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