Pseudomonas aeruginosa: Biology, Pathogenesis and Control Strategies (Advances in Experimental Medicine and Biology, 1386)

This book covers the wide set of well-regulated virulence factors and defense mechanisms of Pseudomonas aeruginosa focusing on stress responses and the evolution of this opportunistic human pathogen. Pseudomonas aeruginosa is responsible for one out of ten hospital infections. Additionally, this Gram-negative bacterium is accountable for persistent infections in immunocompromised individuals and the leading cause of chronic lung infections in cystic fibrosis patients. This book provides insight on the metabolic versatility of Pseudomonas aeruginosa and its mechanisms for biofilm formation that make this organism highly efficient in causing infections. The book invites the readers to learn more about the intrinsic ability of Pseudomonas aeruginosa to resist a wide variety of antimicrobial agents due to the concerted action of multidrug efflux pumps, antibiotic-degrading enzymes, and the low permeability of bacterial cellular envelopes. Particular focus is put on the evolutionary role of different types of protein-secretion systems in pathogenesis, flagella and their role in chemotaxis and surface sensing, and host-pathogen interactions. This book is a useful introduction to the field for junior scientists interested in the biology and pathogenesis of Pseudomonas aeruginosa . It is also an interesting read for advanced scientists and medical specialists working within this field, providing a broader view of the topic beyond their specific area of specialization. Preface Contents Contributors Part I: Biology and Evolution of Pseudomonas aeruginosa 1: Pseudomonas aeruginosa Pangenome: Core and Accessory Genes of a Highly Resourceful Opportunistic Pathogen 1.1 Pseudomonas aeruginosa Environment and Main Genomic Characteristics 1.1.1 Pangenomics and Populations Structure Analyses in Population Genomics 1.2 The Population Structure of Pseudomonas aeruginosa 1.3 The Pangenome of Pseudomonas aeruginosa 1.3.1 Characterization of the Core Genome of Pseudomonas aeruginosa 1.3.2 Comparison of Antibiotic Resistance Profiles Among Phylogroups of Pseudomonas aeruginosa Species 1.4 The Highly Variable Accessory Genome of Pseudomonas aeruginosa 1.5 Conclusions References 2: Iron Homeostasis in Pseudomonas aeruginosa: Targeting Iron Acquisition and Storage as an Antimicrobial Strategy 2.1 Introduction 2.2 Iron Acquisition Systems in P. aeruginosa 2.2.1 Production and Utilization of the Endogenous Siderophores Pyoverdine and Pyochelin 2.2.2 Xenosiderophore-Mediated Iron Acquisition 2.2.3 Iron Acquisition from the Host Heme Molecule 2.2.4 Fe2+ Acquisition by the Feo System 2.2.5 Iron Acquisition Mediated by PQS Molecule and TseF 2.3 Iron Storage Systems in P. aeruginosa 2.4 Iron Efflux Systems in P. aeruginosa 2.5 Regulation of Iron Homeostasis in P. aeruginosa by General Regulators 2.5.1 Iron Sensing and Regulation by the Ferric Uptake Transcriptional Regulator Fur 2.5.2 Regulation of Iron Homeostasis by Small RNAs 2.6 Siderophore Signaling in the Regulation of Iron Homeostasis 2.6.1 Siderophore Signaling by σECF Factors and Cell-Surface Signaling 2.6.2 Siderophore Signaling by Two-Component Systems 2.6.3 Siderophore Signaling by One-Component Systems 2.7 Other Systems Involved in the Regulation of Iron Homeostasis in P. aeruginosa 2.8 Iron and P. aeruginosa Virulence 2.9 Strategies to Block P. aeruginosa Infections by Disrupting Iron Homeostasis 2.9.1 Neutralization of Siderophores with Lipocalin-Based Proteins 2.9.2 Utilization of Iron Chelators 2.9.3 Utilization of the Iron Mimicking Metal Gallium 2.9.4 Use of Siderophore-Dependent Uptake Systems to Deliver Antimicrobials: The `Trojan-Horse ́ Strategy 2.9.5 Other Strategies References 3: Controlling Biofilm Development Through Cyclic di-GMP Signaling 3.1 Introduction 3.2 The First Contact with the Surface: Timing and Heterogeneity of Contact-Dependent Modulation of c-di-GMP Levels 3.3 Consequences of Surface Contact and Downstream Factors 3.4 Key Players Contributing to Biofilm Maturation 3.5 c-di-GMP Levels and Maintenance of the Mature Biofilm Structure 3.6 Biofilm Dispersion: The Return to Low c-di-GMP Levels 3.7 Turnover and Modulation of the c-di-GMP Pool in Biofilms 3.8 Blocking c-di-GMP for Biofilm Control 3.9 Conclusion References 4: Pseudomonas aeruginosa Quorum Sensing 4.1 History and Introduction to P. aeruginosa Quorum Sensing 4.2 QS and Virulence of P. aeruginosa 4.3 Ecological and Evolutionary Considerations 4.4 Quorum Sensing Inhibition Strategies 4.5 A Look Ahead References 5: Antibiotic Resistance in Pseudomonas 5.1 Introduction 5.2 Reasons Behind the Intrinsic Low Susceptibility to Antibiotics of P. aeruginosa 5.3 Mutational Resistance in P. aeruginosa 5.4 Acquisition of Antibiotic Resistance Genes 5.5 High-Risk MDR P. aeruginosa Clones 5.6 Habitat- and Physiology-Dependent Antibiotic Resistance 5.7 Transient Antibiotic Resistance 5.8 Tolerance and Persistence 5.9 Biofilms 5.10 Concluding Remarks References Part II: Cell Envelope and Secretion Systems 6: Cell Envelope Stress Response in Pseudomonas aeruginosa 6.1 Introduction 6.2 The Gram-Negative Cell Envelope 6.3 Cell Envelope Stresses in P. aeruginosa 6.3.1 Antibiotic Stresses Inducing a CESR 6.3.2 Some Examples of Abiotic Stresses Leading to CESR 6.3.2.1 Temperature 6.3.2.2 Osmolarity 6.3.2.3 Mechanical Stresses 6.4 Cell Envelope Stress Responses (CESRs) in P. aeruginosa 6.4.1 CESR-Related Sigma Factors 6.4.1.1 The E. coli σE Homologue AlgU 6.4.1.1.1 The Case of Mucoidy 6.4.1.2 The Bacillus subtilis SigW ECFσ Homologue SigX 6.4.1.2.1 The SigX ECFσ Controls Membrane Homeostasis in P. aeruginosa 6.4.1.2.2 Conditions Leading to Increased SigX Expression or Activity Absence of the Major Porin OprF Hypo-Osmolarity but Not Hyperosmolarity Cold Temperature Adaptation Sublethal Concentration of Valinomycin Super-infective Phage Infection Results in High Expression and Activity of SigX 6.4.1.2.3 Conditions Decreasing SigX Expression or Activity Absence of CmpX Changes in sigX Expression and Activity Caused by Some Plant Metabolites 6.4.1.2.4 The Elusive SigX Regulon Definition 6.4.1.3 The SbrI ECFσ Factor, Another Cell Wall Stress Regulator? 6.4.1.4 Hyperosmolarity Induces the Expression of AlgU-Regulated Genes 6.4.1.5 AlgU Is Involved in Heat Shock Response via RpoH Activation 6.4.1.6 Low-Shear Modeled Microgravity Involves AlgU, RpoH, and SigX Responses 6.4.1.7 Contact with Epithelial Cells Causes an AlgU-Related CESR 6.4.1.8 d-Cycloserine Antibiotic Induces an AlgU-Related CESR 6.4.1.8.1 d-Cycloserine Activates the AlgU Regulon 6.4.1.8.2 DCS Treatment Failed to Trigger Alginate Production Despite Strong AlgU Induction 6.4.1.8.3 DCS Exposure Causes Many AlgU-Dependent Transcript Upregulation 6.4.1.8.4 Many Lipoprotein Genes Are Upregulated upon DCS Exposure 6.4.1.8.5 DCS Triggers Expression of Some H1-T6SS Secretion Genes 6.4.2 CESR-Related Two-Component Systems 6.4.2.1 The AmgRS Two-Component System Is Involved in CESR 6.4.2.2 Polymyxin-Induced Adaptative Resistance in Response to CESR 6.4.2.3 Response to β-Lactams 6.4.3 Mechanosensitive Channels as CESR Actors 6.4.3.1 Mechanosensitive Channels as CESR Actors 6.5 Concluding Remarks References 7: Flagella, Chemotaxis and Surface Sensing 7.1 Introduction 7.2 Flagella 7.2.1 The Flagellum Is the Most Complex Protein Assembly in Bacteria 7.2.2 PA Contains a Single Polar Flagellum 7.2.3 PA Employs a ``Run-Reverse-Turn ́ ́ Chemotaxis Mechanism That Is Different to That of Enterobacteria 7.2.4 The Cost of Flagella and Strategies to Reduce It 7.2.5 PA Has a Dual Stator Motor 7.2.6 Understanding Filament Function 7.2.7 The Multiple Roles of Flagella 7.2.8 The Flagellum and Its Effect on Virulence and Virulence-Related Phenotypes 7.2.9 Flagellar Proteins as Anti-PA Vaccine Antigens or Targets for Antimicrobial Agents 7.3 Chemotaxis 7.3.1 PA Chemosensory Pathways 7.3.2 Core and Auxiliary Proteins of Chemosensory Pathways 7.3.3 Canonical Modes of Signal Perception at Chemoreceptors 7.3.4 Chemotaxis and the Che Pathway 7.3.4.1 Chemotaxis to Histamine and Polyamines 7.3.4.2 Chemotaxis to Inorganic Phosphate 7.3.4.3 Chemotaxis to Nitrate 7.3.4.4 Chemotaxis to Amino Acids 7.3.4.5 Chemotaxis to Autoinducer-2 7.3.4.6 Chemotaxis to Organic Acids 7.3.4.7 Other Chemoreceptors Predicted to Stimulate the Che Pathway 7.3.5 The Che2 Pathway 7.3.6 Transcriptional and Post-transcriptional Regulation of Chemoreceptors and Chemosensory Pathways 7.4 Surface Sensing 7.4.1 Modulation of c-di-GMP Levels by the Wsp Pathway 7.4.2 Twitching Motility and the Chp Pathway 7.4.3 The Role of the Wsp and Chp Pathways in Surface Sensing 7.4.4 Outlook References 8: Antimicrobial Weapons of Pseudomonas aeruginosa 8.1 Introduction 8.2 Contact-Dependent Antimicrobial Weapons 8.2.1 T5SS/CDI 8.2.1.1 Components and Mode of Action 8.2.1.2 Mechanisms of Prey Cell Targeting and Toxin Action 8.2.1.3 Role of CDI Weapons in Antimicrobial Competition 8.2.2 T6SS 8.2.2.1 Components and Mode of Action 8.2.2.2 Mechanism of Prey Cell Targeting and Toxin Action 8.2.2.3 Role of T6SS Weapons in Intermicrobial Competition 8.3 Contact-Independent Antimicrobial Weapons 8.3.1 Pyocins 8.3.1.1 R-and F-Type Tailocins 8.3.1.2 S-, L- and M-Type Pyocins 8.3.1.3 Pyocins as Epidemiological Markers 8.3.1.4 Role of Tailocins and Pyocins in Interbacterial Competition 8.3.1.5 Pyocins as Antibacterial Agents 8.3.2 Small Antimicrobial Molecules 8.3.2.1 Quorum Sensing Molecules as Antimicrobial Agents 8.3.2.2 Quorum Sensing-Regulated Production of Antimicrobial Agents 8.3.2.2.1 Staphylolytic Protease, LasA 8.3.2.2.2 Rhamnolipids 8.3.2.2.3 Hydrogen Cyanide 8.3.2.2.4 Phenazines 8.3.3 Siderophores Pyoverdine and Pyochelin 8.4 Membrane Vesicle-Packaged Antimicrobials 8.5 Conclusions and Future Directions References 9: Pseudomonas aeruginosa Antivirulence Strategies: Targeting the Type III Secretion System 9.1 Introduction 9.2 Small Molecule Inhibitors 9.2.1 ExoU Inhibitors 9.2.2 ExoS Inhibitors 9.3 Active Vaccines 9.3.1 PopB 9.3.2 PscC 9.3.3 PscF 9.3.4 PcrV 9.3.5 Killed Cells 9.4 Passive Antibody Approaches 9.5 Future Directions 9.6 Perspective References Part III: Pathogenesis and Virulence 10: What Makes Pseudomonas aeruginosa a Pathogen? 10.1 P. aeruginosa Is a Cosmopolitan Inhabitant of the Aquatic Environment 10.2 The Hospital Environment: Favorable Aquatic Habitats for an Antibiotic-Resistant Frugal Omnivore 10.3 P. aeruginosa Population Genomics and Biology Are Skewed by Habitat 10.4 The Dynamic Accessory Genome 10.5 The Weapons of Virulence 10.6 The Unpredictable Resistome 10.7 The Adaptation During Infection 10.8 Loose Ends References 11: Transcriptional Profiling of Pseudomonas aeruginosa Infections 11.1 P. aeruginosa, a Versatile Environmental Bacterium and Model Organism 11.2 P. aeruginosa: An Opportunistic Pathogen of High Clinical Relevance 11.3 Old and New Antibacterial Strategies 11.4 Transcriptional Profiling Approaches for a Comprehensive Understanding of P. aeruginosa Adaptation 11.4.1 RNA-seq: Progress and Advances in Mimicking Infections in Laboratory Experiments 11.4.2 Ex Vivo Transcriptomics: Analyzing Gene Expression During an Infection Process 11.4.3 Dual-seq: Understanding the Crosstalk and Interplay Between Host and Pathogen During Infection 11.4.4 Single-Cell RNA-seq: Analyzing the Heterogeneity in Gene Expression Within a Population 11.5 Global Profiling Approaches and Functional Genomics to Study Bacterial Adaptation 11.5.1 Gene Expression Patterns of Individual Genes Across a Collection of Isolates 11.5.2 Identification of Core Phenotypic Traits by Applying Global Correlation Studies 11.5.3 Identification of Group-Specific Traits That Have Evolved via Parallel Evolution 11.5.4 Persistence of Transcriptional Responses as Memory Responses 11.6 Conclusion and Outlook References 12: Molecular Mechanisms Involved in Pseudomonas aeruginosa Bacteremia 12.1 Introduction 12.2 P. aeruginosa Swimming and Attachment to Cells 12.3 Transmigration Across the Epithelial and Endothelial Layers 12.4 Survival Within the Bloodstream 12.4.1 Interaction with Blood Leukocytes 12.4.2 Interaction with the Complement System 12.5 Strain-Specific and Shared Complement-Escape Strategies 12.6 Complement-Evaders and Persistence of P. aeruginosa in Blood 12.7 Conclusions References 13: Pseudomonas aeruginosa in the Cystic Fibrosis Lung 13.1 Background to Cystic Fibrosis 13.2 Genetics and Epidemiology 13.3 Pathophysiology 13.4 Non-CFTR Influences on Lung Disease in pwCF 13.5 Infection in the CF Lung 13.6 P. aeruginosa in CF 13.6.1 Acute/Initial Infection with P. aeruginosa 13.6.2 Risk Factors for and Associations with P. aeruginosa Acquisition 13.6.3 The Evolution of Chronic Infection: Host Factors 13.6.4 The Evolution to Chronicity: Bacterial Factors 13.6.5 The Phenotype of Chronic P. aeruginosa 13.6.6 Pa Mutations Occurring During the Evolution of Chronic Infection 13.6.7 Interactions Between Pa and Co-infecting Pathogens (see also Chap. 15) 13.6.8 Modifier Genes and Environmental Associations with Pulmonary Pa Infection 13.6.9 Pseudomonas aeruginosa in Pulmonary Exacerbations 13.7 Detection/Diagnosis of Pa in CF: Current Practice, Limitations and Future Directions 13.8 Treatment of Pa in CF (see also Chap. 15) 13.8.1 Current Standards of Care: Limitations Despite Recent Advances 13.8.1.1 Initial/Early Infection: Aim to Eradicate 13.8.1.2 Pulmonary Exacerbations 13.8.1.3 Chronic Infection: Aim to Suppress Bacterial Load and Consequent Inflammatory Damage 13.8.1.4 Restoration of CFTR Function: The Impact of CFTR Modulator Therapies on Pa Infection 13.9 Anti-Pseudomonal Therapies in Development for CF 13.9.1 Gallium (Ga3+) 13.9.2 Bacteriophage 13.9.3 Nitric Oxide and NO Donor Molecules 13.9.4 Lactoferrin/Hypothiocyanate 13.9.5 Cysteamine 13.9.6 Quorum Sensing and Virulence Factor Inhibitors 13.9.7 OligoG 13.9.8 Agents Targeting the Bacterial Cell Surface 13.10 Challenges Facing the Future Development of Anti-Pseudomonal Agents for CF References 14: Role of Two-Component System Networks in Pseudomonas aeruginosa Pathogenesis 14.1 Introduction 14.2 Two-Component Systems in Pseudomonas aeruginosa 14.3 TCSs and P. aeruginosa Infection Strategies 14.3.1 The Gac/Rsm Cascade and the Acute-to-Chronic Infection Switch 14.3.2 TCSs Regulating Biofilm Development 14.4 TCSs Regulating P. aeruginosa Antibiotic Resistance 14.4.1 Adaptive Resistance Induced by the Presence of Antimicrobials 14.4.2 Cross-Resistance Between Metals and Antibiotics 14.4.3 Biofilm-Specific Antibiotic Resistance 14.5 TCSs Connecting P. aeruginosa Cell Metabolism and Virulence 14.5.1 The CbrA/CbrB TCS and Carbon Catabolite Repression 14.5.2 The NtrB/NtrC Two-Component System and Nitrogen Metabolism 14.6 Concluding Remarks References 15: Mixed Populations and Co-Infection: Pseudomonas aeruginosa and Staphylococcus aureus 15.1 Introduction 15.2 P. aeruginosa and S. aureus Co-Infection 15.3 Spatial Colocalization and Mixed Biofilm 15.4 Immune Response and Antibiotic Tolerance in Mixed Infection 15.5 Molecular Interactions Between P. aeruginosa and S. aureus 15.5.1 Competition State 15.5.1.1 Direct Action 15.5.1.2 Anti-Biofilm Action 15.5.1.3 Manipulation of the Immune System 15.5.1.4 Nutrient Competition 15.5.2 Transition to Coexistence State 15.5.3 Coexistence or Cooperative Interaction Between S. aureus and P. aeruginosa? 15.6 Conclusion and Perspectives References 16: How to Manage Pseudomonas aeruginosa Infections 16.1 Introduction 16.2 Epidemiology 16.3 Resistance Risk Factors 16.4 Antibiotic Treatment 16.4.1 Empiric and Targeted Treatment for Non-multi-drug Resistant P. aeruginosa 16.4.1.1 Empiric Treatment 16.4.1.2 Targeted Treatment 16.4.2 Empiric and Targeted Treatment for Carbapenem-Resistant P. aeruginosa 16.4.2.1 Empiric Treatment 16.4.2.2 Targeted Treatment 16.4.3 Polymyxins 16.4.4 Fosfomycin 16.4.5 Ceftolozane/Tazobactam 16.4.6 Ceftazidime/Avibactam 16.4.7 Cefiderocol 16.4.8 Newer β-Lactams/β-Lactamase Inhibitor Combination 16.4.9 Plazomicin 16.4.10 Murepavadin 16.4.11 Combination Versus Monotherapy 16.4.12 PDR P. aeruginosa 16.5 Conclusion References