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 

WHO laboratory manual for the Examination and processing of human semen (Fifth Edition)

 

WHO laboratory manual for the Examination and processing of human semen

FIFTH EDITION

Chapter 1 Background 1

1.1 Introduction 1

1.2 The fi fth edition 1 1.3 Scope of the manual 3

PART I. SEMEN ANALYSIS

Chapter 2 Standard procedures 7

2.1 Introduction 7

2.2 Sample collection 10

2.2.1 Preparation 10 2.2.2 Collection of semen for diagnostic or research purposes 11 2.2.3 Sterile collection of semen for assisted reproduction 11 2.2.4 Sterile collection of semen for microbiological analysis 11 2.2.5 Collection of semen at home 12 2.2.6 Collection of semen by condom 12 2.2.7 Safe handling of specimens 13

2.3 Initial macroscopic examination 13

2.3.1 Liquefaction 13 2.3.2 Semen viscosity 14 2.3.3 Appearance of the ejaculate 15 2.3.4 Semen volume 15 2.3.5 Semen pH 16

2.4 Initial microscopic investigation 17

2.4.1 Thorough mixing and representative sampling of semen 17 2.4.2 Making a wet preparation 18 2.4.3 Aggregation of spermatozoa 19 2.4.4 Agglutination of spermatozoa 19 2.4.5 Cellular elements other than spermatozoa 21

2.5 Sperm motility 21

2.5.1 Categories of sperm movement 22 2.5.2 Preparing and assessing a sample for motility 22 2.5.3 Worked examples 25 2.5.4 Lower reference limit 26

2.6 Sperm vitality 26

2.6.1 Vitality test using eosin–nigrosin 27 2.6.2 Vitality test using eosin alone 29 2.6.3 Vitality test using hypo-osmotic swelling 30

2.7 Sperm numbers 32

2.7.1 Types of counting chamber 34 2.7.2 The improved Neubauer haemocytometer 34 2.7.3 Using the haemocytometer grid 35 2.7.4 Care of the counting chamber 35 2.7.5 Fixative for diluting semen 36 2.7.6 Importance of counting suffi cient spermatozoa 36

2.8 Routine counting procedure 37

2.8.1 Determining the required dilution 38 2.8.2 Preparing the dilutions and loading the haemocytometer chambers 39 2.8.3 Assessing sperm numbers in the counting chambers 41 2.8.4 Calculation of the concentration of spermatozoa in semen 43 2.8.5 Worked examples 43 2.8.6 Lower reference limit for sperm concentration 44 2.8.7 Calculation of the total number of spermatozoa in the ejaculate 44 2.8.8 Lower reference limit for total sperm number 44

2.9 Low sperm numbers: cryptozoospermia and suspected azoospermia 45

2.10 When an accurate assessment of low sperm numbers is not required 45

2.10.1 Taking no further action 45 2.10.2 Examination of centrifuged samples to detect spermatozoa 45 2.10.3 Examination of non-centrifuged samples to detect motile spermatozoa 46

2.11 When an accurate assessment of low sperm numbers is required 48

2.11.1 Assessing low sperm numbers in the entire improved Neubauer chamber (phase-contrast microscopy) 48 2.11.2 Assessing low sperm numbers in large-volume disposable chambers (fl uorescence microscopy) 52

2.12 Counting of cells other than spermatozoa 55

2.12.1 Calculation of the concentration of round cells in semen 55 2.12.2 Sensitivity of the method 56 2.12.3 Worked examples 56

2.13 Sperm morphology 56

2.13.1 The concept of normal spermatozoa 57 2.13.2 Preparation of semen smears 58

2.14 Staining methods 62

2.14.1 Traditional fixation and sequential staining 62 2.14.2 Papanicolaou staining procedure for sperm morphology 63 2.14.3 Shorr staining procedure for sperm morphology 65 2.14.4 Rapid staining procedure for sperm morphology 66

2.15 Examining the stained preparation 67

2.15.1 Classification of normal sperm morphology 67 2.15.2 Classifi cation of abnormal sperm morphology 69

2.16 Morphology plates 70

2.17 Analysing a sperm morphology smear 99

2.17.1 Assessment of normal sperm morphology 99 2.17.2 Worked examples 100 2.17.3 Lower reference limit 100 2.17.4 Assessment of abnormal sperm morphology 101 2.17.5 Worked example 101 2.17.6 Assessment of specifi c sperm defects 102

2.18 Assessment of leukocytes in semen 102

2.18.1 Staining cellular peroxidase using ortho-toluidine 103

2.19 Assessment of immature germ cells in semen 107

2.20 Testing for antibody coating of spermatozoa 108 2.20.1 The mixed antiglobulin reaction test 109 2.20.2 The direct immunobead test 111 2.20.3 The indirect immunobead test 113

Chapter 3 Optional procedures 115

3.1 Indices of multiple sperm defects 115

3.1.1 Calculation of indices of multiple morphological defects 115 3.1.2 Worked example 116

3.2 Panleukocyte (CD45) immunocytochemical staining 117

3.2.1 Principle 117 3.2.2 Reagents 118 3.2.3 Procedure 118

3.3 Interaction between spermatozoa and cervical mucus 122

3.3.1 In-vivo (postcoital) test 122 3.3.2 In-vitro tests 125 3.3.3 In-vitro simplifi ed slide test 126

3.3.4 Capillary tube test 127

3.4 Biochemical assays for accessory sex organ function 130 3.4.1 Measurement of zinc in seminal plasma 130 3.4.2 Measurement of fructose in seminal plasma 132 3.4.3 Measurement of neutral -glucosidase in seminal plasma 134

3.5 Computer-aided sperm analysis 136

3.5.1 Introduction 136 3.5.2 Use of CASA to assess sperm motility 137 3.5.3 Use of CASA to estimate sperm concentration 140

3.5.4 Computer-aided sperm morphometric assessment 140

Chapter 4 Research procedures 142

4.1 Reactive oxygen species 142

4.1.1 Introduction 142 4.1.2 Measurement of reactive oxygen species generated by sperm suspensions 143

4.2 Human sperm–oocyte interaction tests 146

4.3 Human zona pellucida binding tests 146

4.4 Assessment of the acrosome reaction 147

4.4.1 Procedure for the fluorescence assessment of acrosomal status 147 4.4.2 Induced acrosome reaction assay 150 4.5 Zona-free hamster oocyte penetration test 152

4.5.1 Protocol 152

4.6 Assessment of sperm chromatin 157

PART II. SPERM PREPARATION

Chapter 5 Sperm preparation techniques 161

5.1 Introduction 161

5.1.1 When spermatozoa may need to be separated from seminal plasma 161 5.1.2 Choice of method 161 5.1.3 Effi ciency of sperm separation from seminal plasma and infectious organisms 162

5.2 General principles 162

5.3 Simple washing 163

5.3.1 Reagents 163 5.3.2 Procedure 163

5.4 Direct swim-up 164

5.4.1 Reagents 164 5.4.2 Procedure 164

5.5 Discontinuous density gradients 165

5.5.1 Reagents 165 5.5.2 Procedure 166

5.6 Preparing HIV-infected semen samples 166

5.7 Preparing testicular and epididymal spermatozoa 167

5.7.1 Enzymatic method 167 5.7.2 Mechanical method 167 5.7.3 Processing sperm suspensions for intracytoplasmic sperm injection 167

5.8 Preparing retrograde ejaculation samples 168

5.9 Preparing assisted ejaculation samples 168

Chapter 6 Cryopreservation of spermatozoa 169

6.1 Introduction 169

6.2 Semen cryopreservation protocols 172

6.2.1 Standard procedure 172 6.2.2 Modifi ed freezing protocols for oligozoospermia and surgically retrieved spermatozoa 175 6.2.3 Labelling of straws and records 176

PART III. QUALITY ASSURANCE

Chapter 7 Quality assurance and quality control 179

7.1 Controlling for quality in the andrology laboratory 179

7.2 The nature of errors in semen analysis 179

7.3 Minimizing statistical sampling error 180

7.4 The quality assurance programme 182

7.5 Laboratory procedures manual 182

7.6 Internal quality control 182

7.6.1 Purchased QC samples 183 7.6.2 Laboratory-made QC samples 183 7.6.3 Stored samples (purchased or laboratory-made) 183 7.6.4 Fresh QC samples (laboratory-made) 184

7.7 Statistical procedures for analysing and reporting within- and among-technician systematic errors 185

7.7.1 The Xbar chart 185 7.7.2 The S chart 188

7.8 QC for percentages 189

7.9 Assessing Xbar and S charts 189

7.9.1 How to recognize out-of-control values 189 7.9.2 Causes of out-of-control values 190 7.9.3 Responses to out-of-control values 191

7.10 Statistical procedures for analysing and reporting among-technician variability 191

7.10.1 Comparing results from two or more technicians 191 7.10.2 Monitoring monthly means 194

7.11 External quality control and quality assurance 194

7.11.1 Assessment of EQC results 196 7.11.2 Responses to out-of-control results 197

7.12 Frequency and priority of quality control 197

7.13 Training 198

7.13.1 Practical hints when experiencing difficulty assessing sperm concentration 198 7.13.2 Practical hints when experiencing diffi culty assessing sperm morphology 200 7.13.3 Practical hints when experiencing diffi culty assessing sperm motility 200 7.13.4 Practical hints when experiencing diffi culty assessing sperm vitality 202

REFERENCES 205

APPENDICES

Appendix 1 Reference values and semen nomenclature 223

A1.1 Reference values 223 A1.2 Nomenclature 225

Appendix 2 Equipment and safety 227

A2.1 Basic supplies needed in an andrology laboratory 227 A2.2 Potential biohazards in an andrology laboratory 230 A2.3 Safety procedures for laboratory personnel 230 A2.4 Safety procedures for laboratory equipment 232 A2.5 Safety precautions when handling liquid nitrogen 233

Appendix 3 Microscopy 234

A3.1 Loading the sample 234 A3.2 Adjusting the oculars 236 A3.3 Focusing the image 236 A3.4 Focusing the oculars 236 A3.5 Focusing the light condenser 236 A3.6 Centring the condenser 237 A3.7 Adjusting the phase rings 237 A3.8 Fluorescence microscopy 237

Appendix 4 Stock solutions 238

A4.1 Biggers, Whitten and Whittingham 238 A4.2 Dulbecco’s phosphate-buffered saline 238 A4.3 Earle’s medium 239 A4.4 Ham’s F-10 medium 239 A4.5 Hanks’ balanced salt solution 240 A4.6 Human tubal fl uid 240 A4.7 Krebs–Ringer medium 240 A4.8 Tris-buffered saline 241 A4.9 Tyrode’s solution 241 A4.10 Papanicolaou stain 241

Appendix 5 Cervical mucus 245

A5.1 Introduction 245 A5.2 Collection and preservation of cervical mucus 246 A5.3 Evaluation of cervical mucus 247

Appendix 6 Record forms for semen and cervical mucus analyses 251

A6.1 Template for a semen analysis recording form 251 A6.2 Template for a cervical mucus recording form 253

Appendix 7 Sampling errors and quality control 254

A7.1 Errors in measurement of sperm concentration 254 A7.2 The importance of understanding sampling errors 256 A7.3 Errors in measurement of percentages 257 A7.4 Production of semen samples for quality control 260 A7.5 Preparation of a video-recording for internal quality control of analysis of sperm motility 261 A7.6 Preparation of diluted semen for internal quality control of determination of sperm concentration 265 A7.7 Preparation of slides for internal quality control of assessment of sperm morphology 268 A7.8 Calibration of equipment 269

Appendix 8 National external quality control programmes for semen analysis 271

Antibiotic Basics for Clinicians: The ABCs of Choosing the Right Antibacterial Agent

 

Antibiotic Basics for Clinicians: The ABCs of Choosing the Right Antibacterial AgentAntibiotic

SECOND EDITION

A Concise Manual of Pathogenic Microbiology

Contents

1 Introduction 

Koch’s Postulate 2

Terminology 3

Major Categories of Pathogenic Microorganisms 4

Transmission of Infectious Disease (Mode of Dissemination) 5

Universal Precautions 6

2 Host-Microbe Interactions 

Resident Microbiota 9

Host Defenses 11

3 Antibiotics and Other Chemotherapeutic Agents 17

Classification of Antibiotics 17

Summary of the Mechanisms of Action 24

4 Antiseptics and Disinfectants 

Physical Control of Microorganisms 25

Chemical Control of Microorganisms 27

5 Gram-Positive Cocci 

Bacterial Taxonomy (An Overview) 31

Clinically Important Gram-Positive Cocci 32

Gram-Positive Cocci Related to Streptococcus Species 38

6 Gram-Positive Bacilli 

Clostridium Species 41

Lactobacillus Species 46

Bacillus Species 46

Listeria Species 49

7 Gram-Positive Bacteria with Rudimentary Filaments 

Corynebacterium diphtheriae 53

Mycobacterium Species 54

8 Gram-Negative Cocci 

Neisseria Species 61

Moraxella catarrhalis 64

Haemophilus influenzae 65

An Overview of Gram-Negative Bacteria 67

9 Gram-Negative Bacilli 

Specimen Collection 69

Media and Laboratory Diagnosis 69

Enterobacteriaceae 71

Glucose Nonfermenters 78

Uncommon Nonfermentative Taxa 81

10 Miscellaneous Gram-Negative Bacteria 

Brucella melitensis 83

Bordetella pertussis 85

Francisella tularensis 86

Pasteurella Species 87

Vibrio cholerae 88

Aeromonas Species 90

Campylobacter Species 90

Legionella Species 92

Gardnerella vaginalis 93

Chlamydia Species 94

Rickettsia rickettsii 95

Bacteroides Species 96

Calymmatobacterium granulomatis 96

Cardiobacterium hominis 96

Streptobacillus moniliformis 96

Spirillum minus 97

11 Spirochetes and Bacteria without a Cell Wall 

Spirochetes 99

Bacteria without a Cell Wall 103

12 Actinomycetes 

Anaerobic Actinomycetes 108

Aerobic Actinomycetes 108

Thermophilic Actinomycetes 112

13 Introduction to Pathogenic Fungi and Superficial Mycoses 

Yeast-Like Fungi 113

Molds or Filamentous Fungi 114

Dimorphic Fungi 114

Superficial Mycoses 115

Mucocutaneous Mycoses 121

14 Subcutaneous and Systemic Mycoses 

Subcutaneous Mycoses 125

Systemic Mycoses 127

Diseases Caused by Dimorphic Fungi 127

Diseases Caused by Yeast-Like Fungi 135

Diseases Caused by Filamentous Fungi 138

Diseases Caused by Miscellaneous Filamentous Fungi 143

15 Unicellular Parasites 

Laboratory Methods in Parasitology 145

Diseases Caused by Lumen-Dwelling Protozoa 146

Blood- and Tissue-Dwelling Protozoa 149

16 Multicellular Parasites 

Lumen-Dwelling Helminths 155

Blood- and Tissue-Dwelling Helminths 161

17 Viruses and Prions 

Laboratory Diagnosis 166

Double-Stranded DNA Viruses 166

Single-Stranded DNA Viruses 171

Double-Stranded RNA Viruses 171

Single-Stranded RNA Viruses 171

Prions 179

Bibliography and Suggested Reading 181

some analytical terms

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كتاب القمة الجزء الاول

 

كتاب القمة الجزء الاول 
فى علم التحاليل الطبية 
رمضان محمد سليمان 

المحتويات 

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دبلومة الفسيولوجى والكيمياء الحيوي جامعة قناة السويس ( الاسماعيلية)2020/2021

دبلومة الفسيولوجى والكيمياء الحيوي 

جامعة قناة السويس ( الاسماعيلية)2020/2021

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