Antimicrobial Drug Resistance (eBook)

Preface 5
Table of Contents Antimicrobial Drug Resistance Volume 1 6
Contributors 13
Part I: General Overview 25
Chapter 1 History of Drug-Resistant Microbes 26
Chapter 2 Evolutionary Biology of Drug Resistance 31
1 Introduction 31
2 Variability: The Substrate of Evolution of Drug Resistance 31
2.1 The Complexity of Antibiotic Action and the Variety of Resistance Phenotypes 31
2.1.1 Adaptation without Change: Redundancy and Degeneracy of Bacterial Systems 32
2.1.2 Phenotypic Tolerance 32
2.2 The Source of Antibiotic-Resistance Genes 33
2.2.1 Origin of Drug Resistance: The Case of Beta-Lactamases 34
2.3 Global Stress Regulation and Antibiotic Resistance 35
2.4 Genetic Variation: Mutation 36
2.4.1 Mutation Frequency and Mutation Rate 36
2.4.2 Hyper-Mutation 36
2.4.3 Antibiotics Inducing Mutations 37
2.5 Genetic Variation: Gene Recombination 37
2.6 Genetic Variation: Modularization 38
2.7 Horizontal Genetic Transfer and Bacterial Variation 39
2.7.1 Plasmids and Drug Resistance Evolution 39
2.7.2 Transposable Elements 40
2.7.3 Phages 40
2.8 Genetic Variation: Clonalization 41
2.9 Generation of Variation in Response to Antibiotic Stress 41
2.10 Phenotypic Variation and Genetic Variation: the Baldwin Effect 42
3 Selection: The Mechanism of Evolution of Drug Resistance 42
3.1 Selection by Low Antibiotic Concentrations 42
3.2 Concentration-Specifi c Selection: the Selective Window 43
3.3 Antibiotic Gradients in Antibiotic Selection 43
3.4 Fluctuating Antibiotic Environments 44
3.5 Selection Towards Multi-Resistance: Genetic Capitalism 44
4 Evolution of Drug Resistance: Future Prospects 45
4.1 Units of Variation and Units of Selection 45
4.2 The Limits of Drug-Resistance Evolution 46
4.2.1 Saturation Constraints, Short-Sighted Evolution 46
4.2.2 Minimizing the Costs of Evolvability 46
4.2.3 Cost of Antibiotic Resistance 46
4.3 Epidemiology and Evolution of Antibiotic Resistance 47
4.3.1 Resistance, Epidemics, Endemics, and Allodemics 47
4.3.2 Resistance as a Colonization Factor 48
4.3.3 Biogeography and Local Biology of Antibiotic Resistance 49
4.3.4 Antibiotics as Ecosystem-Damaging Agents: the Role of Resistance 49
4.3.5 Might Evolution of Antibiotic Resistance Be Predicted? 49
References 51
Chapter 3 Pharmacology of Drug Resistance 55
1 Introduction 55
2 Resistance Defi ned by Breakpoint: Good Clinical Response for “Sensitive” 55
2.1 Goal of Therapy 55
2.2 Protein Binding 56
2.3 Distribution of Drug Exposure 57
2.4 Distribution of MIC Values 57
2.5 Integration of Factors for Dose Choice and Sensitivity Breakpoint 58
3 Resistance Defi ned by Mechanism 59
4 Suppression of Resistance by Dosing 60
5 Choosing a Dose for Suppression of Resistant Subpopulation Amplifi cation 62
6 Summary 63
References 63
Chapter 4 Antimicrobial Resistance Versus the Discovery and Development of New Antimicrobials 65
1 Introduction 65
2 Antibiotics and the Pharmaceutical Industry 65
3 The Rise in Resistance to Penicillin 65
3.1 The Golden Era 66
4 Microbial Genomics: The Failure to Deliver and the Hope for the Future 66
5 Medical Need, Antimicrobial Resistance, and the Anti-Infective Marketplace 67
6 The Regulatory Environment for Antibacterials 68
7 Large Pharmaceutical Companies Consolidate and Abandon Antibacterial Discovery while Biotechnology Enters the Field 69
8 The Future of Antibacterial Research 70
9 Conclusions 70
References 71
Part II: General Mechanisms of Drug Resistance 73
Chapter 5 Genetic Mechanisms of Transfer of Drug Resistance 74
1 Introduction 83
2 Conjugative Plasmids 74
2.1 DNA Replication 74
2.2 Partition and Control of Copy Number 75
2.3 Conjugative Transfer 75
2.4 Antibiotic Resistance and Other Auxiliary Genes 75
3 Composite Transposons 75
3.1 Structure and Mechanism 75
3.2 Newer Elements and Their Antibiotic Resistance Genes 77
4 Simple Transposons 77
4.1 Tn3 and TEM Beta-Lactamase Genes 77
4.2 Tn1546 and Vancomycin Resistance 78
4.3 Site-Specifi c Transposons: Tn7 and the Tn5053 Family 78
5 Conjugative Transposons 78
5.1 Tn916-Like Elements and Their Antibiotic Resistance Genes 78
5.2 Mechanism of Transfer 78
5.3 Related Elements 79
6 Integrons and ISCR Elements 79
6.1 Class 1 Integrons 79
6.2 Recent Evolution of Class 1 Integrons 80
6.3 Antibiotic Resistance Genes Carried by Integrons 81
6.4 Gene Expression in Class 1 Integrons 81
6.5 Chromosomal Integrons 81
6.6 Origin of Integron Cassettes 82
6.7 CR Elements 82
6.8 Antibiotic Resistance Genes Carried by CR Elements 82
7 Outlook 82
References 83
Chapter 6 Mutations as a Basis of Antimicrobial Resistance 86
1 Prefatory Remarks 86
2 Genetic Diversity and Mutator Strains 86
3 Mismatch Repair-Defi cient Permanent Hypermutators 87
4 Transient Hypermutators and the SOS System 87
5 Antimicrobial Resistance Determinants 88
6 Beta-Lactam Resistance Mediated by Low-Affi nity Penicillin Binding Proteins 88
7 Quinolone-Resistance Determining Region in Fluoroquinolone-Resistant Bacteria 89
8 Streptomycin Resistance and Mycobacteria 89
9 Rifampin Resistance 89
10 Fluoroquinolone Resistance Caused by Overexpression of Active Effl ux Pumps 90
11 Constitutive Tetracycline Resistance due to a Mutated Repressor Gene 90
12 Constitutive and Inducible Glycopeptide Resistance Caused by Point Mutations in the Regulatory System 90
13 Unique Regulation of Inducible Macrolide Resistance by Translational Attenuation 91
14 b -Lactam Resistance Caused by AmpC Beta -Lactamase Hyperproduction 91
15 Point Mutations in Acquired Resistance Genes: The New-Generation Beta -Lactamases 91
16 The G238S ESBL Mutation 92
17 Inhibitor-Resistant TEMs 92
18 Complex Mutants of TEM 93
19 CTX-M 93
20 Global Suppressors 93
21 OXA 94
22 Concluding Remarks 94
References 94
Chapter 7 Target-Mediated Antibacterial Resistance 96
1 Introduction 96
2 Point Mutations that Create Resistance 96
3 Mosaic Genes 98
4 Target Overproduction 98
5 Target Substitution 98
6 Target Modifification or Protection 99
7 Conclusion 100
References 100
Chapter 8 Biochemical Logic of Antibiotic Inactivation and Modification 102
1 Introduction 102
2 Destruction of Antibiotics 102
2.1 Beta-Lactam Antibiotics 103
2.2 Fosfomycin 104
2.3 Macrolide Antibiotics 105
2.4 Type B Streptogramins 106
2.5 Tetracycline 107
3 Antibiotic Modification 107
3.1 Aminoglycosides 108
3.1.1 Aminoglycoside Acetyltransferases (AAC Family) 109
3.1.2 Aminoglycoside Phosphotransferases (APH Family) 110
3.1.3 Aminoglycoside Nucleotidyltransferases (ANT Family) 110
3.2 Macrolides 110
3.2.1 Macrolide Kinases (Mph Family) 111
3.2.2 Macrolide Glycosyltransferases (Mgt Family) 112
3.3 Rifamycins 112
3.3.1 ADP-Ribosyltransferases (ARR Family) 112
3.3.2 Rifampicin Kinases 113
3.3.3 Rifampicin Glycosyltransferases 113
4 Summary and Conclusions 113
References 114
Chapter 9 Antibiotic Resistance Due to Reduced Uptake 117
1 Introduction 117
2 Envelope Structure 117
2.1 Cytoplasmic Membrane 117
2.2 Periplasm/Peptidoglycan 118
2.3 Outer Membrane 119
2.4 Mycobacterial Cell Envelope 120
2.5 Capsule 121
3 Intrinsic Resistance 121
3.1 Restricted Permeability 121
3.1.1 Gram-Negative Bacteria 121
3.2 Mycobacteria 122
3.3 Effl ux 122
4 Antibiotic Penetration and Resistance Mechanisms 123
4.1 Porin Pathway 123
4.2 Self-Promoted Uptake and Regulatory Mutants 124
4.3 Hydrophobic Pathway 126
4.4 Inner Membrane Transporters 126
5 Synergy 127
6 Conclusions 127
References 127
Chapter 10 Transport Mechanisms of Resistance to Drugs and Toxic Metals 131
1 Introduction 131
2 H+/Na+-Driven Antiporters 131
3 Structural Analysis of Antiporters 132
4 Tripartite Pumps 133
5 ABC Transporters 133
6 Structural Analysis of ABC ATPases 134
7 Metal Efflux Systems: P-Type ATPases, RND Transporters and the Arsab Pump 135
8 Drug Resistance Can Result from Decreased Uptake 136
9 Circumventing Drug Effl ux 137
10 Reversing P-Glycoprotein-Mediated Multidrug Resistance 137
11 Reversal of Bacterial Multidrug Resistance 137
12 The Future of Multidrug Resistance Inhibition 137
References 138
Chapter 11 The Functional Resistance of Bacterial Biofi lms 141
1 Pathogenic Bacterial Communities 141
2 Stealthy Infections: Flying Below Our Radar 141
3 Biofi lm Structure and Physiology 143
4 Resisting Host Defense 143
5 Why Antimicrobials Fail: Learning from Planktonic Cultures 143
6 Biofi lm-Specifi c Resistance 145
7 Trading Posts for Resistance Genes 147
8 Treating Biofilm Infections 147
9 Conclusion 148
References 148
Part III: Bacterial Drug Resistance - Mechanisms 152
Chapter 12 The Importance of Beta-Lactamases to the Development of New Beta-Lactams 153
1 Introduction 153
2 Hydrolytic Activity 153
3 Beta-lactamase Origins 154
4 Classification Schemes 154
5 Historical Development of Beta-Lactam Antibiotics 156
6 Emergence of Beta-Lactamase Families 158
6.1 Gram-Positive Bacteria 158
6.2 Gram-Negative Bacteria 158
7 Future Directions 159
References 159
Chapter 13 Penicillin-Binding Proteins and Beta-Lactam Resistance 163
1 What Are PBPs? 163
2 Classification of PBPs 164
3 Physiological Function of PBPs 165
4 PBP-Based Beta-Lactam Resistance 166
4.1 Staphylococcus aureus 166
4.2 Enterococci 169
4.3 Streptococcus pneumoniae 172
4.4 Neisseria 179
4.5 Other Pathogens 179
5 Are the PBPs Sustainable Targets? 181
References 182
Chapter 14 Aminoglycosides: Mechanisms of Action and Resistance 189
1 Antimicrobial Mechanism of Action 189
2 Mechanism of Drug Resistance 191
2.1 Ribosomal Mutations 191
2.2 16s rRNA Methylation 191
2.3 Effl ux-Mediated Resistance 192
2.4 Enzymatic Drug Modifi cation 192
2.4.1 Aminoglycoside Adenylyltransferases 193
2.4.2 Aminoglycoside Phosphotransferases 194
2.4.3 Aminoglycoside Acetyltransferases 194
3 Mechanism of the Spread of Resistance 196
4 Cross-Resistance 197
5 Alternative Agents 197
References 197
Chapter 15 Tetracycline and Chloramphenicol Resistance Mechanisms 200
1 Introduction 208
1.1 Tetracycline Resistance 200
1.2 Chloramphenicol Resistance 200
2 Mechanisms of Tetracycline Resistance 201
2.1 Tetracycline Resistance Due to Efflux Proteins 201
2.2 Tetracycline Resistance due to Ribosomal Protection Proteins 204
2.3 Tetracycline Resistance due to Enzymatic Inactivation 204
2.4 Other/Unknown Mechanisms of Resistance 204
2.5 Tetracycline Resistance due to Mutations 205
3 Mechanisms of Chloramphenicol Resistance 205
3.1 Chloramphenicol Resistance due to Chloramphenicol O-Acetyltransferases 205
3.2 Chloramphenicol Resistance due to Specific Exporters 205
3.3 Chloramphenicol Resistance due to Multidrug Transporters, Permeability Barriers, Mutations, Phosphorylation, or Target Site Methylation 206
4 Distribution of Resistance Genes 206
4.1 Distribution of Tetracycline Genes 206
4.2 Distribution of Chloramphenicol Resistance Genes 207
5 Conclusion 208
References 208
Chapter 16 Fluoroquinolone Resistance in Bacteria 211
1 Introduction 211
2 Gram-Negative Bacteria 212
2.1 Target-Mediated Resistance 213
2.2 Decreased Outer Membrane Permeability 214
2.3 Effl ux-Related Resistance 214
2.4 Plasmid-Mediated Quinolone Resistance 216
2.5 Enzymatic Modifi cation of Quinolones 216
3 Gram-Positive Bacteria 216
3.1 Target-Mediated Resistance 217
3.2 Effl ux-Related Resistance 217
4 Means to Limit or Overcome Quinolone Resistance 218
References 219
Chapter 17 Plasmid-Mediated Quinolone Resistance 222
References 224
Chapter 18 Macrolides and Lincosamides 226
1 Introduction 226
2 Mode of Action of Macrolides and Lincosamides 226
3 Spectrum of Activity 227
4 Mechanisms of Resistance to Lincosamides and Clinical Implications 228
4.1 Ribosomal Methylation 228
4.1.1 erm Genes 228
4.1.2 Regulation of Erm Genes Expression 229
Inducible Resistance 229
Constitutive Resistance 230
4.1.3 Clindamycin for Infections Due to S. aureus with the MLSB Inducible Phenotype? 230
4.2 Ribosomal Mutations 231
4.3 Enzymatic Modifi cation of Macrolides 231
4.4 Enzymatic Modifi cation of Lincosamides 231
4.4.1 Expression of the lnu Genes 232
4.5 Effl ux 232
5 Report of Susceptibility Tests by the Laboratory 233
5.1 Staphylococci 233
5.1.1 Strains Resistant to Erythromycin but Susceptible to Clindamycin 233
5.1.2 Strains Susceptible to Erythromycin but Resistant to Lincosamides 233
5.2 Other Organisms 234
6 Conclusion 234
References 234
Chapter 19 Mechanism of Resistance in Metronidazole 237
Mechanism of Resistance in Metronidazole 237
1 Antimicrobial Mechanism of Action 237
2 Mechanism of Resistance 237
2.1 Bacteroides 237
2.2 Helicobacter pylori 238
2.3 Trichomonas 238
2.4 Clostridium spp. 239
2.5 Entamoeba and Giardia 239
3 Cross-Resistance 239
4 Mechanism of Spread of Resistance 239
5 Alternative Agents 239
5.1 Helicobacter Pylori 239
5.2 Trichomonas Vaginalis 239
5.3 Giardia 240
References 240
Chapter 20 Glycopeptide Resistance in Enterococci 242
1 Enterococci 242
2 Glycopeptides 242
3 Glycopeptide Resistance in Enterococci 242
4 The van Alphabet 243
4.1 Glycopeptide Resistance Due to Synthesis of Modified Peptidoglycan Precursors Ending in D-Ala-D-Lac 243
4.1.1 VanA 243
4.1.2 VanB 244
4.1.3 VanD 245
4.2 Glycopeptide Resistance Due to Synthesis of Modified Peptidoglycan Precursors Ending in D-Ala-D-Ser 246
4.2.1 VanC 246
4.2.2 VanE 247
4.2.3 VanG 248
5 Vancomycin-dependent Enterococci 248
6 Origin of the Vancomycin Resistance Genes 248
6.1 Acquired D-Ala:D-Lac Ligases 248
6.2 Acquired D-Ala:D-Ser Ligases 249
7 Transfer of VanA-Type Resistance to S. aureus 250
References 250
Chapter 21 Streptogramin 254
1 Class 254
2 Mechanism of Action 254
3 Mechanisms of Streptogramin Resistance 254
4 Streptogramin Resistance and the Epidemiology of MLSB 256
References 256
Chapter 22 Resistance to Linezolid 259
1 Oxazolidinones: A Brief Description of Chemistry 267
2 Mechanism of Action 259
3 Mechanisms of Resistance 261
3.1 Mutations Affecting 23S rRNA 261
3.2 Other Mechanisms 262
4 Activity of Linezolid Against Clinical Bacterial Isolates 262
5 Linezolid Resistance Among Clinical Isolates 264
5.1 Comparative Clinical Studies 264
5.2 Compassionate Use Program 265
5.3 Independent Observations of Resistance to Linezolid 265
5.3.1 Enterococci 265
5.3.2 Staphylococci 265
5.3.3 Other Organisms 266
6 Clinical Signifi cance of Linezolid Resistance 266
6.1 Enterococci 266
6.2 Staphylococci 266
7 Conclusions 267
References 267
Chapter 23 Sulfonamides and Trimethoprim 270
1 Introduction 270
2 Chromosomal Resistance to Sulfonamides 271
3 Plasmid-Borne Resistance to Sulfonamides 274
4 Chromosomal Resistance to Trimethoprim 275
5 Plasmid-Borne Resistance to Trimethoprim 276
6 Conclusions 277
References 278
Chapter 24 Mechanisms of Action and Resistance of Antimycobacterial Agents 282
1 Introduction 282
2 Isoniazid 282
2.1 Mechanism of Action 283
2.2 Mechanisms of Drug Resistance 285
2.3 katG 285
2.4 inhA 285
2.5 Other Genes 285
3 Rifampin and Other Rifamycins 286
3.1 Mechanism of Action 286
3.2 Mechanism of Resistance 286
4 Pyrazinamide 287
4.1 Mechanism of Action 287
4.2 Mechanisms of Resistance 288
5 Ethambutol 288
5.1 Mechanism of Action 288
5.2 Mechanisms of Resistance 289
6 Aminoglycosides 289
7 Fluoroquinolones 290
8 Macrolides 291
8.1 Cross-Resistance of Antimycobacterial Agents 292
8.2 Mechanism of Spread of Resistance 292
8.3 Alternative Agents 293
References 294
Part IV: Fungal Drug Resisrance - Mechanisms 281
Chapter 25 Amphotericin B: Polyene Resistance Mechanisms 303
1 Introduction 311
1.1 Epidemiology of Polyene Resistance 304
1.2 Emergence of Polyene Resistance 305
2 Mechanism of Action of Amphotericin B 305
2.1 Interaction with Sterols in the Fungal Cell Membrane 306
2.2 Oxidative Damage to the Fungal Cell Membrane 307
3 Mechanisms of Resistance 307
3.1 Polyene Resistance in Experimentally Induced Mutants and Clinical Isolates 307
3.2 Resistance to Oxidation 308
3.3 Biofi lm Formation 310
3.4 Fatty Acid Composition 310
3.5 Cell Wall Alterations 310
3.6 Yeast Cell Cycle 310
4 Conclusions 310
References 311
Chapter 26 Fungal Drug Resistance: Azoles 314
1 Introduction. Azole Antifungal Agents: History, Mode of Action, and Clinical Utility 314
2 Resistance to Azole Antifungal Agents 315
2.1 General Considerations and Defi nitions 315
2.2 Molecular Mechanisms of Azole Resistance 315
2.2.1 Alterations in the Target Enzyme 315
2.2.2 Increased Drug Effl ux 316
2.2.3 Mutations in other Genes in the Ergosterol Biosynthetic Pathway 316
2.2.4 Prevalence and Combinations of Molecular Mechanisms of Azole Resistance 316
2.2.5 Heterogeneity of Molecular Mechanisms of Resistance 316
2.2.6 Biofi lm Resistance 317
3 Genomic and Proteomic Techniques to Study Azole Resistance 317
4 Conclusions 317
References 318
Chapter 27 Flucytosine: Site of Action, Mechanism of Resistance and Use in Combination Therapy 320
1 Background 320
2 Mechanism of Action 320
3 5-Flucytosine Resistance 320
3.1 Epidemiological Factors Responsible for Resistance 322
3.2 Prevention and Control of Resistance 323
4 Mechanism of Resistance 323
5 5-Flucytosine in Combination with Amphotericin B or Fluconazole 324
5.1 5-Flucytosine + Amphotericin B 324
5.1.1 In Vitro Studies 324
5.1.2 In Vivo Studies 324
5.1.3 Clinical Studies 326
5.2 5-Flucytosine + Fluconazole 326
5.2.1 In Vitro Studies 326
5.2.2 In Vivo Studies 327
5.2.3 Clinical Studies 327
5.3 Flucytosine in Combination with Other Triazoles 327
5.3.1 In Vitro Studies 327
5.3.2 In Vivo Studies 328
5.3.3 Clinical Studies 328
5.4 Triple Combination: 5-Fluorocytosine + Amphotericin B + Fluconazole 329
5.4.1 In Vitro Studies 329
5.4.2 In Vivo Studies 329
5.4.3 Clinical Studies 329
6 5-Flucytosine in Combination with New Antifungals 330
7 Conclusions 330
References 330
Chapter 28 Echinocandins: Exploring Susceptibility and Resistance 334
1 Introduction and Background 334
1.1 Fungal Cell Walls and 1,3-Beta-D-Glucan Synthesis 334
1.2 Inhibitors of GS 335
1.3 Echinocandins 335
1.4 Antifungal Spectrum of Echinocandins 336
1.5 Genetics of 1,3-Beta-D-Glucan Synthase 336
2 Measuring Susceptibility to Echinocandins 337
2.1 Yeasts 337
2.2 Moulds 338
3 Exploring Resistance in the Laboratory 339
3.1 Direct Mutant Selection Using Inhibitors 339
3.2 Genetic Screens in S. cerevisiae 341
3.3 Genomic Profi ling 342
3.4 Proteomics 342
3.5 Biochemical Approaches 343
3.6 Animal Models 343
4 Potential for Cross-Resistance 345
5 Perspective Beyond the Laboratory 347
5.1 Paradoxical Effect 347
5.2 Clinical Isolates 348
6 Outlook 348
References 349
Chapter 29 Antifungal Targets, Mechanisms of Action, and Resistance in Candida albicans 354
1 Introduction 354
2 Ergosterol Biosynthesis Genes and Antifungal Resistance 354
2.1 Amphotericin B 362
2.2 Regulation of Ergosterol Biosynthesis Genes 363
2.3 ERG Gene Overexpression Study 365
3 Effl ux of Antifungals as a Resistance Mechanism 365
3.1 ABC Transporters 365
3.1.1 ABC Pump Inhibitors 370
3.2 Regulation of CDR1/CDR2 370
3.2.1 Regulatory Sequences 370
3.2.2 Regulatory Proteins: TAC1 370
3.2.3 Tac1p Regulon 372
3.2.4 NDT80 373
3.3 Drug Effl ux and Membrane Composition 374
3.4 Effl ux by Major Facilitators 374
3.4.1 New Tools for Analysis of Drug Effl ux 375
4 Evidence that Resistance in Clinical Isolates of C. Albicans Is Complex 375
4.1 Tolerance Pathways 376
4.2 cAMP–Protein Kinase A Pathway 377
4.3 Histone Deacetylases as Targets of Azole Adaptive Response 377
4.4 Novel Mechanisms for Azole Resistance? 378
4.4.1 Mitochondrial Respiration and Antifungal Susceptibility 378
5 Hitting Targets outside the Ergosterol Pathway 379
5.1 Echinocandins 379
5.1.1 The Drugs 379
5.1.2 The Target: FKS1 Encoded b-Glucan Synthetase 380
5.1.3 Differential Resistance to the Three Echinocandins 382
5.1.4 Resistance outside FKS1 382
5.1.5 Global Approaches to Resistance Analysis 383
5.1.6 Paradoxical Resistance 383
5.1.7 5-Fluorocytosine and Fluoroorotic Acid 385
5.2 Peptides 388
5.2.1 Histatin 388
5.2.2 Lactoferrin 389
5.2.3 Aminoacyl tRNA Synthetase Inhibitors 390
5.2.4 Sordarins 391
5.2.5 CAN-296 392
5.2.6 Steroidal Saponins 392
5.2.7 Acetominophen 392
6 Resistance in Biofi lms 392
References 395
Part V: Viral Drug Resistance - Mechanisms 415
Chapter 30 Mechanisms of Resistance of Antiviral Drugs Active Against the Human Herpes Viruses 531
1 Introduction 416
2 Thymidine Kinase Herpes Simplex Virus (HSV) Type 1 and Type 2 416
3 HSV DNA Polymerase 417
4 Penciclovir and Famvir 418
5 Human Cytomegalovirus 420
6 Resistance to Ganciclovir 420
7 Maribavir 420
8 CMV DNA Polymerase 421
9 Conclusion 422
References 423
Chapter 31 Influenza M2 Ion-Channel and Neuraminidase Inhibitors 425
1 Introduction 425
1.1 Influenza Viruses 425
1.2 Influenza Virus Replication 425
2 M2 Ion-Channel Inhibitors: Amantadine and Rimantadine 425
2.1 Antimicrobial Mechanisms of Action 426
2.1.1 Direct Studies on the Mechanism of Action in Cells 426
2.1.2 General Structure and Function of the M2 Protein 426
2.1.3 Structure/Function/Inhibitor Binding to the M2 Protein 427
2.1.4 Other Effects of Amantadine/Rimantadine on Virus Replication 427
2.2 Mechanism of Drug Resistance 427
2.2.1 Genetics–Mutations Associated with Resistance 427
2.2.2 Effect of Mutations on Function and Structure of the M2 Ion Channel 428
2.3 Cross-Resistance 430
2.4 Mechanism of Spread of Resistance 430
2.5 Alternative Agents 431
3 Neuraminidase Inhibitors: Zanamivir and Oseltamivir 431
3.1 Antimicrobial Mechanisms of Action 432
3.1.1 Function of the Neuraminidase in Viral Replication 432
3.1.2 Structure of the Neuraminidase and Enzyme Active Site 432
3.1.3 Binding of Substrate and Inhibitors to the Active Site 433
3.2 Mechanism of Drug Resistance 434
3.2.1 Development of Resistance to the NAIs 434
3.2.2 Genetic Analysis of Resistance to the NAIs 435
HA Variants (Mutations Based on H3 Sub-type Numbering) 435
NA Variants and Effects of HA Mutations (NA Mutations Numbered Based on the N2 Sub-type Numbering) 437
NA Variants Selected During In Vitro Passage or During Treatment in the Clinic 437
Variants Detected in Untreated Subjects During Surveillance Programmes 438
Other NA variants from in vitro studies 438
3.2.3 Enzyme Functional Studies 439
3.2.4 Mutant Enzyme Structural Studies 439
3.3 Cross-Resistance 440
3.3.1 Cross-Resistance Analysis with NA Variants Obtained from In Vitro Passage or Clinical Studies with NAIs 440
3.3.2 Cross-Resistance Analysis Using NA Variants Derived by Reverse Genetics or Recombinants Expressed in HeLa, 293T, or Insect Cells 441
3.4 Mechanism of Spread of Resistance 443
3.5 Alternative Agents 444
References 445
Chapter 32 Molecular Mechanisms of Resistance to Nucleoside Reverse Transcriptase Inhibitors 452
1 Introduction 452
2 Nucleoside Reverse Transcriptase Inhibitors 452
3 Resistance Against Nucleoside Analogs 453
4 Mechanisms of Nucleoside Drug Resistance 453
5 Discrimination 454
5.1 The M184V/I 455
5.2 K65R 455
5.3 Q151M 455
5.4 L74V 455
5.5 V75T 455
6 Excision 456
7 Cross-Resistance and Synergy 457
8 Anti-HIV Drugs that Overcome Resistance 458
References 459
Chapter 33 Resistance to HIV Non-Nucleoside Reverse Transcriptase Inhibitors 463
1 Introduction: HIV Reverse Transcriptase 463
2 The Non-Nucleoside RT Inhibitors 463
3 Mechanism of NNRTI Drug Resistance 465
4 Mutations Associated with Resistance to NNRTIs 465
4.1 Nevirapine Resistance 465
4.2 Efavirenz Resistance 466
4.3 Delavirdine Resistance 466
5 Cross-Resistance 466
6 Effect of NNRTI Mutations on Enzyme Activity and Viral Replication 468
7 Natural Resistance to NNRTIs 468
8 NNRTIs Hypersusceptibility 469
9 Prevention of Mother-to-Child Transmission 469
10 The Infl uence of Subtype on Resistance Mutation Pathway 469
11 Transmission of NNRTI Resistance 470
12 Structural Determinants of Resistance to NNRTIs 470
13 New NNRTIs in Development 470
14 Conclusion 472
References 472
Chapter 34 Resistance to HIV-1 Protease Inhibitors 478
1 Mechanism of Action of Protease Inhibitors 478
1.1 The HIV-1 Protease 478
1.2 HIV-1 PIs 478
2 Mechanism of Drug Resistance 480
2.1 Protease Mutations 482
2.2 Structural Effects of Mutations 483
2.3 Effect of Protease Mutations on Enzyme Activity and Viral Replication 484
2.4 Cleavage Site Mutations in PI-Resistant HIV-1 484
2.5 Impact of HIV-1 Subtypes and HIV-2 on PI Susceptibility 484
2.6 PI Boosting 485
3 Cross-Resistance 485
4 Primary or Transmitted PI Resistance 486
5 Other Pls in Development 486
6 Conclusion 488
References 488
Chapter 35 Resistance to Enfuvirtide and Other HIV Entry Inhibitors 494
1 Introduction 494
2 Mechanism of Action 495
2.1 HIV Interaction with Cellular Receptors 495
2.2 The HIV Fusion Process 496
2.3 Inhibition of CCR5 Binding 496
2.4 Inhibition of the HIV Fusion Process 497
3 Mechanism of Drug Resistance 497
3.1 Resistance to CCR5 Binding Inhibitors 497
3.2 Resistance to Enfuvirtide 500
3.3 The Role of Regions Outside gp41 HR1 in Determining Fusion Inhibitor Susceptibility 501
3.4 The Impact of Fusion Inhibitor Resistance Mutations on Viral “Fitness” 502
3.5 Interactions Between Entry Inhibitors 502
4 Conclusion 503
References 503
Chapter 36 Resistance to Inhibitors of Human Immunodefi ciency Virus Type I Integration 508
1 The Role of Integrase in HIV-1 Replication 508
2 Integrase Inhibitor Mechanism of Action 509
3 In Vivo Activity of Integrase Strand Transfer Inhibitors 511
4 Mechanism of Integrase Strand Transfer Inhibitor Resistance and Cross-Resistance: Genetics and Structural Analysis 511
5 Consequences of Resistance 515
6 Alternative Agents 516
References 516
Chapter 37 The Hepatitis B Virus and Antiviral Drug Resistance: Causes, Patterns, and Mechanisms 519
1 Background and Introduction 519
2 Molecular Virology and Lifecycle 519
2.1 Attachment, Penetration, and Uncoating 520
2.2 Conversion of Genomic RC DNA into cccDNA and Transcription of the Viral Minichromosome 520
2.3 Viral Reverse Transcription 521
2.4 Assembly and Release 521
2.5 Replication and Diversity of HBV Genomes 522
3 Antiviral Drug Resistance 522
3.1 Lamivudine Resistance Mutations (L-Nucleosides) 523
3.2 Adefovir Dipivoxil Resistance Mutations (Acyclic Phosphonates) 524
3.3 Entecavir Resistance Mutations (Cyclopenta(e)ne Sugar) 525
3.4 Multidrug Resistance 525
4 Why HBV Antiviral Drug-Resistant Mutants Are Selected 526
4.1 Magnitude and Rate of Virus Replication 526
4.2 Fidelity of the Viral Polymerase 526
4.3 Selective Pressure of the Drug 527
4.4 Amount of Replication Space in the Liver 527
4.5 Replication Fitness of the Drug-Resistant Virus 527
4.6 Other Factors 527
5 Strategies to Overcome Resistance 527
6 Public Health Implications of the Polymerase Envelope Genes Overlap 528
7 Conclusions 528
References 528
Chapter 38 Mechanisms of Hepatitis C Virus Drug Resistance 531
1 HCV-Associated Diseases 531
2 Hepatitis C Virus 531
3 Interferon Therapy 531
4 Advances in HCV Treatment 532
4.1 Patterns of HCV Response 532
4.2 Monotherapy with IFN 532
4.3 Combination IFN and Ribavirin Treatment 533
4.4 Pegylated-IFN 533
5 Mechanisms of Resistance to Current Therapy 533
5.1 HCV Genotype 533
5.2 HCV Quasispecies 533
5.3 Evasion of Immune Responses 534
5.4 Viral Proteins 534
5.5 Negative Regulators of Jak/Stat Signaling Pathway 534
5.6 Host Negative Regulators of IFN Signaling 535
6 Resistance: In Vitro Models 535
6.1 HCV Replicons 535
6.2 NS3 Protease Inhibitors 536
6.3 HCV Polymerase Inhibitors 537
6.3.1 Ribavirin 538
6.3.2 2'-Modifi ed Nucleosides 539
6.3.3 Non-nucleoside Active-Site Inhibitors 539
6.3.4 Allosteric Inhibitors Site 1 540
6.3.5 Allosteric Inhibitors Site 2 540
7 Conclusions and Prospects 541
References 541
Part VI: Parasitc Drug Resistance - Mechanisms 546
Chapter 39 Drug Resistance Mechanisms in Entamoeba histolytica, Giardia lamblia, Trichomonas vaginalis, and Opportunistic Anaerobic Protozoa 547
1 Introduction 547
2 Entamoeba histolytica 549
2.1 Antimicrobial Mechanism of Action in E. histolytica 549
2.2 Mechanisms of Drug Resistance in E. histolytica 549
2.2.1 E. histolytica Metronidazole Resistance 549
2.2.2 Multidrug Resistance in E. histolytica 549
3 Giardia lamblia 550
3.1 Antimicrobial Mechanism of Action in G. lamblia 550
3.2 Drug Resistance Mechanisms in G. lamblia 551
3.2.1 Metronidazole Resistance in G. lamblia 551
3.2.2 Resistance Mechanism to Other Compounds in G. lamblia 551
3.3 Cross-Resistance in G. lamblia 551
4 Trichomonas vaginalis 552
4.1 Antimicrobial Mechanism of Action in T. vaginalis 552
4.2 Drug Resistance Mechanisms in T. vaginalis 552
4.2.1 Metronidazole Resistance in T. vaginalis 552
4.2.2 Multiple Drug Resistance in T. vaginalis 552
4.3 Cross-Resistance in T. vaginalis 553
5 Other Anaerobic Opportunistic Protozoan Parasites 553
5.1 Antimicrobial Treatments Against Opportunistic Protozoan Parasites 553
5.2 Drug Resistance in B. hominis, C. parvum, and Microsporidia 553
6 Spread of Resistance in Anaerobic Protozoa 553
7 Alternative Drugs Against E. histolytica, G. lamblia, T. vaginalis, and Opportunistic Protozoa 554
8 Concluding Remarks 554
References 555
Chapter 40 Mechanisms of Antimalarial Drug Resistance 558
1 Introduction 558
2 Resistance Mechanisms to 4-Aminoquinolines 558
2.1 Access to Haematin Is the Biochemical Basis of CQ Resistance 558
2.2 pfcrt Is the Genetic Determinant of CQ Resistance 560
2.3 Proposed Functional Roles for PfCRT in CQ Resistance 561
2.4 pfmdr1 and Resistance Mechanisms to Mefloquine and Quinine 562
3 Resistance Mechanisms to the Antifolates 564
3.1 Resistance Caused by Mutations in DHPS and DHFR 564
3.2 Further Putative Antifolate Resistance Mechanisms 565
4 Resistance Mechanisms to Naphthoquinones 565
5 Resistance Mechanisms to Artemisinin 566
6 Conclusion 567
References 567
Chapter 41 Drug Resistance in Leishmania 572
1 Introduction 572
2 Mechanisms of Drug Action and Resistance 574
2.1 Antimonials 574
2.1.1 Mechanisms of Action 574
2.1.2 Mechanisms of Resistance 576
2.2 Amphotericin B 577
2.2.1 Mechanisms of Action 577
2.2.2 Mechanisms of Resistance 577
2.3 Pentamidine 577
2.3.1 Mechanisms of Action 577
2.3.2 Mechanisms of Resistance 578
2.4 Alternate Agents 578
2.4.1 Miltefosine 578
Mechanisms of Action 578
Mechanisms of Resistance 578
2.4.2 Allopurinol 579
2.4.3 Atovaquone 579
2.4.4 Paromomycin 579
2.4.5 Other Drugs 579
Fluconazole 579
Sitamaquine 579
alpha-Difl uoromethyl Ornithine 580
Antifolates 580
Mechanisms of Action 580
Mechanisms of Resistance 580
3 Spread of Resistance 581
References 581
Chapter 42 Drug Resistance in African Trypanosomiasis 585
1 Introduction 585
2 Mechanisms of Action of Currently Used Drugs 585
2.1 Suramin (Germanin®, Bayer) 585
2.2 Pentamidine (Pentamidine Isethionate, Aventis) 587
2.3 Melarsoprol (MelB, Arsobal®, Aventis) 587
2.4 alpha-Difl uoromethylonithin (DFMO, Efl ornithin, Ornidyl®, Aventis) 588
3 Cross-Resistance Analysis 589
4 Mechanisms and Spread of Drug Resistance 591
4.1 Origin of Drug Resistance 591
4.2 Multiplication of Drug Resistance 592
4.3 Dissemination of Drug Resistance 593
5 Experimental Drugs 593
6 New Drug Opportunities 593
6.1 Ongoing Developments 594
6.1.1 Inhibitors of Protein Farnesylation and Myristoylation 594
6.1.2 Lipid and Fatty Acid Synthesis Inhibitors 594
6.1.3 Phosphodiesterase Inhibitors 594
6.1.4 Metabolic Inhibitors 595
6.1.5 Interference with Protein Glycosylation 595
6.1.6 New Diamidines 595
6.2 ‘Non-rational’ Drug Finding 595
7 Outlook 595
References 596
Chapter 43 Drug Resistance and Emerging Targets in the Opportunistic Pathogens Toxoplasma gondii and Cryptosporidium parvum 601
1 Toxoplasma gondii: An Opportunistic Pathogen 601
1.1 Antimicrobial Mechanism of Action 601
1.1.1 The Current Treatment of Toxoplasmosis 601
1.1.2 Is Short-Term Treatment Benefi cial in Congenital and Ocular Toxoplasmosis? 602
1.2 Mechanisms of Drug Resistance 602
1.2.1 Is There Drug Resistance in Toxoplasma? 602
1.2.2 Drug-Resistant Parasites Are Easily Generated in the Laboratory 603
1.3 Why Is There Not More Drug Resistance in the Clinic? 603
1.4 Alternative Agents 604
1.4.1 The Challenge of a Dormant Foe 604
2 Cryptosporidiosis: A Widespread Disease in Developing and Industrialized Countries 604
2.1 Antimicrobial Mechanisms of Drug Resistance 604
2.1.1 What Is the Basis of Cryptosporidium’s Formidable Drug Resistance? 604
2.1.2 Living on the Edge, C. parvum Is an Intracellular, but Extracytoplasmatic Parasite 605
2.1.3 Effl ux Pumps Could Contribute to Drug Resistance 606
2.1.4 C. parvum Is a Highly Divergent Apicomplexan 606
2.2 Alternative Agents 607
2.2.1 The Emerging Genome Sequence Provides an Unprecedented View of C. parvum’s Metabolism 607
2.2.2 Gene Loss and Horizontal Transfers Shape C. parvum’s Nucleotide Pathway 608
References 609
Chapter 44 Drug Resistance in Nematodes 616
1 Introduction 616
2 Extent of the Resistance Problem in Nematode Parasites 616
3 Measuring Resistance 618
4 Mechanisms of Resistance 618
4.1 Benzimidazoles 618
4.2 Levamisole 619
4.3 Avermectins and Milbemycins 619
5 Selection for Anthelmintic Resistance 620
6 Management of Nematode Infections in Endemic Regions 621
References 621
Chapter 45 Chemotherapy and Drug Resistance in Schistosomiasis, Fascioliasis and Tapeworm Infections 624
1 Introduction 624
1.1 Schistosomiasis 624
1.2 Fasciolosis 625
1.3 Cestode (Tapeworm) Infections 625
2 Treatment of Schistosomiasis with Praziquantel 626
2.1 History, Chemical Structure and Properties of Praziquantel 626
2.2 Effi cacy of Praziquantel 627
2.3 Metabolism, Toxicity and Side Effects of Praziquantel 627
2.4 Mechanisms of Action of Praziquantel 628
3 Resistance to Praziquantel 628
3.1 Evidence of Resistance to Praziquantel in Schistosomes 628
3.2 Mechanisms and Markers of Resistance to Praziquantel 629
4 Alternative Agents for Schistosomiasis 630
4.1 Oxamniquine 630
4.1.1 The Activity of Oxamniquine Against S. mansoni 630
4.1.2 Schistosome Resistance to Oxamniquine 631
4.2 Artemisinin Derivatives 631
4.3 Ro 15-5458 631
4.4 Ro 11-3128 632
4.5 Myrrh 632
5 Cross-Resistance and Spread of Resistance to Schistosomicides 632
5.1 Refugia 633
6 Drugs for Liver Fluke Infections 633
6.1 Triclabendazole 633
6.2 Uncouplers 634
6.3 Benzimidazoles 634
6.4 Clorsulon 634
7 Other Drugs for Tapeworms 634
7.1 Pyrantel 634
7.2 Benzimidazoles 634
7.3 Nitroscanate 634
7.4 Niclosamide 634
7.5 Treatment of Larval Tapeworms 635
7.5.1 Taenia solium 635
7.5.2 Echinococcus granulosus 635
7.5.3 Echinococcus multilocularis 635
8 Concluding Remarks 635
References 636
Chapter 46 Drug Resistance in Ectoparasites of Medical and Veterinary Importance 642
1 Introduction 642
2 Background 642
3 Defi nition of Resistance 642
4 Mode of Action and Mechanisms of Resistance 643
4.1 The Organophosphates 643
4.2 The Carbamates 643
4.3 The Pyrethroids 643
4.4 The Insect Growth Regulators 643
4.5 The Macrocyclic Lactones 643
4.6 The Arylheterocycles Phenylpyrazoles 644
4.7 The Chloronicotinyl Nitroguanidines 644
5 The Development of Resistance in Individual Genera of Insects 644
5.1 Arachnida 644
5.1.1 Acari (Mites) 644
5.1.2 Ixodida (Ticks) 644
5.2 Insecta 644
5.2.1 Diptera (Flies) 644
5.2.2 Ceratopogonidae (Biting Midges) 645
Psychodidae–Phlebotominae (Sandfl ies) 645
Simuliidae (Blackfl ies) 645
Tabanidae (Horsefl ies, Deer Flies and Clegs) 645
Glossinidae (Tsetse Flies) 645
Muscidae and Fanniidae (Housefl ies and Stablefl ies) 645
Calliphoridae (Blowfl ies) 645
Oestridae (Gad Flies, Warble Flies and Stomach Bots) 646
5.2.3 Hemiptera (Bugs) 646
5.2.4 Phthiraptera (Lice) 646
5.2.5 Siphonaptera (Fleas) 646
6 Cross-Resistance 647
7 Conclusion 647
References 647
Index 650