دبلوم الكیمیاء الحیویة الطبیة
Diploma of Biomedical Chemistry

دبلومة ضبط الجودة (علوم اسيوط ) Professional Diploma in Quality Control

 دبلومة ضبط ورقابة الجودة 

 Professional Diploma in Quality Control

كلية العلوم - جامعة أسيوط 

دبلوم رقابة الجوده (كلية الدراسات العليا بنى سويف ) Diploma in Quality Control

دبلوم رقابة الجوده
 Diploma in Quality Control 

 كلیة الدراسات العلیا للعلوم المتقدمة

جامعة بنى سویف

دبلومات الدرسات العليا التخصصية - كلية العلوم جامعة اسيوط 2020/2021

 تعلن كلية العلوم - جامعة أسيوط 

Basic laboratory procedures in clinical bacteriology

 Contents

Preface viii

Introduction 1

Quality assurance in bacteriology 2

Introduction 2

Definitions 2

Internal quality control 6

External quality assessment 16

PART I : Bacteriological investigations 19

Blood 20

Introduction 20

When and where bacteraemia may occur 20

Blood collection 20

Blood-culture media 22

Processing of blood cultures 23

Cerebrospinal fluid 25

Introduction 25

Collection and transportation of specimens 25

Macroscopic inspection 26

Microscopic examination 26

Preliminary identification 28

Susceptibility testing 29

Urine 30

Introduction 30

Specimen collection 30

Culture and interpretation 32

Interpretation of quantitative urine culture results 34

Identification 35

Susceptibility tests 36

Stool 37

Introduction 37

Etiological agents and clinical features 37

Appropriate use of laboratory resources 39

Collection and transport of stool specimens 40

Visual examination of stool specimens 41

Enrichment and inoculation of stool specimens 41

Media for enteric pathogens 42

Primary isolation 42

Preliminary identification of isolates 44

Final microbiological identification 50

Serological identification 54

Upper respiratory tract infections 60

Introduction 60

Normal flora of the pharynx 60

Bacterial agents of pharyngitis 61

Collection and dispatch of specimens 62

Direct microscopy 62

Culture and identification 63

Susceptibility testing 65

Lower respiratory tract infections 66

Introduction 66

The most common infections 66

Collection of sputum specimens 68

Processing of sputum in the laboratory (for

non-tuberculous infections) 68

Culture for Mycobacterium tuberculosis 72

Interpretation of cultures for M. tuberculosis 74

General note on safety 74

Sexually transmitted diseases 76

Introduction 76

Urethritis in men 77

Genital specimens from women 79

Specimens from genital ulcers 82

Purulent exudates, wounds and abscesses 86

Introduction 86

Commonly encountered clinical conditions and the

most frequent etiological agents 86

Collection and transportation of specimens 89

Macroscopic evaluation 90

Microscopic examination 91

Culture 92

Identification 93

Susceptibility testing 97

Anaerobic bacteriology 98

Introduction 98

Description of bacteria in relation to oxygen requirement 98 

Bacteriology 98

Antimicrobial susceptibility testing 103

Introduction 103

General principles of antimicrobial susceptibility testing 103

Clinical definition of terms “resistant” and “susceptible”:

the three category system 104

Indications for routine susceptibility tests 106

Choice of drugs for routine susceptibility tests in the

clinical laboratory 107

The modified Kirby–Bauer method 109

Direct versus indirect susceptibility tests 117

Technical factors influencing the size of the zone in the

disc-diffusion method 118

Quality control 120

Serological tests 122

Introduction 122

Quality control measures 122

Serological reactions 125

Serological tests for syphilis 126

Febrile agglutinins tests 133

Antistreptolysin O test 135

Bacterial antigen tests 137

PART II: Essential media and reagents 141

Introduction 142

Pathogens, media and diagnostic reagents 143

Blood 144

Cerebrospinal fluid 144

Urine 145

Stool 146

Upper respiratory tract 147

Lower respiratory tract 148

Urogenital specimens for exclusion of sexually transmitted

diseases 149

Pus and exudates 149

List of recommended media and diagnostic reagents for the intermediate microbiological laboratory 150

Selected further reading 154

Index 155

Bacteriology of Humans

An Ecological Perspective

Michael Wilson
University College London

CONTENTS

 Preface, ix

Abbreviations of genera, xi

1 THE HUMAN–MICROBE SYMBIOSIS

1.1 Overview of the nature and distribution of the microbial communities inhabiting humans

1.1.1 Difficulties encountered in determining the composition of a microbial community, 2

1.1.2 Structural aspects of microbial communities, 5

1.1.2.1 Microcolonies, 5

1.1.2.2 Intracellular colonization, 5

1.1.2.3 Biofilms, 6

1.1.3 Communication in microbial communities, 8

1.2 Environmental determinants that affect the distribution and composition of microbial communities

1.2.1 Nutritional determinants, 14

1.2.2 Physicochemical determinants, 18

1.2.3 Mechanical determinants, 22

1.2.4 Biological determinants, 23

1.3 Host characteristics that affect the indigenous microbiota

1.3.1 Age, 28

1.3.2 Host genotype, 29

1.3.3 Gender, 29

1.4 Techniques used to characterize the microbial communities inhabiting humans

1.4.1 Microscopy, 31

1.4.2 Culture-dependent approaches, 33

1.4.3 Culture-independent, molecular approaches, 35

1.4.4 Functional analysis of microbial communities, 37

1.5 The epithelium – site of host–microbe interactions

1.5.1 Structure of epithelia, 38

1.5.2 The epithelium as an excluder of microbes, 41

1.5.3 Mucus and mucins, 41

1.5.4 Innate and acquired immune responses at the mucosal surface, 46

1.6 Further reading

1.6.1 Books, 53

1.6.2 Reviews and papers, 53

2 THE INDIGENOUS MICROBIOTA OF THE SKIN

2.1 Anatomy and physiology of human skin, 56

2.2 Cutaneous antimicrobial defense systems, 56

2.2.1 Innate defense systems, 58

2.2.2 Acquired immune defense systems, 60

2.3 Environmental determinants operating at different skin regions, 61

2.4 The indigenous microbiota of the skin, 67

2.4.1 Members of the cutaneous microbiota, 67

2.4.1.1 Corynebacterium spp., 67

2.4.1.2 Propionibacterium spp., 70

2.4.1.3 Staphylococcusspp., 71

2.4.1.4 Micrococcusspp., 73

2.4.1.5 Malassezia spp., 75

2.4.1.6 Acinetobacterspp., 76

2.4.1.7 Brevibacterium spp., 78

2.4.1.8 Dermabacter hominis, 79

2.4.1.9 Methylobacterium spp., 79

2.4.2 Community composition at different sites,80

2.4.3 Culture-independent studies of the cutaneous microbiota, 86

2.4.4 Interactions among members of the cutaneous microbiota, 88

2.5 Overview of the cutaneous microbiota, 90

2.6 Sources of data used to compile figures , 92

2.7 Further reading, 92

2.7.1 Books, 92

2.7.2 Reviews and papers, 92

3 THE INDIGENOUS MICROBIOTA OF THE EYE

3.1 Anatomy and physiology of the eye, 95

3.2 Antimicrobial defense systems of the eye, 97

3.3 Environmental determinants on the conjunctival surface, 99

3.4 The indigenous microbiota of the eye, 103

3.4.1 Members of the ocular microbiota, 103

3.4.2 Composition of the ocular microbiota, 104

3.4.3 Interactions among members of the ocular microbiota, 107

3.5 Overview of the ocular microbiota, 111

3.6 Sources of data used to compile figures, 111

3.7 Further reading, 111

4 THE INDIGENOUS MICROBIOTA OF THE RESPIRATORY TRACT

4.1 Anatomy and physiology of the respiratory tract, 113

4.1.1 Nose, 113

4.1.2 Pharynx, 114

4.1.3 Larynx, 114

4.1.4 Trachea, 114

4.1.5 Bronchi and bronchioles, 114

4.1.6 Alveolus, 115

4.2 Antimicrobial defense systems of the respiratory tract, 117

4.2.1 Nasal cavity, 117

4.2.2 Other regions of the conducting portion, 119

4.2.3 Respiratory portion, 119

4.3 Environmental determinants within the respiratory tract, 119

4.3.1 Atmospheric composition, 119

4.3.2 pH, 120

4.3.3 Nutrients, 120

4.3.3.1 Composition of nasal fluid, ASL, and alveolar lining fluid, 120

4.3.3.2 Contribution of microbial residents of the respiratory tract to nutrient availability, 122

4.4 Indigenous microbiota of the respiratory tract, 123

4.4.1 Members of the respiratory microbiota,123

4.4.1.1 Streptococcusspp., 123

           4.4.1.1.1 Strep. pyogenes, 124

          4.4.1.1.2 Strep. pneumoniae, 126

         4.4.1.1.3 Viridans group streptococci, 128

4.4.1.2 Neisseria spp., 128

     4.4.1.2.1 N. meningitidis, 129

     4.4.1.2.2 Other Neisseria spp.,131

4.4.1.3 Haemophilusspp., 131

    4.4.1.3.1 H. influenzae, 132

   4.4.1.3.2 Other Haemophilusspp.,134

4.4.1.4 Moraxella catarrhalis, 135

4.4.1.5 Staphylococci, 136

        4.4.1.5.1 Staph. aureus, 136

       4.4.1.5.2 CNS, 138

       4.4.1.6 Mollicutes, 139

4.4.1.7 Kingella kingae, 140

4.4.2 Community composition at the various sites within the respiratory tract, 140

4.4.2.1 Nasal vestibule, 142

4.4.2.2 Nasal cavity, 143

4.4.2.3 Nasopharynx, 146

4.4.2.4 Oropharynx, 146

4.4.2.5 Lower respiratory tract, 151

4.4.3 Interactions among members of the respiratory microbiota, 152

4.5 Overview of the respiratory microbiota, 152

4.6 Sources of data used to compile figures, 155

4.7 Further reading, 157

5 THE INDIGENOUS MICROBIOTA OF THE URINARY SYSTEM OF FEMALES

5.1 Anatomy and physiology of the urinary system of females, 159

5.2 Antimicrobial defenses of the female urinary system, 160

5.3 Environmental determinants within the female urethra, 161

5.4 The indigenous microbiota of the female urethra, 162

5.4.1 Members of the urethral microbiota, 163

5.4.2 Community composition in the female urethra, 164

5.5 Overview of the microbiota of the urinary tract of females, 167

5.6 Sources of data used to compile figures, 168

5.7 Further reading, 168

6 THE INDIGENOUS MICROBIOTA OF THE REPRODUCTIVE SYSTEM OF FEMALES

6.1 Anatomy and physiology of the female reproductive system, 170

6.2 Antimicrobial defense systems of the female reproductive system, 172

6.2.1 Innate defense systems, 173

6.2.2 Acquired immune defense systems, 174

6.3 Environmental determinants at different regions of the reproductive system, 176

6.3.1 Vagina, 176

6.3.2 Cervix, 179

6.3.3 Vulva, 179

6.3.4 Contribution of the indigenous microbiota to nutrient supply within the reproductive system, 179

6.4 The indigenous microbiota of the female reproductive system, 181

6.4.1 Members of the microbiota, 181

6.4.1.1 Lactobacillusspp., 181

6.4.1.2 Gardnerella vaginalis, 184

6.4.1.3 Candida albicans, 184

6.4.1.4 Streptococcus agalactiae(Group B streptococcus), 186

6.4.1.5 Mycoplasma hominis, 186

6.4.1.6 Ureaplasma urealyticum, 186

6.4.1.7 Atopobium vaginae, 187

6.4.1.8 Mobiluncusspp., 187

6.4.2 Community composition at different sites within the female reproductive system, 187

6.4.2.1 Vagina, 187

6.4.2.1.1 Post-menarcheal/pre- menopausal females, 187

6.4.2.1.2 Pre-menarcheal girls,191

6.4.2.1.3 Post-menopausal women, 192

6.4.2.1.4 Vaginal microbiota during pregnancy, 193

6.4.2.2 Cervix, 193

6.4.2.2.1 Post-menarcheal/pre- menopausal females, 197

6.4.2.2.2 Cervical microbiota during pregnancy, 197

6.4.2.3 Vulva, 199

6.4.3 Interactions between organisms colonizing the female reproductive system, 200

6.5 Overview of the microbiota of the female reproductive system, 202

6.6 Sources of data used to compile figures, 202

6.7 Further reading, 204

6.7.1 Books, 204

6.7.2 Reviews and papers, 204

7 THE INDIGENOUS MICROBIOTA OF THE URINARY AND REPRODUCTIVE SYSTEMS OF MALES

7.1 Anatomy and physiology, 207

7.2 Antimicrobial defenses of the male urinary and reproductive systems, 207

7.3 Environmental determinants within the male urinary and reproductive systems

7.4 The indigenous microbiota of the male urinary and reproductive systems, 211

7.4.1 Members of the microbiota, 211

7.4.2 Microbiota of the male urethra, 212

7.4.3 Microbiota of the glans penis, 216

7.4.4 Microbiota of the prostate, 218

7.5 Overview of the microbiota of the male urinary and reproductive systems, 218

7.6 Sources of data used to compile figures, 219

7.7 Further reading, 220

8 THE INDIGENOUS MICROBIOTA OF THE ORAL CAVITY

8.1 Anatomy and physiology of the oral cavity, 222

8.2 Antimicrobial defense systems of the oral cavity,225

8.3 Environmental determinants at the various siteswithin the oral cavity, 228

8.3.1 Mechanical determinants, 228

8.3.2 Nutritional determinants, 228

8.3.3 Physicochemical determinants, 231

8.4 The indigenous microbiota of the oral cavity, 232

8.4.1 Members of the oral microbiota, 235

8.4.1.1 Oral streptococci and related Gram-positive cocci, 235

8.4.1.2 Gemella spp., 235

8.4.1.3 Actinomycesspp., 236

8.4.1.4 Rothia dentocariosa, 237

8.4.1.5 Veillonella spp., 237

8.4.1.6 Anaerobic and microaerophilic Gram-negative rods, 237

8.4.1.6.1 Fusobacterium spp., 237

8.4.1.6.2 Porphyromonasspp.,

8.4.1.6.3 Prevotella spp., 239

8.4.1.6.4 Spirochaetes, 239

8.4.1.6.5 Other anaerobic species, 239

8.4.1.7 Facultatively anaerobic Gram-negative bacilli, 240

8.4.1.8 Mycoplasma spp., 240

8.4.1.9 Megasphaera spp., 241

8.4.2 Community composition at different sites, 241

8.4.2.1 Supragingival plaque, 241

8.4.2.2 Gingival crevice, 253

8.4.2.3 Tongue, 256

8.4.2.4 Other mucosal surfaces, 257

8.5 Overview of the oral microbiota, 261

8.6 Sources of data used to compile figures, 263

8.7 Further reading, 264

8.7.1 Books, 264

8.7.2 Reviews and papers, 264

9 THE INDIGENOUS MICROBIOTA OF THE GASTROINTESTINAL TRACT

9.1 Anatomy and physiology of the gastrointestinal tract, 267

9.2 Antimicrobial defense systems of the gastrointestinal tract, 272

9.2.1 Innate defense systems, 272

9.2.2 Acquired immune defense system, 275

9.3 Environmental determinants within different regions of the gastrointestinal tract, 276

9.3.1 Esophagus, 276

9.3.2 Stomach, 277

9.3.3 Small intestine, 277

9.3.4 Large intestine, 278

9.4 The indigenous microbiota of the gastrointestinal tract, 280

9.4.1 Members of the intestinal microbiota, 282

9.4.1.1 Bacteroides, 282

9.4.1.2 Eubacterium, 283

9.4.1.3 Roseburia, 284

9.4.1.4 Clostridium, 284

9.4.1.5 Bifidobacterium, 284

9.4.1.6 Enterococcus, 285

9.4.1.7 Helicobacter pylori, 286

9.4.1.8 Enterobacteriaceae, 286

9.4.1.9 Ruminococcus, 287

9.4.1.10 Methanogenic organisms, 287

9.4.1.11 Desulfovibrio, 287

9.4.1.12 Acidaminococcus, 288

9.4.1.13 Faecalibacterium prausnitzii, 288

9.4.2 Community composition in different regions of the intestinal tract, 288

9.4.2.1 Esophagus, 288

9.4.2.2 Stomach, 289

9.4.2.3 Small intestine, 295

9.4.2.3.1 Duodenum, 295

9.4.2.3.2 Jejunum, 295

9.4.2.3.3 Ileum, 301

9.4.2.4 Large intestine, 302

9.4.2.4.1 Cecum, 304

9.4.2.4.2 Colon, 306

9.4.2.4.3 Rectum, 316

9.4.3 Microbial interactions in the gastrointestinal tract, 317

9.5 Overview of the indigenous microbiota of the gastrointestinal tract, 320

9.6 Sources of data used to compile figures, 320

9.7 Further reading, 322

9.7.1 Books, 322

9.7.2 Reviews and papers, 322

10 THE FUTURE, 327

10.1 Further reading, 329

Index, 331

كتاب القمة الجزء الثانى

 

كتاب القمة الجزء الثانى 

يشمل العلوم التالية 

الميكروبيولوجى 

الدم هيماتولوجى 

الطفيليات 

البول والبراز