感染微生态学 理论与实践 英文版PDF电子书下载

1 Infectious Microecology 1

1.1 ConceptionofInfectious Microecology 2

1.1.1 Defmition 2

1.1.2 Classification of Normal Microbiota α 2

1.2 History of Infectious Microecology 5

1.2.1 The Embryonic Stage of Microecology 5

1.2.2 The Lag Phase of Microecology 6

1.2.3 The Developmental Stage of Microecology 6

1.2.4 The Establishment and Development of Infectious Microecology 7

1.3 The Subject Characteristics of Infectious Microecology 8

1.3.1 Subiect Relations 8

1.3.2 Subject Core 9

1.3.3 Infectious Microecology Is a Basic Subject 9

1.3.4 Infectious Microecology Is an Applied Subject 10

1.4 The Classification of Infection 11

1.4.1 Types of Infection 11

1.4.2 The Evolution of Infection 13

1.4.3 The Outcome of Infection 13

1.5 Microecological Characteristics of Infection 13

1.5.1 Microecology Helps to Build and Maintain the Host's Immune Systems 14

1.5.2 Dynamic Balances between Microecology and Host 15

1.5.3 Many Infections are Correlated with Microecological Imbalance 15

1.6 The Microecological Mechanism of Infection 16

1.6.1 Occurrence of Infection 16

1.6.2 Development of Infection 17

1.6.3 Outcome of Infection 17

1.7 Prevention and Control of Infections Using Infectious Microecology Theories 18

1.7.1 The Revolution in Infection Prevention and Control Strategy 18

1.7.2 Mechanisms for Preventing and Controlling Infections with Microecological Modulators 19

1.7.3 Frequently Used Microecological Modulators 19

1.7.4 Prospects of Infection Prevention and Control Using Infectious Microecology Theories 19

References 20

2 Human Microbiota and Its Function 23

2.1 Metabolic Functions 24

2.2 Trophic Functions 27

2.3 Interaction between Gut Bacteria and Host Immunity 27

2.4 Protective Functions:The Barrier Effect 28

References 29

3 Infectious Microecology and Immunology 33

3.1 Infection and Immunity 33

3.1.1 Immunity Response to Microbes 34

3.1.2 Immune Responses to Extracellular Bacteria 34

3.1.3 Immune Responses to Intracellular Bacteria 35

3.1.4 Immune Responses to Fungi 36

3.2 Infectious Microecology and Immunology 36

3.2.1 Intestinal Microbes and Intestinal Barrier 37

3.2.2 Intestinal Microecology and Host Immunity 39

3.3 Hepatic Microecology and Immunity 42

3.3.1 Liver Involvement in Innate Immunity 42

3.3.2 Liver Involvement in Adaptive Immunity 45

3.4 Liver's Immune Privilege 46

References 49

4 Microecology Disturbance and Infection 59

4.1 Microecology Disturbance 59

4.1.1 Concept of Microecology Disturbance 60

4.1.2 Classification of Microecology Disturbance 60

4.1.3 Influencing Factors of Microecology Disturbance 64

4.2 Infection 68

4.2.1 The Concept of Infection 69

4.2.2 Types of Infection 70

4.2.3 Etiologic Agent of Infection 71

4.2.4 Epidemic Links of Infection 74

4.3 The Relation between Microecology Disturbance and Infection 75

4.3.1 Traditional Biological Pathogeny Theory 76

4.3.2 Ecological Pathogeny Theory 76

4.3.3 The Significance of Infection 76

4.3.4 Microdysbiosis Induces Infection Diseases 78

4.3.5 Mechanism of Microorganisms and Host 79

References 80

5 Nosocomial Infections and Bacterial Resistance 83

5.1 Nosocomial Infections 84

5.1.1 Introduction 84

5.1.2 Epidemiology of Nosocomial Infections 85

5.1.3 Pathogens of Nosocomial Infections 89

5.1.4 Common Nosocomial Infections 91

5.1.5 Prevention of Nosocomial Infections 99

5.2 Bacterial Resistance 103

5.2.1 Prevalence of Bacterial Resistance 103

5.2.2 Mechanisms of Bacterial Resistance 110

5.2.3 Strategies to Control Bacterial Resistance 124

References 124

6 Microbial Culture and Its Clinical Application 133

6.1 Conventional Microbial Culture and Clinical Application 133

6.1.1 Clinical Blood Culture 133

6.1.2 Clinical Body Fluids Culture 135

6.1.3 Clinical Urine Culture 136

6.1.4 Culture of Specimens from Gastrointestinal Tract 137

6.2 Requirements for Collection of Cultural or Non-Cultural Specimens 137

6.2.1 Conventional Principles for Collection and Transportation of Specimens Used for Culture 137

6.2.2 Special Conditions for Collecting Specimens Used for'Non-Routine'Culture 139

6.2.3 Inoculating Samples in an Optimal Media:Selection of the Culture Media 140

6.3 Clinical Choice ofMicrobial Culture or Non-Culture 142

6.3.1 Overview of Microbial Culture and Non-Culture Based Methods 142

6.3.2 Clinical Indication of Microbial Culture and Non-Culture 144

6.4 Interpretation of the Microbial Culture Results 146

6.4.1 Interpreting the Positive Results of the Microbial Culture 147

6.4.2 Interpreting the Negative Results of the Microbial Culture 149

References 150

7 Molecular Microecological Techniques 153

7.1 Introduction 154

7.2 Size Pattern Analysis—T-RFLP Polymorphism Analysis of 16S rRNA Genes 156

7.3 Melting Pattern Analysis—PCR-DGGE Analysis of 16S rRNA Genes 159

7.4 FISH 165

7.5 Microarray Applications in Microbial Ecology Research 168

7.6 Cloning Library Construction and Sequencing 172

7.7 Next-Generation Sequencing Techniques for Microbial Ecology Research 174

7.8 Conclusion 180

References 180

8 Metabonomic Phenotyping for the Gut Microbiota and Mammal Interactions 189

8.1 Mammals Are'Superorganisms' 189

8.2 Co-Metabolisms and the Mammal-Microbiome Interactions 190

8.3 Metabonomic Phenotyping for Mammals 191

8.4 Future Perspectives 194

References 194

9 Bioinformatics for Genomes and Metagenomes in Ecology Studies 203

9.1 Introduction to Advances in Microbial Ecology 203

9.2 16S rDNA in Ecology Studies 204

9.3 16S rDNA Gene Analysis 205

9.4 Metagenomics 207

9.5 Recent Applications of Environmental Metagenomic Sequencing 208

9.6 Analysis of Viral Communities 209

9.7 Assembly of Sequence Data 209

9.8 Assembly:Strategies 211

9.9 Assembly:Future Directions 212

9.10 Fragment Recruitment 215

9.11 Taxonomic Classification 216

9.12 MGTAXA 216

9.13 High Performance Computing 217

9.14 Functional Annotation 218

9.15 Analysis of Eukaryotes in Ecology Studies 218

9.16 Challenges Presented by Data Volume(Computational and Storage Requirements,Cloud Computing Solutions) 219

9.17 Future Directions 221

References 222

10 Ecology of Oral Infectious Diseases 227

10.1 Ecological Basis 228

10.1.1 Oral Biotic Area 229

10.1.2 Normal Oral Microflora 231

10.1.3 Saliva and Dental Plaque Biofilm 244

10.2 Oral Infectious Diseases 253

10.2.1 Dental Caries 253

10.2.2 Pulpal and Periapical Diseases 267

10.2.3 Periodontal Disease 273

10.2.4 Maxillofacial Infectious Diseases 285

10.2.5 Oral Mucosal Infections 287

10.2.6 Secondary Infection from the Wearing of Dentures 290

References 291

11 Gastrointestinal Infectious Microecology 293

11.1 Microbiota in Health 293

11.1.1 Normal Microbiota in the Stomach 293

11.1.2 Normal Microbiota in the Intestine 294

11.1.3 Physiological Functions of Gastrointestinal Microbiota 295

11.1.4 Factors Affecting Gastrointestinal Microecological Balance of the Host 296

11.2 Helicobacter Pylori and Gastroduodenal Disease 298

11.2.1 Helicobacter Pylori and Chronic Gastritis 298

11.2.2 Helicobacter Pylori and Peptic Ulcer 298

11.2.3 Helicobacter Pylori and Gastric Cancer 299

11.2.4 Diagnosis for H. Pylori Infection 299

11.2.5 Treatment 301

11.3 Inflammatory Bowel Disease 301

11.3.1 Role of Microbiota 301

11.3.2 Immune Response 302

11.3.3 Clinical Findings and Diagnosis 302

11.3.4 Treatment 303

11.4 Infectious Diarrhea 304

11.4.1 Diarrhea Caused by Toxins 304

11.4.2 Diarrhea Caused by Invasive Pathogens 305

11.4.3 Diarrhea Caused by Viruses 305

11.4.4 Diagnosis 305

11.4.5 Treatment 306

11.5 Irritable Bowel Syndrome 306

11.5.1 Etiology 307

11.5.2 Clinical Findings and Diagnosis 308

11.5.3 Treatment 309

11.6 Antibiotic-Associated Diarrhea 309

11.6.1 Pathogenesis 309

11.6.2 Clinical Findings and Diagnosis 310

11.6.3 Treatment 311

11.7 Colorectal Cancer 311

11.7.1 Pathogenesis 312

11.7.2 Symptoms 313

11.7.3 Diagnosis 313

11.7.4 Treatment 314

11.8 Gastrointestinal Tuberculosis 314

References 315

12 Infectious Microecology in Liver Disease 317

12.1 An Overview ofInfectious Microecology in Liver Disease 318

12.1.1 Liver Anatomy and Enterohepatic Recycling 318

12.1.2 Gut-Liver Axis 318

12.1.3 The Role of Kupffer Cells in Liver Disease 319

12.1.4 Endotoxin Activates Kupffer Cells in Liver Disease 319

12.1.5 Pathogenesis of Bacterial Translocation in Liver Disease 321

12.2 Gut Microflora in the Pathogenesis of the Complications of Cirrhosis 322

12.2.1 Bacterial Infections in Cirrhosis 323

12.2.2 Sources and Types of Bacterial Infection in Cirrhosis 323

12.2.3 Bacteria Translocation in the Pathogenesis of Spontaneous Bacterial Peritonitis in Cirrhosis 324

12.2.4 Gut Flora and the Hyperdynamic Circulatory State in Cirrhosis 324

12.2.5 The Gut Flora and Hepatic Encephalopathy 325

12.3 Modulation of Intestinal Microbiota as a Therapeutic Strategy of Liver Disease 326

12.3.1 Manipulation of Gut Flora and Its Effect on Infections in Cirrhosis 326

12.3.2 Manipulation of Gut Flora and Its Effect on Infections in Liver Transplants 329

References 329

13 Biliary Infection,Pancreatic Infection and Microecology 333

13.1 Biliary Infection and Microecology 333

13.1.1 Microecology Foundation of Biliary Tract System 334

13.1.2 Biliary Infection and Microecology 338

13.1.3 Microecology Treatment of Biliary Tract Infection 343

13.2 Pancreatic Infection and Microecology 349

13.2.1 Microecology Foundation of the Pancreas 350

13.2.2 Pancreatic Infection and Microecology 351

13.2.3 Microecology Therapies for Pancreatic Infection 359

References 367

14 Infectious Microecology in Urinary Tract and Reproductive System 377

14.1 Introduction 377

14.2 Infections of the Urinary Tract 378

14.2.1 Definitions 378

14.2.2 Classification 379

14.3 Diagnosis 380

14.3.1 Upper Urinary Tract Infection(UUTI) 381

14.3.2 Lowerr Urinaru Tract Infections (LUTI) 390

14.3.3 Factors Increasing Morbidity and/or Mortality 395

14.4 Prostatitis and Related Disorders 396

14.4.1 Epidemiology 397

14.4.2 Pathophysiology 398

14.4.3 Clinical Presentation and Diagnostic Evaluation 398

14.4.4 Causative Pathogens in Prostatitis 399

14.4.5 Treatment of Bacterial Prostatitis 400

14.4.6 Conclusions 403

References 403

15 Infectious Microecology in the Diseases of the Respiratory System 411

15.1 Ecological Space and Microecological Characteristics of the Respiratory System 411

15.1.1 Non-Specific Defense Mechanism 411

15.1.2 Specific Defense Mechanism 413

15.2 Microecology and Microecology Changes in Respiratory System Infection 414

15.3 Microecology of Respiratory System Fungal Infection 416

15.3.1 Pulmonary Candidiasis 416

15.3.2 Pulmonary Aspergillosis 417

15.3.3 Pulmonary Cryptococcosis 417

15.3.4 Pulmonary Coccidioidomycosis 418

15.4 Microecology of Respiratory System Viral Infection 418

15.5 Microecology of Respiratory System Mycobacterial Infection 419

15.5.1 Pulmonary Tuberculosis 420

15.5.2 Non-Tuberculous Mycobacterial Disease 424

15.6 Main Measures of Microecological Prevention/Treatment and Respiratory System Ecological Prevention/Treatment in Anti-Infective Therapy 426

References 428

16 Infectious Microecology of Skin 431

16.1 Histological Structures of Skin 431

16.1.1 Epidermis 432

16.1.2 The Dermis 433

16.1.3 Subcutaneous Tissue 434

16.1.4 Cutaneous Appendages:The Adnexa 434

16.2 Functions of Skin 436

16.2.1 Biological Barrier Function of Skin 436

16.2.2 Immune Function of Skin 437

16.2.3 Functions of the Sweat Gland and Sebaceous Gland 439

16.2.4 Nutritional Metabolism of Skin 441

16.2.5 Thermo-Regulation of Skin 442

16.3 Characteristics of Cutaneous Microecology 443

16.3.1 Normal Microbial Community of the Skin 443

16.3.2 Influential Factors of Cutaneous Normal Microflora 448

16.3.3 Physiological Function of Normal Cutaneous Microfloras 454

16.4 Microecological Disturbance and Cutaneous Disorders 455

16.4.1 Bacteria and Cutaneous Diseases 455

16.4.2 Fungi and Cutaneous Diseases 457

16.4.3 Virus and Cutaneous Diseases 463

16.4.4 Warts 466

16.5 Ecological Prevention and Treatment of Cutaneous Diseases 468

16.5.1 Protect the Macroecological Environment 468

16.5.2 Improve the Microecological Environment 468

16.5.3 Use Antibiotics Appropriately 470

16.5.4 Apply the Microecological Reagents 470

16.6 Prospects 473

References 474

17 Infectious Microecology of the Hematological System 477

17.1 Defensive Function of Blood 477

17.1.1 Cellular Components of Blood 478

17.1.2 Non-Cellular Components of Blood 479

17.2 Molecular Ecology and Hematological Disease 480

17.2.1 Apoptosis and Hematological Disease 481

17.2.2 Oncogenes,Tumor Suppressor Genes and Signal Conducting Molecules 487

17.2.3 Telomere Telomerase 491

17.3 Microecological Changes and Hematologic Diseases 493

17.3.1 Helicobacter Pylori and Primary Gastric Lymphoma 493

17.3.2 Microecological Changes and Erythrocyte Disorders 495

17.3.3 Microecological Changes and Leukocyte Diseases 499

17.3.4 Infection and Bleeding Disorders 502

17.4 Treatment of Hematologic Diseases and Infective Microecology 507

17.4.1 Predisposing Factors and Pathogens 507

17.4.2 The Principles of Treatment 509

17.5 Molecular Ecological Treatment 510

17.5.1 Genic Ecological Treatment 510

17.5.2 Immune Ecological Treatment 513

References 515

18 Infectious Microecology in Solid-Organ Transplantation 519

18.1 Screening of Donor and Recipient Prior to Solid-Organ Transplantation 520

18.1.1 Donor-Derived Infections 520

18.1.2 Recipient-Derived Infections 521

18.2 Timeline ofInfection Post-Transplantation 522

18.2.1 Early Period(1-4 weeks) 523

18.2.2 Intermediate Period(1-6 months) 523

18.2.3 Late Period (After 6 months) 523

18.3 Prevention of Infection in Solid-Organ Transplantation 524

18.3.1 Viral Infections 524

18.3.2 Bacterial Infections 527

18.3.3 Fungal Infections 528

18.3.4 Parasitic Infections 530

References 531

19 Microecology of Infections Associated with Surgery and Trauma 533

19.1 Main Pathogenic Bacteria Associated with Surgical and Trauma-Related Infections 534

19.1.1 Changes to the Spectrum of the Pathogenic Bacteria 534

19.1.2 Predominant Pathogenic Bacteria 538

19.1.3 Primary Pathogenic Factors 541

19.2 Post-Surgery-and Post-Trauma-Related Wound Infections 542

19.2.1 Etiology and Pathogenesis of Wound Infections 543

19.2.2 Prevention and Treatment of Wound Infections 543

19.3 Intra-Abdominal Infections Associated with Surgery and Trauma 547

19.3.1 Acute Peritonitis Resulting from Surgery and Trauma 547

19.3.2 Intra-Abdominal Abscesses after Surgery and Trauma 549

19.4 Enterogenic Infections Associated with Post-Surgery and Trauma 550

19.4.1 Intestinal Barrier Function 551

19.4.2 Intestinal Barrier Function and Bacterial Translocation 554

19.4.3 Clinical Manifestations of Enterogenic Infections 556

19.4.4 Prevention and Treatment of Enterogenic Infections 557

19.5 Preventionand Prognosis of Surgical and TraumaticInfections 558

19.5.1 Prevention of Post-Surgical and Post-Traumatic Infections 559

19.5.2 Conventional Treatments Associated with Surgery and Wound Infections 561

19.5.3 Complications of Severe Surgical and Wound Infections Prevention and Treatment of Sepsis and MOF 563

19.5.4 Future Directions 566

References 566

20 Infective Microecology of Chemotherapy and Radiotherapy 569

20.1 Mechanisrn of Chemotherapy and Radiotherapy 569

20.1.1 Chemotherapy 569

20.1.2 Radiotherapy 572

20.2 Chemotherapy and Radiotherapy Effect on Microecology 574

20.2.1 Cancer Patients and Microecology 574

20.2.2 Microdysbiosis in Cancer Patients 578

20.3 Microecology of Infection Caused by Radiotherapy and Chemotherapy 580

20.3.1 Prevention and Treatment of Infection-Related Chemotherapy Toxicity 581

20.3.2 Prevention and Treatment of Infection-Related Radiotherapy Toxicity 582

20.3.3 Prevention and Treatment of Cancer Patients Infection 584

20.3.4 Microecological Control of Cancer Patients 587

20.4 Prospects 589

References 590

21 Infectious Microecology in Immunodeficiency Diseases 593

21.1 HIV Immune Deficiency,Old View 594

21.2 Immune Activation in HIV Infection 595

21.3 Breakdown of Mucosal Immunity 596

21.4 Solving the Problem from the Microecological Viewpoint 598

21.5 HIV-1 Infection in Mucosa Scope 600

21.6 Through Microbiota and Beyond 601

21.7 Probiotics and HIV 604

References 605

22 Microecology Intervention in Prevention and Treatment of Infectious Diseases 611

22.1 Theoretical Basis of Microecological Prevention and Treatment 611

22.1.1 The Principle of Microecology Balance 612

22.1.2 Principles of Biological Antagonism 612

22.1.3 Biological Oxygen Consumption Hypothesis 613

22.1.4 Immune Activating 613

22.1.5 Nutritional Effect 613

22.1.6 Three Circulations Theory 614

22.1.7 Continuous Succession Effect 614

22.2 Microecological Modulators 615

22.2.1 Probiotics Definitions 615

22.2.2 Characteristics and Classification of Probiotics 616

22.2.3 Bio-Safety of Probiotics 617

22.2.4 Bifidobacterium Products 619

22.2.5 Lactobacillus Products 620

22.2.6 Bacillus Products 622

22.2.7 Saccharomyces Preparations 623

22.2.8 Enterococcus Preparations 624

22.2.9 Clostridium Butyricum Preparation 625

22.3 Prebiotics Preparation 625

22.3.1 Definition 626

22.3.2 Oligosaccharide as Prebiotics 627

22.3.3 Physiological Function 628

22.4 Application of Probiotics and Prebiotics 631

22.4.1 Gastrointestinal Tract Infection Diseases Prevention 631

22.4.2 Constipation Treatment 632

22.4.3 Prevention and Treatment of Hepatic Diseases 633

22.4.4 Prevention of Hypercholesterolemia 635

22.4.5 Treatment of Irritable Bowel Syndrome 635

22.4.6 Prevention and Treatment of Vaginal Infection Diseases 636

22.4.7 Application in Pediatric Diseases and Infant Care 636

22.4.8 Application in Antitumor 637

References 638

23 Future Development of Infectious Microecology 639

23.1 Evolving View of Infectious Disease 639

23.2 Advances in Molecular Ecological Techniques 640

23.3 Normal Human Microbiota 641

23.4 Interactions between Infectious Diseases and Microbiota 642

23.4.1 Disturbance of Normal Microbiota by Therapy 642

23.4.2 Microbiota and Viral Infection 643

23.4.3 Microbiota and Autoimmunity Disease 644

23.5 Therapy 644

23.5.1 Probiotics or Prebiotics 644

23.5.2 Other Bacteriologic Therapy 645

23.5.3 The Role of Microbiota in Drug Metabolism 646

23.6 Summary and Prospects 646

References 647

Index 649