Microbial Genomic Islands in Adaptation and Pathogenicity

Foreword
Preface
Acknowledgements
Contents
Editors and Contributors
1: An Introduction to Microbial Genomic Islands for Evolutionary Adaptation and Pathogenicity
1.1 Introduction
1.2 Types of Genomic Islands
1.2.1 Pathogenicity Islands
1.2.2 Resistance Islands
1.2.3 Fitness and Metabolic Islands
1.2.4 Symbiotic Islands
1.3 In Silico Prediction Tools and Databases of Genomic Islands
1.4 Pangenome
1.4.1 Open and Closed Pangenome
1.5 Concluding Remarks
References
2: Computation Tools for Prediction and Analysis of Genomic Islands
2.1 Introduction
2.1.1 Major Features of GIs
2.1.2 Subclasses of GIs
2.1.3 Detection of Genomic Islands
2.2 Tools for Prediction and Analysis of Genomic Islands
2.3 Conclusion and Future Perspectives
References
3: An Overview of Genomic Islands´ Main Features and Computational Prediction: The CMNR Group of Bacteria As a Case Study
3.1 Introduction to the Genomic Age and Comparative Genomics of Microorganisms
3.2 Main Characteristics of Genomic Islands
3.2.1 Genomic Plasticity and Genomic Features of Horizontally Acquired Regions
3.2.2 Codon Usage
3.2.3 GC Content
3.2.4 Transposases and Insertion Sequences
3.2.5 Specific Factors (Virulence, Resistance, Metabolic, and Symbiotic Factors)
3.3 Software/Databases for Prediction and Visualization of Genomic Islands
3.4 Examples of Bacteria of the Group CMNR in the Context of Genomic Islands
3.4.1 Genus Corynebacterium
3.4.1.1 Corynebacterium pseudotuberculosis
3.4.2 Rhodococcus
3.4.3 Genus Mycobacterium
3.4.3.1 Mycobacterium tuberculosis Complex
3.4.3.2 Mycobacterium tuberculosis
3.4.4 Genus Nocardia
3.4.5 Artificial Intelligence As an Improving Approach to Genomic Islands Prediction
3.5 Conclusions
References
4: Microbial Genomic Island Discovery: Visualization and Analysis
4.1 Microbial Genomic Islands (GIs): An Overview
4.2 Origin and Acquisition of GIs
4.2.1 Islands Related to Pollution Degradation
4.2.2 Islands Related to Pathogenicity
4.3 Islands in Extremophiles
4.3.1 Thermophiles
4.3.2 Psychrophiles
4.3.3 Halophiles
4.3.4 Acidophiles and Alkaliphiles
4.4 Antibiotic Resistance Islands
4.5 Catabolic Genomic Islands
4.6 Symbiosis Islands
4.7 Prediction of GIs
4.7.1 Tools
4.7.2 Databases
4.8 Significance of GIs in Prokaryotic Evolution
4.9 Conclusion
References
5: Genomic Islands in Bacterial Genome Evolution and Speciation
5.1 Genome Plasticity, Horizontal Gene Transfer and Evolution of the Bacterial Genome
5.2 GIs: Features, Types, Significance, and Plasticity
5.2.1 Features Attributed to a GI
5.2.2 Types of GIs
5.2.3 Significance of GIs
5.2.4 Plasticity in GIs
5.2.4.1 Driving Forces for GIs Plasticity
Recombination
Deletion
Insertion
Duplication and Inversion
Tandem Accretion
5.3 GIs and Bacterial Evolution
5.3.1 GIs in Bacterial Genome Evolution and Shapiro´s Geographical Metaphors
5.3.2 GI and Heavy Metal Tolerance
5.3.3 GIs in Secondary Metabolism, Pathway Evolution and Xenobiotic Degradation
5.3.4 GIs and Siderophore Expressing Bacteria
5.3.5 GIs and Bacterial Secretion Systems
5.3.6 GIs and Antimicrobial Resistance
5.3.7 In Planta GI Mediated Bacterial Evolution
5.3.8 GIs in Evolution of Pathogenic Bacteria
References
6: Genomic Islands in the Gut Microbiome: Current Knowledge and the Application in the Probiotics Field
6.1 Introduction
6.2 Common and Specific Features of Gut Microbiome
6.3 The Gut Microbiome Flexible Gene Pool
6.4 Genomic Islands of the Gut Microbiome
6.4.1 Pathogenicity Islands
6.4.2 Symbiosis Islands
6.4.3 Antibiotic Resistance Genes
6.4.4 Chromosomal Mobile Genetic Elements
6.5 The Application in the Probiotics Field
6.6 Conclusion
References
7: Genomic Islands in Nutritional Fitness and Adaptation
7.1 Introduction
7.2 Genomic Islands and Pathogens
7.3 Pathogenicity Island (PAIs) and Its Correlation with Virulence
7.4 Resistance Islands (REIs) for Pathogen Adaptation
7.5 Pathogen Fitness
7.6 Pathogenicity of Clostridium Species
7.7 Pathogenicity Locus of Clostridium difficile
7.8 Pathogenicity Islands of Citrobacter Species
7.9 Genomic Islands in Environmental Microorganisms
7.10 GEIs for Adaptation in Toxic Environments
7.11 Gene Acquisitions and Adaptation of Marine Bacterial Species
7.12 Extremophiles and Horizontal Gene Transfer
7.13 Gene Exchange Between Archaea and Bacteria
7.14 Conclusion
References
8: Genomic Islands Involved in Iron Uptake
8.1 Introduction
8.2 Iron Uptake in Bacteria
8.2.1 Siderophore-Mediated Iron Transport Systems
8.2.2 Iron Acquisition Through Ferrous and Ferric Ions
8.2.3 Iron Acquisition from Heme
8.2.4 Iron Uptake via Transferrin and Lactoferrin
8.2.5 Low-Affinity Iron Uptake Systems
8.2.6 Iron Uptake Mechanisms in Pathogenic Bacteria
8.3 Bacterial Iron Homeostasis
8.4 Genetic Aspects of Iron Uptake Mechanisms in Bacteria
8.4.1 Genomic Islands
8.4.2 GEIs-General Features
8.4.3 Genomic Island Identification Methods
8.4.4 Types of Genomic Islands-Contributions to Ecological Adaptation and the Pathogenesis
8.5 Genomic Islands Implicated in Iron Acquisition
8.5.1 Yersiniabactin
8.5.2 Pseudochelin
8.5.3 Yersiniachelin
8.5.4 Specific PAIs Involved in Iron Uptake
8.6 Model for Horizontal Transfer of PAIs
8.7 Siderophores and Colibactin Genotoxin Biosynthetic Pathway Interactions in Escherichia coli
8.8 Conclusion
References
9: Genomic Islands in Uropathogenic Escherichia coli
9.1 General Introduction
9.2 Genomic Islands in E. coli
9.3 Characteristics of Pathogenic Genomic Islands in E. Coli
9.3.1 Molecular Characteristics of PAI I536
9.3.2 Molecular Characteristics of PAI II536
9.3.3 Molecular Characteristics of PAI III536
9.3.4 Molecular Characteristics of PAI IV536
9.3.5 Comparative Account of PAIs in E. Coli Including Uropathogenic E. Coli
9.4 Genes Governing Hardiness and Virulence in Uropathogenic E. coli
9.4.1 Lipopolysaccharide (LPS)
9.4.2 Pili
9.4.3 Curli
9.4.4 Non-pilus Adhesins
9.4.5 Flagella
9.4.6 Secreted Toxins
9.4.7 Outer Membrane Vesicles (OMVs)
9.4.8 Iron Acquisition
9.4.9 Siderophores
9.4.10 Two-Component Signaling System
9.5 Omics Studies in Revealing Virulence of Uropathogenic E. Coli
9.6 Conclusion
References
10: Genomic Islands in Helicobacter Species
10.1 Introduction
10.2 Genomic Islands and its Contribution to Pathogenesis
10.2.1 Evolution of PAIs
10.2.2 Antibiotic Resistance Islands
10.2.3 Secondary Metabolism
10.3 Identification of GIs in Helicobacter Species
10.4 Adaptation and Pathogenicity of GI in Helicobacter Species
10.5 Computational Tools Involved in GI Prediction
10.5.1 Prediction Methods Based on One Genome
10.5.2 Prediction Methods Focussed on Multiple Genomes
10.6 Future Perspectives of GIs
10.7 Conclusion
References
11: Genomic Islands in Staphylococcus
11.1 Staphylococcus Species
11.2 Staphylococcus aureus
11.3 S. epidermidis and Other CoNS
11.4 Mobile Genetic Elements of Staphylococcus Species
11.5 Staphylococcal Cassette Chromosome mec (SCCmec)
11.6 Arginine Catabolic Mobile Element (ACME)
11.7 Copper and Mercury Resistance (COMER)
11.8 The Mechanism of SCCmec Transfer
11.9 Plasmids
11.10 Multi-Resistant (Conjugative) Plasmids and their Mobilization System
11.11 Mobilization System of RC-Replicating Plasmids
11.12 Bacteriophages
11.13 Staphylococcus aureus Pathogenicity Islands (SaPIs)
11.14 Insertion Sequences (IS) and Composite Transposons (Tn)
11.15 Integrative and Conjugative Elements
11.16 Others
11.17 Conclusion Remarks
References
12: Genomic Islands in Pseudomonas Species
12.1 Genus Pseudomonas
12.2 Ecological and Marine Habitat of Pseudomonas
12.3 Marine Pseudomonas Diversity and Important Role
12.4 Pseudomonas and Marine Macroorganisms
12.5 Bioactive Compounds and Enzyme Kinetics Production Isolated from Marine Pseudomonas
12.6 Pathogenicity of Pseudomonas sp. in Marine Habitats
12.7 Future Perspectives
References
13: Genomic Islands in Klebsiella pneumoniae
13.1 Introduction
13.2 Integrative and Conjugative Elements-Kp (ICEKp)
13.2.1 ICEKp1
13.2.2 ICEKp2
13.2.3 ICEKp3
13.2.4 ICEKp4 and ICEKp12
13.2.5 ICEKp5
13.2.6 ICEKp10
13.3 Prophages
13.3.1 Integration of Phages in Genome
13.4 Integrons
13.4.1 Integrons Associated with Antibiotic Resistance
13.5 Conjugative Transposons
13.5.1 Antibiotic Resistance
13.5.1.1 Tn916
13.5.1.2 Tn6009
13.5.1.3 Tn6497
13.6 Concluding Remarks
References
14: Molecular Insights into Genomic Islands and Evolution of Vibrio cholerae
14.1 Introduction
14.1.1 Taxonomic Classification of Vibrio cholerae
14.1.2 Clinical Spectrum and Pathogenesis of V. cholerae
14.1.3 Epidemiology of Pathogenic V. cholerae
14.2 Mobile Genetic Elements in V. cholerae
14.2.1 Types of MGEs
14.2.2 Types of Genomic Islands
14.2.2.1 Vibrio Pathogenicity Island-1 (VPI-1)
14.2.2.2 Vibrio Pathogenicity Island-2 (VPI-2)
14.2.2.3 Vibrio Seventh Pandemic Island-I (VSP-I)
14.2.2.4 Vibrio Seventh Pandemic Island-II (VSP-II)
14.3 Vibrio cholerae CRISPR-Cas System
14.3.1 General Structure of CRISPR-Cas
14.3.2 CRISPR-Cas in Clinical and Environmental V. cholerae Isolates
14.3.3 Resistance Against CRISPR-Cas System
14.4 Tools to Study Evolution of V. cholerae and Its Genomic Islands
14.4.1 Tools to Study GIs
14.5 Antimicrobial Resistance in V. cholerae
14.5.1 Drugs and Their Targets Used for the Treatment of Cholera
14.5.2 Genomics of Antimicrobial Resistance and Its Mechanisms in Vibrio cholerae
14.5.3 Genetic Factors for Biofilm Formation in Vibrio cholerae
14.6 Role of Genomic Islands in Development of Cholera Vaccines
14.7 Future Perspectives and Conclusions
References
15: Genomic Islands in Marine Bacteria
15.1 Introduction
15.2 Mining of Genomes in Actinomycetes from Marine Environments
15.3 Relative Significance of Genomic Island in Marine Bacteria
15.4 GIs Quantitative Significance in Marine Bacteriological Genomes
15.5 Architecture of Marine Bacterial GIs
15.6 Differences in GI Gene Content Among Marine Bacteriological Classes
15.7 Biologically Important Genes Found in Marine Bacterial GIs
15.8 Conclusions
References
16: Challenges in Eventing Horizontal Gene Transfer
16.1 Introduction
16.2 Conclusions and Future Outlook
References
17: Artificial Intelligence and Machine Learning for Prediction and Analysis of Genomic Islands
17.1 Introduction
17.2 Deficiency in Benchmark for GIs Datasets
17.2.1 GI Prediction Methods
17.2.2 Genomic Islands Prediction Approaches
17.3 Genomic Islands Prediction
17.3.1 Data Quality
17.3.2 Computational Programme for GIs Identification
17.4 Future Improvements
References