	The Promise and the Caution
	Selected Readings
	Questions
	Solving Problems in Bacterial Pathogenesis
Chapter 11: Bacterial Strategies for Colonization and Survival in the Host
	What Does Not Kill You Makes You Stronger—Or, a Better Pathogen
	Preinfection
		Survival in the External Environment
		Biofilms
		Motility and Chemotaxis
	Colonization of Host Surfaces
		Penetrating Intact Skin
		Penetrating the Mucin Layer
		Evading the Host’s Innate Immunity
		Nutrient and Iron Acquisition Mechanisms
		Adherence
	Evading the Host Immune Response
		Avoiding Complement and Phagocytosis
		Invasion and Uptake by Host Cells
		Surviving Phagocytosis
		Cell-to-Cell Spread
		Tissue Penetration and Dissemination
		Beyond Virulence Factors
	Selected Readings
	Questions
	Solving Problems in Bacterial Pathogenesis
	Special Global Perspective Problem: Integrating Concepts in Pathogenesis
Chapter 12: Toxins and Other Toxic Virulence Factors
	Bacterial Toxins
		Transparent Mechanisms, Exciting Applications, Mysterious Purposes
		Toxin Characteristics and Nomenclature
		Nonprotein Toxins
		Peptide and Protein Exotoxins
		Toxic Effector Proteins of Specialized Secretion Systems
	Examples of Toxin-Mediated Diseases
		Diphtheria Toxin
		Clostridial Neurotoxins
		Cholera Toxin
	Toxin-Based Therapeutics and Research Tools
		Immunotoxins
	Selected Readings
	Questions
	Solving Problems in Bacterial Pathogenesis
Chapter 13: Delivery of Virulence Factors
	Bacterial Secretion Systems and Virulence
	Common Secretory Systems
		The General Secretory (Sec) System
		The Accessory Secretory (Sec) System
		The Cotranslational Signal-Recognition Particle (SRP) System
		The Twin-Arginine Transport (TAT) System
	Secretion Systems Specific to Gram-Negative Bacteria
		Sec-Dependent Secretion Systems
		Sec-Independent Secretion Systems
	Specialized Secretion Systems Specific to Gram-Positive Bacteria
		General Secretory Transporter Systems in Gram-Positive Bacteria
		Cytolysin-Mediated Translocation (CMT) in S. pyogenes (Group A Strep
		Type 7 Secretion System (T7SS
	Selected Readings
	Questions
	Solving Problems in Bacterial Pathogenesis
Chapter 14: Virulence Regulation
	Virulence Gene Regulation
	Mechanisms of Regulation
		Operons, Regulons, and Global Regulators
		Activators and Repressors
		Two-Component Regulatory Systems
		Sigma Factors
		Transcriptional Terminators and Antiterminators
		Regulation of Translation Initiation
		Regulatory Small RNAs
		Bacterial Chromatin
	Responding to Environmental Signals
		Phase Variation and Bistable Switches
		Hypermutability, Intragenomic Recombination, and Positive Selection
		Coordinate Virulence Regulation
		Quorum Sensing
		Chemotaxis
	Selected Readings
	Questions
	Solving Problems in Bacterial Pathogenesis
	Special Global Perspective Problems: Integrating Concepts in Pathogenesis
Chapter 15: Antimicrobial Compounds and Their Targets
	Antimicrobial Compounds: The Safety Net of Modern Medicine
		The Importance of Antimicrobial Compounds
		Avoiding, Reducing, and Preventing Exposure
		Killing versus Inhibiting Growth
		Tests Used To Assess Antibiotics
	Antiseptics and Disinfectants
	Antibiotics
		Characteristics of Antibiotics
		The Process of Antibiotic Discovery
		The Economics of Antibiotic Discovery
	Mechanisms of Antibiotic Action
		Targets of Antibiotic Action
		Cell Wall Synthesis Inhibitors
		Protein Synthesis Inhibitors
		Antibiotics That Target DNA and RNA Synthesis
		Inhibitors of Tetrahydrofolate Biosynthesis
		The Newest Antibiotics
		The Newest Antibiotic Targets
		Strategies for Enhancing Antibiotic Efficacy
	The Continuing Challenge
	Selected Readings
	Questions
	Solving Problems in Bacterial Pathogenesis
Chapter 16: Antibiotic Resistance
	The Dawning of Awareness—Uh,We Have a Problem!
	How Did We Get to Where We Are?
	And Now the Really Scary Part
		Emergence and Challenge of Multidrug Resistance (MDR)
		Multiple Resistance and Genetic Linkage
		Next-Generation MDR Pathogens: The “Superbugs"!
	Mechanisms of Antibiotic Resistance
		Overview of Resistance Mechanisms
		Resistance to Antiseptics and Disinfectants
		Limiting Access of the Antibiotic
		Enzymatic Inactivation of the Antibiotic
		Modification or Protection of the Antibiotic Target
		Failure to Activate an Antibiotic
		Regulation of Resistance Genes
	Antibiotic Tolerance and Persister Cells
		Antibiotic Tolerance
		Persistence
		Toxin-Antitoxin Systems
	Horizontal Gene Transfer (HGT) of Resistance Genes
	Propagating and Maintaining Antibiotic Resistance through Selective Pressure and Changes in Fitness
	Will We Return to the Pre-Antibiotic Era
		Returning to Status Quo or Moving Forward
		The Hunt for Alternative Approaches to Antibiotics
	Selected Readings
	Questions
	Solving Problems in Bacterial Pathogenesis
	Special Global Perspective Problems: Integrating Concepts in Pathogenesis
Chapter 17: Vaccination: A Critical Component of the Modern Medical Armamentarium
	Vaccines: A Major Health Care Bargain
	What Makes an Ideal Vaccine
	Immunization Programs
		Barriers to Implementation and Success of Immunization Programs
		The Antivaccination Movement
	Vaccine Success Stories
		Subunit Vaccines
		Conjugate Vaccines
	Vaccine “Less-than-Success” Stories
	A New Age of Vaccine Development: Making Vaccines Better
		Approaches to Enhancing Immunogenicity
		Adjuvants
		Programming Adaptive Immunity
		Targeting Mucosal Immunity
	Storage of Vaccines—Strategies to Increase Shelf Life
	Passive Immunization
	Selected Readings
	Questions
	Solving Problems in Bacterial Pathogenesis
	Special Global Perspective Problems: Integrating Concepts in Pathogenesis
Chapter 18: The Gram-Positive Opportunistic Pathogens
	What Is an Opportunist
		Characteristics of Gram-Positive Opportunists
	Notable Gram-Positive Opportunists
		Staphylococcus aureus—Commensal Ready for a Fight
		Staphylococcus epidermidis—Accidental Pathogen
		Streptococcus pneumoniae—“Captain of All the Men of Death"
		Clostridium difficile—True Opportunist
	Other Gram-Positive Opportunists
	Selected Readings
	Questions
	Solving Problems in Bacterial Pathogenesis
Chapter 19: The Gram-Negative Opportunistic Pathogens
	Jumping Over the (Cell) Wall: Gram-Negative Bacteria Can Be Opportunistic Pathogens Too
		Common Traits of Gram-Negative Opportunists
	The Dark Side of Some Residents of the Human Body
		The Ever-Changing Face of E. coli
		Klebsiella pneumoniae Nosocomial Infections
		Bacteroides fragilis—The Bad Sheep of the Family
		Porphyromonas gingivalis—A Keystone Pathogen
	Environmental Inhabitants Weigh in as Opportunists
		Pseudomonas aeruginosa—A Versatile Opportunist of the Highest Order
		Burkholderia cepacia Complex—P.aeruginosa’s Evil Twin
		Acinetobacter baumannii—A Deadly Threat Emerges from the Iraq War
	Don’t Forget the Arthropods
		Ehrlichia spp
	Selected Readings
	Questions
	Solving Problems in Bacterial Pathogenesis
	Special Global Perspective Problems: Integrating Concepts in Pathogenesis
Chapter 20: The Changing Roles of Microbiologists in an Age of Bioterrorism and Emerging Diseases
	When Microbiologists Are Called to the Front Line
	Tracking Down a Bioterrorist
		Unintentional or Deliberate
		Timing
		Tracing the Source
	Lessons Learned
	The “Top Four” Bioterror Agents
		Bacillus anthracis Spores
		Smallpox
		Yersinia pestis
		Botulinum Neurotoxin
	What If Bioterrorists Hit Us with Something Completely New
	Biosecurity in a Complex, Dynamic, and Ever-Changing World
	Food Safety and Biosecurity
		The Case for Food Irradiation
	The Future of Biosecurity
	Selected Readings
	Questions
	Solving Problems in Bacterial Pathogenesis
Glossary
Index