Biofilm-Mediated Diseases: Causes and Controls

Preface
Contents
Editors and Contributors
1: Introduction to Bacterial Biofilm and Acute Infections
1.1 Introduction
1.2 Description of Biofilm
1.3 History of Discovery of Biofilm
1.4 Composition of Bacterial Biofilm
1.5 Planktonic to Biofilm-Growing Bacteria
1.6 Quorum Sensing and Its Role in Bacterial Biofilm
1.6.1 Quorum Sensing in Gram-Positive Bacteria
1.6.1.1 Quorum Sensing in Staphylococcus aureus
1.6.2 Quorum Sensing in Gram-Negative Bacteria
1.6.2.1 Quorum Sensing in Pseudomonas aeruginosa
1.7 Biofilm-Associated Infection and Pathogenesis
1.8 Biofilm-Associated Acute Infections
1.8.1 Biofilm-Associated Acute Infection of the Skin
1.8.2 Biofilm-Associated Respiratory Tract Infections
1.8.3 Biofilm-Associated Acute Digestive Tract Infection
1.8.4 Biofilm-Associated Urinary Tract Infections
1.9 Antimicrobial Resistance of the Biofilm
1.10 Conclusion
References
2: Quorum Sensing
2.1 Introduction
2.2 Mechanism of Quorum Sensing in Gram-Negative Bacteria
2.2.1 Cellular Communication in P. aeruginosa via Quorum Sensing
2.2.2 QS in Burkholderia cepacia
2.2.3 QS in Erwinia carotovora
2.3 Mechanism of QS in Gram-Positive Bacteria
2.3.1 QS in S. aureus
2.4 QS and Virulence
2.4.1 Virulence in Staphylococcus aureus
2.4.2 Virulence in Pseudomonas aeruginosa
2.4.3 Virulence in E. coli
2.5 Pharmacological Perspective of Quorum Sensing
2.5.1 Targeting QS for Antimicrobial Therapy
2.5.2 Strategies to Control Biofilm Formation
2.5.2.1 Targeting the AHL-Mediated QS
2.5.2.2 Preventing the Stringent Response in Bacteria
2.5.2.3 Enzymatic Dispersion of EPS
2.5.2.4 Disrupting the Peptidoglycan Layer
2.5.2.5 Molecules Causing Biofilm Dispersal
2.5.2.6 Disassembly of Lipopolysaccharides/Membrane Permeabilization
2.5.2.7 Prevention of Cell Division and Adhesion Molecule Synthesis
2.6 Conclusion
References
3: Bacteria and Biofilms as Natural Inhabitants of Our Body
3.1 Introduction
3.2 Oral Biofilms
3.2.1 Human Oral Microbiome
3.2.2 Ecological Determinants for the Nature of Inhabitants
3.2.3 Establishment of Oral Biofilm
3.2.4 Formation of Oral Biofilm Is Done Through the Following Steps
3.2.4.1 Adsorption of Host and Bacterial Molecules to the Tooth Surface
3.2.4.2 Passive Transport of Oral Bacteria to the Tooth Surface
3.2.4.3 Co-adhesion of Later Colonizers to Already Attached Early Colonizers
3.2.4.4 Multiplication of the Attached Microorganisms
3.2.4.5 Active Detachment and Dispersal
3.2.5 Genetic Background of Oral Biofilm Formation
3.2.6 Diseases Caused by Oral Biofilm
3.2.7 Systemic Consequences of Oral Dysbiosis
3.2.8 Advantages of Oral Biofilm
3.3 Skin Microbiology
3.3.1 Human Skin Microbiome
3.3.2 The Skin as an Ecosystem
3.3.3 Composition of Skin Microbiota
3.3.4 Variation by Skin Site
3.3.5 Biofilms in Skin Microbiota
3.3.6 Diseases
3.4 Gut Microbiome
3.4.1 Introduction to Gut Microbiome
3.4.2 Formation of Biofilm in Gut
3.4.3 Composition of Gut Biofilm
3.4.4 Architecture of Gut Biofilm
3.4.4.1 Biofilm in the Oesophagus
3.4.4.2 Biofilm in the Stomach
3.4.4.3 Biofilm in the Large Intestine
3.4.4.4 Biofilm in the Colon
3.4.5 Functions of Gut Biofilm
3.4.6 Diseases and Gut Biofilm
3.4.6.1 Crohn´s Disease
3.5 Bacterial Biofilms on Other Body Parts
3.5.1 Vaginal Biofilm
3.5.2 Middle Ear Biofilm
3.5.3 Lung Biofilm
3.5.4 Biofilm in the Pancreatic Duct
3.5.5 Biofilm on Renal Tissues
3.5.6 Biofilm in the Eye
3.6 Conclusion
References
4: Biofilms and Acute and Chronic Infections
4.1 Introduction
4.2 Biofilm in Acute Infections
4.3 Chronic Infections Persistency
4.4 Biofilms and Drug Resistance
4.5 Pseudomonas aeruginosa Biofilms in Cystic Fibrosis Lung Infections
4.6 Biofilms on Chronic Wounds
4.7 Endocarditis
4.8 Periodontitis
4.9 Chronic Infections: Host Response
4.9.1 Immune Response in Chronic Biofilm Infections
4.9.1.1 Innate Immune Response in Chronic Biofilm Infections
4.9.2 Acquired/Adapted Immune Response in Chronic Biofilm Infections
4.9.3 Host Immune Responses to Biofilm Constituents
4.9.3.1 The Immune Response to Exopolysaccharides
4.9.3.2 Immune Response to Extracellular DNA
4.9.3.3 Immune Response to Exoproteins
4.9.3.4 Immune Responses to Biofilm-Associated Small Molecules
4.10 Treatments for Biofilm-Associated Diseases
4.10.1 Current Treatment Approaches
4.10.2 Reasons Behind Treatment Failure in Device-Related Osteomyelitis
4.10.3 Reasons Behind Treatment Failure and Recurrence in Vaginal Infections
4.10.4 Reasons Behind Treatment Failure and Recurrence in Otitis Media
4.10.5 Reasons Behind Treatment Failure and Recurrence in Orthopaedic Infections
4.10.6 Reasons Behind Treatment Failure and Recurrence in Coccidioidal Meningitis
4.10.7 Reasons Behind Treatment Failure and Recurrence of Osteomyelitis
4.11 Conclusion
References
5: Bacteria and Biofilms in Chronic Infections and Nosocomial Diseases
5.1 Introduction
5.2 Biofilm and Lung Cystic Fibrosis (CF)
5.2.1 Origin and Demonstration of Biofilm in CF of Lungs
5.2.2 Mechanism Underlying the Biofilm Organization in Lungs in Chronic CF
5.3 Biofilm and Chronic Wounds
5.3.1 Signaling Events Leading to Biofilm Formation in Chronic Wounds
5.4 Biofilm and Endophthalmitis
5.4.1 Endophthalmitis and Biofilm
5.5 Biofilm and Keratitis
5.6 Prospective Antibiofilm Agents
5.6.1 EPS-Degrading Enzymes
5.6.2 Targeting EPS (Extrapolymeric Network) by Alginate Oligosaccharides
5.6.3 Targeting e-DNA by DNase
5.6.4 Targeting Quorum Sensing Molecules
5.6.5 Imposing Negative Pressure to Distract Biofilm
5.6.6 Biofilm Gene Knockout Strategies
5.6.7 Nanoparticle-Based Technology
5.7 Conclusion and Prospective
References
6: Immune Response to Biofilm
6.1 Introduction
6.2 Immune Response for Pathogens and Pathobionts
6.2.1 Local Immune Response
6.2.1.1 Immune Response from Host Tissues
6.2.1.2 Immune Response due to Implant
6.2.2 Systemic Immune Response
6.2.2.1 Immune Response from Host Tissues
6.2.2.2 Immune Response due to Implant
6.3 Immune Response for Commensal Microorganisms
6.4 Immune Evasion by Biofilm
6.4.1 Evasion of Innate Immune Reaction
6.4.2 Evasion of Adaptive Immune Response
6.5 Skewing of Immune Response
6.6 Induction of Biofilm Production by Immunogenic Cells of the Host
6.7 Conclusion
References
7: Biofilm on Medical Appliances
7.1 Introduction
7.2 Infections Associated with Medical Devices
7.2.1 Biofilm of Gram-Positive Bacteria and Infections
7.2.2 Biofilm of Gram-Negative Bacteria and Infections
7.3 Device-Associated Biofilm Formation
7.3.1 Non-invasive Medical Devices
7.3.2 Invasive Medical Devices
7.3.3 Short-Term Use of Medical Devices
7.3.4 Long-Term Use of Medical Devices
7.4 Mechanisms of Bacterial Attachment on the Surface of Appliances
7.4.1 Bacterial Motility and Surface Attachment
7.4.1.1 Brownian Motion
7.4.1.2 Motility of the Flagella
7.4.1.3 Non-flagellar Motility
7.4.2 Environmental Factors Regulating Bacterial Movements
7.4.2.1 Chemotaxis
7.4.2.2 Quorum Sensing
7.4.2.3 Bis-(3′-5′)-Cyclic Dimeric Guanosine Monophosphate (c-di-GMP)
7.4.3 Mechanism of Development of Biofilm upon Medical Implants
7.4.3.1 Initiation of the Biofilm Formation
7.4.3.2 Adhesion by Proteins
7.4.3.3 Amyloid Fibers
7.4.3.4 Maturation of Biofilm
7.4.3.5 Dispersal of Biofilm
7.5 Characteristics of Medical Device-Associated Infections
7.5.1 Host Factors
7.5.2 Nature of Biomaterials
7.5.3 Microbial Factors
7.6 Common Appliances and Implants with Biofilm
7.6.1 Contact Lenses
7.6.2 Central Venous Catheters (CVC)
7.6.3 Endotracheal Tubes (ETT)
7.6.4 Intrauterine Devices (IUD)
7.6.5 Mechanical Heart Valves
7.6.6 Pacemakers
7.6.7 Dialysis Catheters
7.6.8 Urinary Catheters
7.6.9 Voice Prostheses
7.6.10 Intracardiac Prostheses
7.7 Conclusion and Future Prospects
References
8: Biofilm and Antimicrobial Resistance
8.1 Introduction
8.2 Ultrastructure of Biofilm
8.3 Structure of Biofilm and Associated Places
8.4 Antibiotic Resistance by Biofilm
8.5 Mechanisms of Development of Antibiotic Resistance
8.5.1 Antimicrobial Penetration
8.5.2 Polysaccharide-Associated Development of Resistance Within the Biofilm
8.5.3 Development of Resistance by the Antibiotic-Modifying Enzymes Being Present in Matrix
8.5.4 Intrinsic Resistances: Acquired and Adaptive Resistance
8.5.5 Mutation
8.5.6 Extracellular DNA-Dependent Development of Resistance
8.5.7 Stress Responses Resulting in the Development of Antibiotic Resistance and Hypoxia-Associated Antimicrobial Resistance
8.5.8 Oxidative Stress Responses Resulting in the Development of Resistance
8.5.9 Starvation of Amino Acids Results in the Development of Resistance
8.5.10 Cell Wall-Modifying Enzyme-Associated Development of Resistance
8.5.11 Genetic Basis of Resistance: Mobile Genetic Elements
8.5.12 Insertion Sequence (IS)
8.5.13 Transposons
8.5.14 Plasmids
8.6 Effects of Antibiotic Resistance
8.7 Conclusion
References
9: Inhibition of Biofilm Formation
9.1 Introduction
9.2 Inhibition of Quorum Sensing and Signalling Pathways
9.2.1 Quorum Quenching (QQ)
9.3 Other Interacting Members in a Bacterial Biofilm
9.3.1 Role of EPS Molecules in the Formation of Biofilm
9.4 Natural Antibiofilm Compounds
9.4.1 Antimicrobial Resistance Versus Phytotherapy
9.4.2 Phytochemicals and Biofilm
9.5 Conclusion
References
10: Novel and Future Treatment Strategies for Biofilm-Associated Infections
10.1 Introduction
10.2 Biofilm Formation in Infections
10.3 Biofilm Control Strategies
10.3.1 Phytomedicine
10.3.2 New Biofilm Control Strategies
10.3.2.1 Ultrasonic Disruption
10.3.2.2 Enzyme-Mediated Disruption
10.3.2.3 Electrolyzed Water
10.3.2.4 Bacteriophages
10.3.3 Nanotechnology-Driven Solutions
10.3.3.1 Gold Nanoparticles
10.3.3.2 Silver Nanoparticles
10.3.3.3 Gold-Silver Bimetallic Nanoparticles
10.3.3.4 Nanocomposites and Magnetic Nanomaterials
Silver-SPION Nanocomposite
Carboxylate Functionalized SPIONs
SPION-Encapsulated Polymersome
10.4 Conclusions and Future Perspectives
References
11: Biofilm: The Unknown Armor in the Arsenal of Bacteria: A Case Study
11.1 Introduction
11.2 Case History
11.3 On Examination
11.4 Lab Investigations
11.5 Diagnosis
11.6 Identification of Microorganism
11.7 Antimicrobial Susceptibility Testing
11.7.1 Qualitative Biofilm Production Assay by Congo Red Method
11.7.2 Quantitative Biofilm Detection Assay by Tube Method
11.8 Discussion
11.9 Conclusion
References