تمكن فريق بحثى يابانى مصري من تطوير وسيله جديده قابله للتطبيق على المسحات الخاصه بالكشف عن فيروس" SARS-CoV-2 " المستجد بمختلف سلالاته بهدف تحسين حساسيه الكشف عن الفيروس باستخدام احد البوليمرات الذكيه لتجنب مشكله التشخيص السلبى الكاذب التى تواجه المتخصصين فى الوقت الراهن استعدادا للموجه القادمه من الفيروس التى يتوقع ان تكون بالغه الضراوه.
Introduction 2
Definitions 2
Internal quality control 6
External quality assessment 16
Introduction 20
When and where bacteraemia may occur 20
Blood collection 20
Blood-culture media 22
Processing of blood cultures 23
Introduction 25
Collection and transportation of specimens 25
Macroscopic inspection 26
Microscopic examination 26
Preliminary identification 28
Susceptibility testing 29
Introduction 30
Specimen collection 30
Culture and interpretation 32
Interpretation of quantitative urine culture results 34
Identification 35
Susceptibility tests 36
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
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
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
Introduction 76
Urethritis in men 77
Genital specimens from women 79
Specimens from genital ulcers 82
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
Introduction 98
Description of bacteria in relation to oxygen requirement 98
Bacteriology 98
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
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
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
Preface, ix
Abbreviations of genera, xi
1.1.2.1 Microcolonies, 5
1.1.2.2 Intracellular colonization, 5
1.1.2.3 Biofilms, 6
1.2.1 Nutritional determinants, 14
1.2.2 Physicochemical determinants, 18
1.2.3 Mechanical determinants, 22
1.2.4 Biological determinants, 23
1.3.1 Age, 28
1.3.2 Host genotype, 29
1.3.3 Gender, 29
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
1.5.1 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
1.6.1 Books, 53
1.6.2 Reviews and papers, 53
2.2.1 Innate defense systems, 58
2.2.2 Acquired immune defense systems, 60
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
2.7.1 Books, 92
2.7.2 Reviews and papers, 92
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
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
4.2.1 Nasal cavity, 117
4.2.2 Other regions of the conducting portion, 119
4.2.3 Respiratory portion, 119
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
4.4.1.1 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
4.4.2.1 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
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
6.1 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
7.4.1 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
8.3.1 Mechanical determinants, 228
8.3.2 Nutritional determinants, 228
8.3.3 Physicochemical determinants, 231
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
8.7.1 Books, 264
8.7.2 Reviews and papers, 264
9.2.1 Innate defense systems, 272
9.2.2 Acquired immune defense system, 275
9.3.1 Esophagus, 276
9.3.2 Stomach, 277
9.3.3 Small intestine, 277
9.3.4 Large intestine, 278
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
9.4.2.1 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
9.7.1 Books, 322
9.7.2 Reviews and papers, 322
10.1 Further reading, 329
Index, 331