Koneman's Color atlas and textbook of diagnostic microbiology:
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Philadelphia [u.a.]
Lippincott Williams & Wilkins
2006
|
| Edition: | 6. ed. |
| Subjects: | |
| Online Access: | Publisher description Inhaltsverzeichnis |
| Item Description: | 5. Aufl. u.d.T.: Color atlas and textbook of diagnostic microbiology |
| Physical Description: | XXXI, 1535, 30 S. Ill. |
| ISBN: | 0781730147 9780781730143 |
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MARC
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| 245 | 1 | 0 | |a Koneman's Color atlas and textbook of diagnostic microbiology |c Washington C. Winn ... |
| 246 | 1 | 3 | |a Color atlas and textbook of diagnostic microbiology |
| 250 | |a 6. ed. | ||
| 264 | 1 | |a Philadelphia [u.a.] |b Lippincott Williams & Wilkins |c 2006 | |
| 300 | |a XXXI, 1535, 30 S. |b Ill. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 500 | |a 5. Aufl. u.d.T.: Color atlas and textbook of diagnostic microbiology | ||
| 650 | 4 | |a Microbiologie clinique - Atlas | |
| 650 | 2 | |a Techniques et procédures de laboratoire | |
| 650 | 4 | |a Diagnostic microbiology |v Atlases | |
| 650 | 4 | |a Microbiology |v Laboratory Manuals | |
| 650 | 4 | |a Laboratory Techniques and Procedures | |
| 650 | 0 | 7 | |a Mikrobiologische Diagnostik |0 (DE-588)4194941-9 |2 gnd |9 rswk-swf |
| 689 | 0 | 0 | |a Mikrobiologische Diagnostik |0 (DE-588)4194941-9 |D s |
| 689 | 0 | |5 DE-604 | |
| 700 | 1 | |a Winn, Washington C. |e Sonstige |4 oth | |
| 700 | 1 | |a Koneman, Elmer W. |d 1932- |e Sonstige |0 (DE-588)125010613 |4 oth | |
| 856 | 4 | |u http://www.loc.gov/catdir/enhancements/fy0712/2005008049-d.html |3 Publisher description | |
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Record in the Search Index
| _version_ | 1804136588220825600 |
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| adam_text | Brief C
Chapter 1
Introduction to Microbiology: Part I: The
Role of the Microbiology Laboratory in the
Diagnosis of Infectious Diseases: Guidelines
to Practice and Management I
Chapter 2
Introduction to Microbiology: Part II:
Guidelines for the Collection, Transport,
Processing, Analysis, and Reporting of
Cultures From Specific Specimen Sources 67
Chapter 3 Laboratory Diagnosis by Immunologic
Methods 111
Chapter 4 Molecular Microbiology 132
Chapter 5
Medical Bacteriology: Taxonomy,
Morphology, Physiology, and Virulence 166
Chapter 6
The Enterohacteriaceae 211
Chapter 7
The Nonfermentath e (• ram Negati ve
Bacilli 303
Chapter 8
Curved Gram Negative Bacilli and
(Kidase Positive Fermenters:
Campylobaeteraceae and Yibrionaccae 392
Dntents
Chapter 9
Miscellaneous Fastidious Gram Negative
Bacilli 429
Chapter 1O
Legionella 549
Chapter 11 Neisseria Species and Moraxella
catarrhalis 566
Chapter 12 Gram Positive Cocci: Part I: Staphylococci
and Related (»ram Positive Cocci 623
Chapter 13
Gram Positive Cocci: Part II: Streptococci,
Enterococci, and the Streptococcus Like
Bacteria 672
Chapter 14
Aerobic and Facultative
Gram Positive Bacilli 765
Chapter 15 Aerobic Actinomycetes 858
Chapter 16 The Anaerobic Bacteria 877
Chapter 17
Antimicrobial Susceptibility Festing 945
ix
X Brief Contents
Chapter 18 Mycoplasmas and Ureapiasmas 1022
Chapter 19 Mycobacteria 1064
Chapter 2O Spirochetal Infections 1125
Chapter 21 Mycology 1151
Chapter 22 Parasitology 1244
Chapter 23 Diagnosis of Infections Caused by
Viruses, Chlamydia, Rickettsia,
and Related Organisms 1327
Appendix I Ectoparasites and Other Invertebrates In
the Clinical Laboratory: A Brief Guide 1420
Appendix II Free Living Antebae 1437
Charts 1442
Color Plates
Index i i
Expanded
Chapter 1
Introduction to Microbiology Part I: The Role of the Microbiology
Laboratory in the Diagnosis of Infectious
Diseases: Guidelines to Practice and
Management
INTRODUCTION 2
Outline of the Book 2
The World of Infectious Disease 2
THE TRIAD OF INFECTIOUS DISEASE 2
The Infectious Agent 3
Classes of Infectious Agents 3
Interactions Between Hosts and Infectious Agents 4
Purpose of Infectious Agents in Nature 4
Virulence 4
The Environment 5
The Infected Host 5
Innate Humoral (Noncellular) Defenses 6
Innate Cellular Defenses 7
Types of Inflammation 7
Adaptive Immunologic Cellular Defenses 7
Adaptive Immunologic Noncellular (Humoral) Defenses 8
Clinical Signs and Symptoms of Infection 8
Indirect Effects of Infectious Agents on Humans 9
PHASES OF THE DIAGNOSTIC CYCLE 9
Preanalytic Phase 10
Specimen Collection 10
Specimen Transport 14
Specimen Receipt and Preliminary Observations 14
Criteria for Rejection of Specimens 14
Cost Effective Approaches in the Preanalytic Phase 15
Analytic Phase 15
Microscopic Examination 15
Processing Specimens 27
Interpretation of Cultures 33
Procedures for Preliminary Identification of Bacterial Isolates 38
Identification of Organisms Other Than Bacteria 39
Testing of Susceptibility to Antimicrobial Agents 39
Cost Effective Approaches in the Analytic Phase 39
Postanalytic Phase 43
Reporting Results 43
Interactions With Epidemiologists 44
Analysis of Results 44
Maintenance of Samples and Records 44
Contents
ADMINISTRATIVE ASPECTS OF THE
MICROBIOLOGY LABORA TORY 45
Government Regulations 45
Risk Management 47
Laboratory Safety 47
General Safety Rules and Regulations 47
Routine Safety Precautions 48
Biologic Agents 50
Universal Precautions 51
Shipping of Specimens and Etiologic Agents 55
Nonbiologic Hazards 56
Bioterrorism 58
Quality Assurance 58
Quality Control 59
Components of a Quality Control Program 60
Monitoring Laboratory Equipment 60
Monitoring Culture Media, Reagents, and Supplies 61
Chapter 2
Introduction to Microbiology Part III Guidelines for the Collection,
Transport, Processing, Analysis, and
Reporting of Cultures from Specific
Specimen Sources
INFECTIONS OF THE RESPIRATORY TRACT 68
Infections of the Upper Respiratory Tract 71
Indigenous Flora 71
Pharyngitis 72
Infections of the Oral Cavity Other Than Pharyngitis 73
Infections of the Nasopharynx and Nasopharyngeal Cultures 74
Otitis Media and Sinusitis 74
Epiglottitis 74
Laryngitis 74
Other Infections of the Upper Respiratory Tract 74
Infections of the Lower Respiratory Tract 75
Tracheobronchitis 75
Bronchiolitis 75
Pneumonia 75
Chronic Pneumonia 76
Empyema 76
Pneumonia in Special Populations 76
Collection of Specimens for the Diagnosis of Lower
Respiratory Infection 76
Laboratory Diagnosis of Pneumonia 78
xi
XII Expanded Contents
INFECTIONS OF THE GASTROINTESTINAL
TRACT 79
Lower Intestinal Infections 79
Clinical Symptoms 79
Collection of Fecal Specimens 81
Epidemiologic Considerations in the Evaluation of Patients With
Gastroenteritis 81
Upper Intestinal Infections 81
Clinical Symptoms 81
Obtaining Specimens From the Upper Gastrointestinal Tract 82
URINARY TRACT INFECTIONS 82
Clinical Signs and Symptoms 82
Host Factors 83
Collection of Urine Samples for Culture 83
Midstream Urine Specimens 83
Other Voided Urine Specimens 84
Catheter Collections 85
Suprapubic Aspiration 85
Culture of Urine Specimens 85
Screening Tests for Urinary Tract Infection 86
Screening Tests for Bacteriuria 86
Screening Tests for Pyuria 86
INFECTIONS OF THE GENITAL TRACT 87
Sexually Transmitted Infections 87
Urethritis and Cervicitis 87
Genital Ulcer Disease 88
Genital Infections Transmitted by Nonsexual Means 88
Vaginitis and Vaginosis 88
Infections of the Upper Female Genital Tract 89
Systemic Complications of Genital Infections 89
Diagnosis of Genital Tract Infections 89
Diagnosis of Urethritis, Cervicitis, and Vaginitis 89
Diagnosis of Genital Ulcer Disease and Venereal Warts 90
Collection of Genital Specimens 90
INFECTIONS OF THE BONES AND JOINTS 91
Clinical Presentation 91
Diagnosis of Infections of the Bones and Joints 91
INFECTIONS OF THE CENTRAL NERVOUS
SYSTEM 92
Meningitis 92
Encephalitis and Brain Abscess 93
Diagnosis of Central Nervous System Infections 93
Collection of Specimens 93
Assessing the Inflammatory Response and Microscopic Techniques 93
Direct Detection of Antigen and Nucleic Acid 94
Serologic Diagnosis 95
Diagnosis by Culture 95
WOUNDS, ABSCESSES, AND CELLULITIS 95
Clinical Presentation 95
Diagnosis of Wound Infections, Abscesses, and Cellulitis 95
Collection of Specimens 95
Microscopic Examination of Specimens 96
Culture 96
EYE INFECTIONS 96
Clinical Presentation 96
Conjunctivitis 96
Keratitis 97
Uveitis and Endophthalmitis 97
Diagnosis of Eye Infections 97
Collection of Specimens 97
Microscopic Examination 97
Culture 97
INFECTIONS OF THE BLOOD 97
Clinical Presentation and Pathogenesis 97
Bacteremia and Septicemia 97
Types of Bacteremia 97
Intravascular Infection 98
Catheter Associated Bacteremia and Sepsis 100
Collection of Blood Cultures 100
Contamination With Skin Flora 100
Number and Timing of Cultures 101
Culture Media 101
Systems for Processing Blood Cultures 102
Manual Blood Culture Systems 102
Lysis Centrifugation Blood Culture System 103
Automated and Computerized Blood Culture Systems 103
Comparative Studies 104
Special Considerations 105
Fastidious Organisms and Endocarditis 105
Catheter Associated Bacteremia and Sepsis 105
Tissues and Biopsies 105
Chapter 3
Laboratory Diagnosis by Immunologic
Methods ANTIGENS AND ANTIBODIES: BASIC
DEFINITIONS 112
MONOCLONAL ANTIBODIES 113
TYPES OF ANTIGEN ANTIBODY REACTIONS
USED IN DIAGNOSTIC SEROLOGY 114
Precipitin Reactions 114
Complement Fixation and Hemagglutination Inhibition 116
Agglutination Reactions 116
SOLID PHASE IMMUNOASSA Y METHODS 119
Enzyme Immunoassays for Antibody Detection 119
Enzyme Immunoassay Antibody Capture Methods for
IgM Detection 122
Enzyme Immunoassays for Antigen Detection 122
IMMUNOFLUORESCENCE TECHNIQUES 125
Immunofluorescence Techniques for Antigen Detection 125
Immunofluorescence Techniques for Antibody Detection 125
Chapter 4
Molecular Microbiology NUCLEIC ACIDS—THE BASICS OF DNA
ANDRNA 133
Structure of DNA 133
Structure of RNA 134
Function of DNA—Information Storage 135
Function of RNA—Information Transfer 135
Reading (Transcription) and Interpretation (Translation)
of the Genetic Code 135
SIGNAL AMPLIFICA TION METHODS 137
Nucleic Acid Probes 137
Clinical Applications 137
Hybrid Capture 137
Clinical Applications 138
Branched DNA 139
Clinical Applications 139
In Situ Hybridization 139
Clinical Applications 140
NUCLEIC ACID AMPLIFICA TION 141
Basics of the Polymerase Chain Reaction 141
Clinical Applications 143
Other Methods of Nucleic Acid Amplification 143
Clinical Applications 144
Modifications of PCR 144
RT PCR 144
Clinical Applications 145
Broad Range PCR 145
Clinical Applications 145
Multiplex PCR 146
Clinical Applications 146
Nested PCR 146
Clinical Applications 146
POSTAMPLIFICA TION ANAL YSIS 147
Traditional Methods of Detection 147
Gel Electrophoresis/Southern Blot Analysis 147
Enzymatic Detection of Amplified Products 147
Clinical Applications 148
Reverse Hybridization 148
Clinical Applications 148
DNA Sequencing 148
Traditional DNA Sequencing 149
Clinical Applications 149
Sequencing by Synthesis (Pyrosequencing) 149
Clinical Applications 150
Microarray Analysis 150
Clinical Applications 151
REAL TIME NUCLEIC ACID AMPLIFICA TION 151
Methods of Detecting the Products of Real Time Amplification 151
SYBR Green 151
Hybridization Probes 151
Clinical Applications 154
STRAIN TYPING 156
Non Amplification Based Typing 156
Pulsed Field Gel Electrophoresis 156
Amplification Based Typing 157
PCR RFLP 157
Rep PCR 158
Clinical Applications of Microbial Typing 158
CONCLUSION 158
Chapter 5
Medical Bacteriology: Taxonomy,
Morphology, Physiology, and Virulence TAXONOMY: CLASSIFICATION,
NOMENCLATURE, AND IDENTIFICATION
OF BACTERIA 167
Expanded Contents XJH
The Naming of Bacteria 167
Phenotypic Identification of Bacteria 168
Phylogenetic Criteria for Classification of Bacteria 168
BASIC BACTERIAL ANATOMY AND
PHYSIOLOGY 177
Bacterial Size and Shape 177
Nuclear Structure, DNA Replication, Transcription,
and Translation 178
Cytoplasm 181
Cytoplasmic Membrane 182
Bacterial Cell Wall Structure 182
Gram Positive Bacterial Cell Walls 184
Gram Negative Bacterial Cell Walls 185
Acid Fast Bacterial Cell Walls 188
Bacterial Endospores 189
Bacterial Surface Structures 190
Capsules 190
Flagelia 190
Fimbriae (Pili) 191
Genetic Exchange and Recombination in Bacteria 192
Requirements for Bacterial Growth and Metabolism 195
Carbon 195
Carbon Dioxide 195
Oxygen 195
Nitrogen 195
Growth Factors 196
Kinetics of Bacterial Cell Growth 196
General Bacterial Metabolism and Energy Generation 196
Fermentation 196
Utilization of Pyruvate 198
BACTERIAL VIRULENCE FACTORS AND
PATHOGENICITY 200
Definitions and Concepts 200
Requirements for Pathogenicity 203
Virulence Factors of Microorganisms 204
Adhesins 204
Aggressins 204
Exotoxins and Endotoxins 205
Bacterial Superantigens 207
Chapter 6
The Enterobacteriaceae CHARACTERISTICS FOR PRESUMPTIVE
IDENTIFICATION 213
Screening Characteristics 213
Carbohydrate Utilization 213
Cytochrome Oxidase Activity 215
Nitrate Reduction 216
CULTURE MEDIA USED FOR DETECTION OF
CARBOHYDRA TE FERMENT A TION 216
Use of Kligler Iron Agar and Triple Sugar Iron Agar 216
Biochemical Principles 217
SELECTION OF PRIMARY ISOLA TION MEDIA 218
Chemicals and Compounds Used in Selective Media 219
Selective Isolation Media 221
XIV Expanded Contents
Highly Selective Isolation Media Used Primarily for
Gastrointestinal Specimens 222
Enrichment Media 222
Guidelines for Choosing Selective Isolation Media 222
DIFFERENTIAL IDENTIFICATION
CHARACTERISTICS 223
Indole Production 224
Methyl Red Test 224
Voges Proskauer Test 225
Citrate Utilization 225
Urease Production 225
Decarboxylation of Lysine, Ornithine, and Arginine 225
Phenylalanine Deaminase Production 226
Hydrogen Sulfide Production 226
Motility 227
TAXONOMY OF THE ENTEROBACTERIACEAE 228
Classification of Enterobacteriaceae by Tribes 228
Key Identification Characteristics for the Most Common Species 228
Tribe Escherichieae 235
Tribe Edwardsielleae 250
Tribe Salmonelleae 251
Tribe Citrobactereae 258
Tribe Klebsielleae 259
Tribe Proteeae 267
Tribe Yersinieae 269
Tribe Erwinieae 274
Miscellaneous New Genera of Enterobacteriaceae 274
Identification Characteristics of Newer Enterobacteriaceae Til
Clinical Significance of Newer Enterobacteriaceae Til
QUICK SCREENING METHODS FOR RAPID
IDENTIFICATION 282
Commercial Screening Kits 282
Chromogenic Agar Media 283
CLASSIC IDENTIFICA TION SYSTEMS 284
Checkerboard Matrix 284
Branching Flow Diagrams 284
Computer Aided Schemes 285
NUMERIC CODING SYSTEMS 285
Reading Octal Codes in Numeric Code Registers 286
Estimated Frequency of Occurrence 287
Calculation of Likelihood 287
Resolving Discrepancies 287
PACKAGED KIT IDENTIFICA TION SYSTEMS 287
Overview of Packaged Systems 287
Specific Identification Systems 289
API 20E 289
BBL Crystal Entenc Noi.fernienter ID System 289
RapID onE System 289
Enterotube ii 290
Micro ID 291
Bioiog GN2 Micropiate 291
MicroScan System 291
Sensititre System 291
SEMIAUTOMATED AND AUTOMATED
IDENTIFICATION SYSTEMS 292
MicroScan Walkaway 292
Vitek System 292
Sensititre Gram Negative Autoldentification System 293
The Phoenix System 293
The OmniLog ID System 293
Chapter 7
The Nonfermentative Gram Negative Bacilli
Part I: Metabolism of the Nonfermenters
FERMENTATIVE AND OXIDATIVE
METABOLISM 309
The Embden Meyerhof Parnas Pathway 309
The Entner Doudoroff Pathway 311
The Warburg Dickens Hexose Monophosphate Pathway 312
INITIAL CLUES THAT AN UNKNOWN
ISOLA TE IS A NONFERMENTER 312
Lack of Evidence for Glucose Fermentation 312
Positive Cytochrome Oxidase Reaction 312
Failure to Grow on MacConkey Agar 313
TESTS USED IN THE IDENTIFICATION OF
NONFERMENTERS 313
Utilization of Glucose 313
Motility 313
Pigment Production 314
Hydrolysis of Urea 314
Nitrate Reduction 315
Denitrification of Nitrates and Nitrites 315
Indole Production 315
Decarboxylation 315
Esculin Hydrolysis 315
Flagella Stains 315
Leifson Method 315
Ryu Method 316
Wet Mount Technique 316
Flagellar Morphology 316
Part III Taxonomy, Biochemical
Characteristics, and Clinical Significance of
Medically Important Genera of
Nonfermenters
ORGANISMS THAT ARE MOTILE WITH
POLAR FLAGELLA 316
Pseudomonads 316
Family Pseudomonadaceae 317
Genus Pseudomonas—rRNA Group I 317
Family Burkholderiaceae 323
rRNA Group II 323
Genus Burkholderia—Pseudomallei Group 323
Genus Ralstonia and Genus Cupriavidus 328
Genus Pandoraea 329
Genus Inquilinus 331
Genua Lautropia 331
Family Comamonadaceae 331
rRNA Group III 331
Acidovorans Group 331
Facilis Delafieldii Group 332
Family Caulobacteraceae 332
rRNA Group IV 332
Brevundimonas Diminuta Group 332
Family Xanthomonadaceae 332
rRNA Group V 332
Genus Stenotrophomonas 332
Family Sphingomonadaceae 334
Genus Sphingomonas 334
Family Oceanospirillaceae 334
Genus Balneatrix 334
Family Oxalobacteraceae 334
Genus Massilia 334
Genus Herbaspirillum 334
Family Alteromonadaceae 336
Genus Shewanella—Hydrogen Sulfide Producing Group 336
Genus Alishewanella—Halophilic Group 337
Family Halomonadaceae 337
Genus Halomonas 337
Family Methylobacteriaceae 337
Genus Methylobacterium 337
Genus Roseomonas 338
Unnamed Species 339
Laribacter hongkongensis 339
ORGANISMS THAT ARE MOTILE WITH
PERITRICHOUS FLAGELLA 340
Family Alcaligenaceae 340
Genus Alcaligenes 340
Genus Achromobacter 340
Genus Bordetella 343
Genus Kerstersia 344
Genus 0/#e//a 344
Family Rhizobiaceae 344
Genus Rhizobium (Formerly Agrobacterium) 344
Family Brucellaceae 345
Genus Ochrobactrum 345
ORGANISMS THAT ARE NONMOTILE AND
OXIDASE POSITIVE 345
Family Flavobacteriaceae 345
Chryseobacterium, Empedobacter, and Unnamed CDC Groups 346
Weeksella and Bergeyella 348
Genus Myroides 348
Family Sphingobacteriaceae 348
Sphingobacterium and Pedobacter 348
Family Moraxellaceae 349
Genus Moraxella 349
Genus Psychrobacter and CDC EO Groups 350
Family Neisseriaceae 353
Genus Neisseria 353
Gilardi Rod Group 1 353
ORGANISMS THAT ARE NONMOTILE AND
OXIDASE NEGATIVE 353
Genus Acinetobacter 353
CDC Group NO 1 355
Bordetella holmesii (CDC Group NO 2) 355
CDC Group EO 5 355
Expanded Contents XV
Part III: Approach to Recovery and
Identification of Nonfermenters
LEVELS OF SERVICE IN IDENTIFICATION OF
NONFERMENTERS 355
GUIDELINES FOR RECOVERY OF
NONFERMENTERS 356
IDENTIFICATION OF MOST COMMON SPECIES 356
Pseudomonas aeruginosa 356
Acinetobacter baumannii 357
Stenotrophomonas maltophilia 357
METHODS FOR IDENTIFICATION USING
CONVENTIONAL TESTS 357
Weyant (CDC), Gilardi, and Pickett Identification Schemes 358
Practical Approach to Identification of Nonfermenters 358
Computer Aided Schemes 359
COMMERCIAL KIT SYSTEMS 359
The Oxi/Ferm Tube 359
The API 20E System 362
The API 20NE System 362
The Remel N/F System 362
The Crystal Enteric/Nonfermenter System 367
The RapID NF Plus System 367
The Biolog System 373
AUTOMA TED IDENTIFICA TION SYSTEMS 373
The Vitek Legacy System 373
The Vitek 2 System 374
The Microscan Walkaway 96, Walkaway 40, and
Autoscan 4 Systems 375
The Sensititre AP80 System 375
The Phoenix System 375
SELECTION OF A SYSTEM 375
Chapter 8
Curved Gram Negative Bacilli and Oxidase
Positive Fermenters: Campylobacteraceae and
Vibrionaceae Part I: Curved Rods: Campylobacter,
Wolinella, Arcobacter Helicobacter, and
Related Bacteria
HISTORICAL BACKGROUND 393
CLASSIFICATION OF CAMPYLOBACTER AND
RELATED TAXA 393
Campylobacter Species 395
Campylobacter jejuni Subsp. jejuni 395
Other Campylobacter Species 398
Former Wolinella and Bacteroides Species Included in the Family
Campylobacteraceae 402
Genus Arcobacter 403
Genus Helicobacter 403
H. pylori 404
Other Medically Important Helicobacter Species 404
Nonhuman Helicobacter Species 405
Other Microaerophilic Gram Negative Bacilli 405
XVi Expanded Contents
DEFINITIVE IDENTIFICATION OF
CAMPYLOBACTERS AND RELATED
BACTERIA 406
Rapid Identification of Campylobacters From Colonies and
From Stool Specimens 406
Nonculture Tests 406
Direct Detection Methods 407
Culture and Isolation of Helicobacter pylori 407
Specimens for Recovery of H. pylori 407
Isolation Procedure 407
Identification of H. pylori 407
Biopsy Urease Test (CLO Test) 408
Noninvasive Tests To Diagnose H. pylori Infection 408
Accuracy of Invasive and Noninvasive Tests To Diagnose
H. pylori Infection 408
Enterohepatic Helicobacters 408
Part II: The Families Vibrionaceae and
Aeromonadaceae
PHYLOGENY OF THE VIBRIONACEAE 408
Genus Vibrio 408
Taxonomy 409
Description and Associated Clinical Syndromes of Vibrio
Species of Human Importance 409
Methods for Laboratory Isolation of Vibrios 414
Biochemical Characterization and Laboratory Identification
of Vibrio Species 416
GENERA LISTONELLA, PHOTOBACTERIUM AND
SHEWANELLA 417
AEROMONAS AND PLESIOMONAS 417
Genus Aeromonas 417
Taxonomy 419
Clinical Significance 419
Aeromonas Species in Medicinal Leeches 420
Laboratory Recovery of Aeromonas Species From Clinical Specimens 420
Laboratory Identification of Aeromonas Species 420
Genus Plesiomonas 422
Laboratory Isolation and Identification 422
GENUS CHROMOBACTERIUM 422
Chapter 9
Miscellaneous Fastidious Gram Negative
Bacilli HAEMOPHILUS SPECIES 431
Taxonomy of Haemophilus and Related Organisms 431
Haemophilus influenzae 433
Haemophilus influenzae Type B Vaccines 433
Infections Caused by Haemophilus Species 435
Meningitis 435
Epiglottitis 439
Otitis Media 439
Sinusitis 440
Bronchitis and Chronic Obstructive Pulmonary Disease 440
Pneumonia 440
Bacteremia and Infectious Complications of Bacteremia 441
Endocarditis 441
Urogenital, Maternal, and Perinatal Infections 441
Ocular Infections 442
Brazilian Purpuric Fever 442
Miscellaneous Haemophilus influenzae Infections 443
Haemophilus parainfluenzae 443
Haemophilus aphrophilus and Haemophilus paraphrophilus 444
Other Haemophilus Species 444
Haemophilus ducreyi 444
Laboratory Diagnosis of Haemophilus Infections 444
Direct Examination of Clinical Specimens 444
Culture of Haemophilus Species 445
Identification of Haemophilus Species 446
Laboratory Diagnosis of Haemophilus ducreyi Infection 449
Antimicrobial Susceptibility of Haemophilus Species 451
ACTINOBACILLUS SPECIES 452
Actinobacillus actinomycetemcomitans 452
Clinical Significance 452
Cultural Characteristics and Identification 453
Antimicrobial Susceptibility 455
Actinobacillus ureae 455
Actinobacillus hominis 458
Animal Species in the Genus Actinobacillus 458
PASTEURELLA AND MANNHEIMIA
SPECIES 458
Taxonomy and Characteristics of the Genus Pasteurella 458
Pasteurella multocida 459
Clinical Significance and Virulence 459
Cultural Characteristics and Identification 462
Antimicrobial Susceptibility 464
Other Pasteurella Species Isolated From Human Infections 465
Pasteurella pneumotropica [ Actinobacillus pneumotropica ) 465
Pasteurella aerogenes { Actinobacillus aerogenes ) 465
Pasteurella dagmatis 465
Pasteurella canis and Pasteurella stomatis 466
Pasteurella bettyae 466
Pasteurella caballi 466
Pasteurella gallinarum 466
Mannheimia Species (Formerly the Pasteurella
haemolyticalPasteurella granulomatis Complex) 467
CARDIOBACTERIUM HOMINIS 467
Taxonomy 467
Clinical Significance 468
Cultural Characteristics and Identification 468
Antimicrobial Susceptibility 468
EIKENELLA CORRODENS 470
Taxonomy and Virulence 470
Clinical Significance 470
Cultural Characteristics and Identification 471
Antimicrobial Susceptibility 471
KINGELLA AND SUTTONELLA SPECIES 472
Taxonomy 472
Clinical Significance 472
Cultural Characteristics and Identification 473
Antimicrobial Susceptibility 474
HUMAN CAPNOCYTOPHAGA SPECIES 474
Taxonomy 474
Clinical Significance 474
Cultural Characteristics and Identification 475
Antimicrobial Susceptibility 475
CANINE CAPNOCYTOPHAGA SPECIES 477
Taxonomy 477
Clinical Significance 477
Cultural Characteristics and Identification 477
Antimicrobial Susceptibility 478
DYSGONOMONAS SPECIES 479
CDC GROUPS EF 4A AND EF 4B 479
SIMONSIELLA SPECIES 481
STREPTOBACILLUS MONIUFORMIS 481
Taxonomy 481
Clinical Significance 481
Cultural Characteristics and Identification 481
Antimicrobial Susceptibility 482
BRUCELLA SPECIES 482
Epidemiology of Brucellosis 482
Taxonomy of Brucella Species 484
Virulence of Brucella Species 484
Clinical Spectrum of Brucellosis 486
Serologic Diagnosis of Brucellosis 486
Isolation and Cultural Characteristics 488
Identification of Brucella Species 488
Treatment of Brucellosis 490
FRANCISELLA TULARENSIS 491
Epidemiology of Tularemia 491
History and Taxonomy 491
Virulence of F. tularensis 492
Clinical Spectrum of Tularemia 493
Isolation and Cultural Characteristics 494
Serologic Diagnosis of Tularemia 495
Treatment of Tularemia 495
BARTONELLA SPECIES 497
Taxonomy and Epidemiology of Bartonella Species 497
Clinical Significance of Bartonella Species 499
Oroya Fever and Verruga Peruana 500
Classical and Urban Trench Fever 500
Bacillary Angiomatosis 501
Peliosis 501
Fever and Bacteremia 502
Endocarditis 502
Cat Scratch Disease (CSD) 503
Miscellaneous Infections 504
Detection, Isolation, and Identification of Bartonella Species 505
Specimen Types 505
Culture 505
Gram Stain and Colony Morphology 505
Identification Methods 505
Serologic Diagnosis of Bartonella Infections 507
In Vitro Antimicrobial Susceptibility 509
AFIPIA SPECIES 510
Taxonomy and Clinical Significance 510
Isolation and Identification 510
Antimicrobial Susceptibility 510
BORDETELLA SPECIES 510
Background and Taxonomy of Bordetella Species 510
Epidemiology of Pertussis 512
Clinical Significance of Bordetella pertussis 512
Pertussis Vaccines 513
Clinical Significance of Other Bordetella Species 516
Bordetella parapertussis 516
Bordetella bronchiseptica 516
Bordetella hinzii 517
Bordetella holmesii 517
Bordetella trematum 517
Expanded Contents XVH
Isolation and Identification of Bordetella Species 517
Specimens and Culture Media 517
Direct Fluorescent Antibody Test 518
Cultural Characteristics and Identification 519
New Technologies for Detection and Identification
of Bordetella pertussis 519
Serologic Tests for Diagnosis of Pertussis 521
Treatment of Pertussis 522
Antimicrobial Susceptibility Testing of Bordetella Species 522
Chapter 1O
Legionella TAXONOMY AND CHARACTERISTICS OF THE
GENUS LEGIONELLA 550
CLINICAL AND PATHOLOGIC SPECTRUM OF
LEGIONELLOSIS 551
Predisposing Factors 552
Pathology and Pathogenesis 552
EPIDEMIOLOGIC AND ECOLOGIC ASPECTS OF
LEGIONELLOSIS 553
Incidence 553
Legionellaceae in the Environment 553
Natural Habitats 553
Man Made (Artificial) Aquatic Habitats 554
Legionellosis in Travelers 554
Nosocomial Outbreaks of Legionellosis 555
LABORATORY DIAGNOSIS 555
Selection, Collection, and Transport of Clinical Specimens 555
Direct Examination of Clinical Specimens 556
Gross Examination and Microscopic Examination of Stained Materials 556
Microscopic Examination of Stained Materials 556
Direct Fluorescent Antibody (DFA) Procedure 556
Antigen Detection in Urine and Body Fluids 557
DETECTION OF LEGIONELLA
IN CLINICAL SPECIMENS 557
Isolation of Legionella Species From Clinical Specimens 557
Biopsy, Surgical Removal, and Autopsy Tissue 557
Pleural Fluid and Transtracheal Aspirates 557
Acid Wash Decontamination Procedure for Sputum and Other
Contaminated Specimens 557
Blood Cultures 557
Identification of Legionella Species 558
Antimicrobial Susceptibility and Treatment 558
Serum Indirect Immunofluorescent Antibody Test 560
Molecular Diagnosis 560
ENVIRONMENTAL MICROBIOLOGY STUDIES 561
Isolation of Legionella From Environmental Samples 561
Typing of Legionella Isolates 561
Chapter 11
Neisseria Species and Moraxella catarrhalis
TAXONOMY OF THE FAMILY NEISSERIACEAE
AND THE FAMIL Y MORAXELLACEAE 568
GENERAL CHARACTERISTICS OF THE GENUS
NEISSERIA 569
XViM Expanded Contents
CLINICAL SIGNIFICANCE OF NEISSERIA
SPECIES 570
Neisseria gonorrhoeae 570
Epidemiology 570
Infections Caused by N. gonorrhoeae 573
Neisseria meningitidis 578
Epidemiology 578
Infections Caused by N. meningitidis 580
Meningococcal Prophylaxis and Meningococcal Vaccines 582
Other Neisseria Species 584
CLINICAL SIGNIFICANCE OF MORAXELLA
CATARRHALIS 585
ISOLA TION OF NEISSERIA SPECIES 588
Neisseria gonorrhoeae 588
Direct Gram Stained Smears 588
Specimen Collection 588
Specimen Transport 589
Selective Culture Media: Inoculation and Incubation 590
Neisseria meningitidis 591
Laboratory Safety 591
Direct Gram Stained Smears and Direct Capsular Antigen Tests 591
Specimen Collection and Transport 591
Isolation and Incubation 591
IDENTIFICATION OF NEISSERIA SPECIES 592
Colony Morphology 592
Gram Stain and Oxidase Test 593
Superoxol Test 593
Differentiation of Other Organisms on Selective Media 593
Presumptive Criteria for Identification of N. gonorrhoeae 593
Identification Tests for Neisseria Species 593
Carbohydrate Utilization Tests 594
Conventional CTA Carbohydrates 594
Rapid Carbohydrate Utilization Test 594
RIM Neisseria Test (Rapid Identification Method Neisseria) 594
Other Carbohydrate Utilization Methods. 594
Chromogenic Enzyme Substrate Tests 594
Gonochek II 595
BactiCard Neisseria 595
Immunologic Methods for Culture Confirmation of N. gonorrhoeae 596
Direct Fluorescent Monoclonal Antibody Test 596
Coagglutination Tests 596
GonoGen II Test 596
Multitest Identification Systems 597
DNA Probe Test for Culture Confirmation of N. gonorrhoeae 597
Nucleic Acid Hybridization and Amplification Tests for
N. gonorrhoeae 597
Molecular Methods for Detection of N. meningitidis 599
CULTURAL CHARACTERISTICS OF NEISSERIA
SPECIES 600
Neisseria gonorrhoeae 600
Neisseria meningitidis 602
Other Neisseria Species 603
Neisseria lactamica 603
Neisseria cinerea 603
Neisseria flavescens 603
Neisseria subflava Biovars, Neisseria mucosa. and Neisseria sicca 603
Neisseria polysaccharea 604
Neisseria eiongata Subspecies 604
Neisseria gonorrhoeae Subspecies kochii (¦¦Neisseria kochii ) 604
Atypical and Non Human Neisseria Species 604
CULTURAL CHARACTERISTICS AND
IDENTIFICATION OF MORAXELLA
CATARRHALIS 604
ANTIMICROBIAL SUSCEPTIBILITY OF
NEISSERIA SPECIES 605
Neisseria gonorrhoeae 605
Neisseria meningitidis 607
ANTIMICROBIAL SUSCEPTIBILITY OF
MORAXELLA CATARRHALIS 608
Chapter 12
Gram Positive Cocci Part I: Staphylococd and Related Gram
Positive Cocci
TAXONOMY OF STAPHYLOCOCCI AND
RELA TED GRAM POSITIVE COCCI 624
CLINICAL SIGNIFICANCE OF STAPHYLOCOCCI
AND RELA TED GRAM POSITIVE COCCI 625
Staphylococcus aureus Subsp. aureus 625
Coagulase Negative Staphylococci 638
Staphylococcus epidermidis 638
Staphylococcus saprophyticus Subsp. saprophyticus 641
Other Coagulase Negative Staphylococci 642
Micrococcus Species and Related Genera 642
Rothia mucilaginosa 642
ISOLATION AND PRELIMINARY
DIFFERENTIATION OF STAPHYLOCOCCI
AND RELA TED GRAM POSITIVE COCCI 643
Direct Gram Stained Smears 643
Isolation From Clinical Specimens 643
Colony Morphology 643
The Catalase Test 644
Methods for Differentiating Micrococci and Staphylococci 644
Fermentation of Glucose 644
Susceptibility to Lysostaphin 645
Production of Acid From Glycerol in the Presence of Erythromycin 645
Susceptibility to Furazolidone 645
Modified Oxidase Test 645
Susceptibility to Bacitracin 645
IDENTIFICATION OF STAPHYLOCOCCUS
AUREUS 645
Slide Coagulase Test 645
Tube Coagulase Test 646
Alternative Coagulase Test Procedures 646
Latex Agglutination 646
Passive Hemagglutination 646
Additional Confirmatory Tests 647
Deoxyribonuclease (DNase) Test 647
Thermostable Endonuclease Test 648
Mannitol Fermentation 648
Other Methods for Identification of Staphylococcus aureus 648
Rapid Tests for Detection of Methicillin Resistance 648
Differentiation of Coagulase Positive Staphylococci
of Veterinary Origin 648
IDENTIFICATION OF COAGULASE NEGATIVE
STAPHYLOCOCCI 649
Conventional Identification Methods 649
Production of Phosphatase for Identification of
Staphylococcus epidermidis 650
Pyrrolidonyl Arylamidase Activity 650
Susceptibility to Polymyxin B 652
Omithine Decarboxylase Test (ODC) 652
Urease Production 655
Acetoin Production 655
Susceptibility to Deferoxamine 655
Susceptibility to Novobiocin for Identification of Staphylococcus
saprophyticus 655
Commercial Identification Systems 655
RapiDEC Staph 656
API Staph IDENT 656
API Staph 656
API ID32 Staph 656
Vitek Gram Positive Identification (GPI) Card 657
MicroScan Rapid Pos Combo Panel 657
MicroScan Pos ID Panel 657
BBL Crystal Gram Positive (GP) Identification System 657
Staf Sistem 18 R 658
Staph Zym 658
Microbact Staphylococcal 12S 658
Microbial Identification System 658
Biolog Microplate Identification System 658
Molecular Identification and Typing Methods for Staphylococci 658
Identification of Micmcoccus and Related Species 661
Identification of Rothia mucilaginosa 661
LABORATORY APPROACH TO THE
IDENTIFICATION OF STAPHYLOCOCCI 661
Chapter 13
Gram Positive Cocci Part III Streptococci, Enterococci, and the
Streptococcus Like Bacteria
GENERAL CHARACTERISTICS OF THE
STREPTOCOCCI 674
GROUP A p HEMOLYTIC STREPTOCOCCI
(STREPTOCOCCUS PYOGENES) 676
Virulence Factors 676
Clinical Significance 679
GROUP B p HEMOLYTIC STREPTOCOCCI
(STREPTOCOCCUS AGALACTIAE) 683
Virulence Factors 683
Clinical Significance 684
GROUP C AND GROUP G /3 HEMOLYTIC
STREPTOCOCCI 688
GROUP F p HEMOL YTIC STREPTOCOCCI 689
OTHER STREPTOCOCCI IN THE PYOGENIC
COCCI GROUP 689
STREPTOCOCCUS PNEUMONIAE 689
Virulence Factors 689
Pneumococcal Vaccines 690
Clinical Significance 691
Expanded Contents XJX
VIRIDANS STREPTOCOCCI 693
THEANGINOSUS GROUP: STREPTOCOCCUS
ANGINOSUS, STREPTOCOCCUS
CONSTELLATUS, AND STREPTOCOCCUS
INTERMEDIUS 695
GROUP D STREPTOCOCCI: THE
STREPTOCOCCUS BOVIS/STREPTOCOCCUS
EQUINUS COMPLEX AND RELATED
SPECIES 697
STREPTOCOCCUS SUIS 698
OTHER VIRIDANS STREPTOCOCCI ISOLATED
FROM ANIMALS 700
MISCELLANEOUS STREPTOCOCCI 700
ENTEROCOCCUS SPECIES 700
Taxonomy 700
Virulence Factors 701
Clinical Significance 701
Genus Melissococcus 704
THE STREPTOCOCCUS LIKE BACTERIA 704
Abiotrophia and Granulicatella Species 704
Aerococcus and Helcococcus Species 705
Leuconostoc Species 706
Pediococcus and Tetragenococcus Species 706
Gemella Species 707
Vagococcus Species 707
Alloiococcus Species 708
Globicatella Species 708
Facklamia Species 708
Dolosigranulum, Ignavigranum, and Dolosicoccus Species 709
Eremococcus Species 709
Genus Lactococcus 709
ISOLATION AND IDENTIFICATION OF
STREPTOCOCCI AND
STREPTOCOCCUS LIKE BACTERIA 709
Direct Gram Stained Smears 709
Culture Media 710
Hemolysis on Blood Agar 710
Nonculture, Direct Detection Techniques for Group A
|5 Hemolytic Streptococci in Pharyngeal Specimens 711
Nonculture, Direct Detection Techniques for Group B
fj Hemolytic Streptococci and Streptococcus pneumoniae 712
Colony Morphology and Catalase Testing 713
Recognition and Preliminary Characterization of Streptococci
and the Streptococcus Like Bacteria 713
Presumptive Identification of Streptococci 715
Susceptibility to Bacitracin 715
Susceptibility to Sulfamethoxazole Trimethoprim (SXT) 715
CAMP Test and Pigment Production 717
Hydrolysis of Sodium Hippurate 717
Bile Esculin Test 717
Sait Tolerance Test (6.5% NaCI Broth) 717
Leucine Aminopeptidase (LAP) Test 718
Pyrrolidonyl Arylamidase (PYR) Test 718
Susceptibility to Optochin 718
Bile Solubility Test 718
Commercial Presumptive Identification Tests 718
XX Expanded Contents
Serologic Identification of [1 Hemolytic Streptococci 718
Capillary Precipitin Test 718
Coagglutination 718
Latex Agglutination 719
Serologic Identification of Streptococcus pneumoniae 719
Biochemical Characteristics for Identification of
Groupable Streptococci 719
Identification of the Viridans Streptococci 719
Sanguis Group 722
Mitis Group 722
Mutans Group 722
Salivarius Group 722
Anginosus Group 725
Bovis Group 726
Identification of Streptococcus suis and Other Streptococci
Isolated From Animals 726
Identification of Enterococcus Species 726
Identification of Abiotrophia and Granulicatella Species 731
Identification of Aerococcus and Helcococcus Species 731
Identification of Leuconostoc, Pediococcus, and
Tetragenococcus Species 734
Identification of Gemella Species 736
Identification of Vagococcus Species 736
Identification of Alloiococcus, Globicatella, Facklamia,
Dolosigranulum, Ignavigranum, and Dolosicoccus Species 738
Identification of Lactococcus Species 742
Commercially Available Systems for Identification of Streptococci,
Enterococci, and Selected Streptococcus Like Bacteria 742
API Rapid Strep 743
BBL Crystal Gram Positive Identification System 743
Rapid ID 32 Strep 744
RapID STR 744
Vitek Gram Positive Identification (GPI) Card 744
Microscan Gram Positive Breakpoint Combo Panel 745
Chapter 14
Aerobic and Facultative Gram Positive
Bacilli LISTERIA SPECIES AND LISTERIA
MONOCYTOGENES 766
Taxonomy of the Genus Listeria 766
Virulence Factors of L monocytogenes 768
Epidemiology of L monocytogenes 768
Clinical Significance of L. monocytogenes 768
Isolation of L monocytogenes From Clinical Specimens 770
Identification of Listeria Species 770
Antimicrobial Susceptibility and Treatment of Listeria Infections 773
Pathogenicity of Other Listeria Species 773
ERYSIPELOTHRIX SPECIES: ERYSIPELOTHRIX
RHUSIOPATHIAE AND ERYSIPELOTHRIX
TONSILLARUM 773
Taxonomy of the Genus Erysipelothrix 773
Virulence Factors of £ rhusiopathiae 774
Clinical Significance of £ rhusiopathiae 774
Isolation and Identification of £ rhusiopathiae 775
Antimicrobial Susceptibility of £ rhusiopathiae 775
BACILLUS SPECIES AND RELA TED GENERA 775
Taxonomy and the Taxonomic Dissection of the Genus Bacillus 775
Bacillus anthracis 776
Epidemiology of Anthrax 776
Virulence Factors of B. anthracis 111
Clinical Presentations of Anthrax 777
Treatment of Anthrax 778
Prevention of Anthrax 778
Bacillus cereus 778
Virulence Factors of B. cereus 778
B. cereus Gastroenteritis 779
Opportunistic Bacillus Species Infections 779
Bacteremia and Endocarditis 779
Infections in Compromised Hosts 780
Ocular Infections 780
Musculoskeletal Infections 780
Nosocomial Infections 780
Laboratory Safety, Specimen Collection, and Processing 781
Isolation and Identification of Bacillus Species: The
Bacillus cereus Group : B. anthracis, B. cereus,
B. thuringiensis, and B. mycoides 781
Antimicrobial Susceptibility of Bacillus Species 783
CORYNEBACTERIUM SPECIES 783
Introduction and Taxonomy 783
Identification of Corynebacterium Species and the
Coryneform Bacteria 785
Antimicrobial Susceptibility Testing of Corynebacterium
Species and the Coryneform Bacteria 797
Members of the Genus Corynebacterium Isolated From Humans 797
Corynebacterium amycolatuin 798
Corynebacterium diphtheriae 803
Corynebacterium jeikeium 807
Corynebacterium pseudodiphtheriticum 808
Corynebacterium striatum 808
Corynebacterium urealyticum 808
Corynebacterium Species Associated With Animals 809
Corynebacterium Species Isolated From Foods and
the Environment 810
OTHER CORYNEFORM BACTERIA 810
Actinobaculum Species 810
Actinomyces Species Isolated From Humans 811
Actinomyces Species Isolated From Animals 817
Arcanobacterium Species 817
Arthrobacter Species 823
Brevibacterium Species 823
Cellulomonas, Cellulosimicrobium, and Oerskovia Species 826
Dermabacter Species 828
Exiguobacterium Species 828
Leifsonia Species 830
Microbacterium (Aureobacteriuni) Species 830
Rothia and Rothia Like Species (CDC Group 4) 832
Turicella Species 834
GARDNERELLA VAGINAL IS 834
Taxonomy and Cellular Morphology 834
Virulence Factors of 6. vaginalis 835
Clinical Significance of G. vaginalis 835
Isolation and Identification 836
Antimicrobial Susceptibility 838
LACTOBACILLUS SPECIES 838
Taxonomy and Epidemiology 838
Clinical Significance 839
Isolation and Identification 840
Antimicrobial Susceptibility 840
Chapter 15
Aerobic Actinomycetes INTRODUCTION, CLASSIFICATION, AND
TAXONOMY 858
THE NOCARDIOFORM GROUP 860
Nocardia 860
Epidemiology, Pathology, and Pathogenesis 861
Clinical Disease 862
Rhodococcus 863
Epidemiology, Pathology, and Pathogenesis 863
Clinical Disease 863
Other Nocardioform Bacteria 863
THE MADUROMYCETES AND
THERMOMONOSPORAS 864
Actinomadura 864
Epidemiology 864
Clinical Disease and Pathology 864
Nocardiopsis 864
THE STREPTOMYCETES 865
Streptomyces 865
THERMOPHILIC ACTINOMYCETES 865
MISCELLANEOUS ACTINOMYCETES 865
Oerskovia 865
Dermatophilus 865
Tropheryma whipplei 865
History and Taxonomy 865
Ecology 866
Clinical Disease and Pathology 866
LABORATORY DIAGNOSIS OF INFECTIONS
CAUSED BY AEROBIC ACTINOMYCETES 866
Primary Isolation 866
Differentiation of Nocardia From Other Genera of
Aerobic Actinomycetes 867
Identification of Thermophilic Actinomycetes 871
Identification of Tropheryma whipplei 871
In Vitro Susceptibility of Nocardia and Related Bacteria to
Antimicrobial Agents and Therapy of Infections 871
Chapter 16
The Anaerobic Bacteria RELATIONSHIPS OF BACTERIA TO OXYGEN 878
Oxygen Tolerance 879
Oxidation Reduction Potential 879
HABITATS 880
TAXONOMIC CLASSIFICATION AND
NOMENCLATURE 880
HUMAN INFECTIONS 887
ISOLA TION OF ANAEROBIC BACTERIA 890
Selection of Specimens for Culture 890
Collection and Transport of Specimens 891
Anaerobic Blood Culture (Summary of Guidelines for
Traditional Broth and Instrumented Systems) 891
Direct Examination of Clinical Materials 892
Selection and Use of Media 893
Expanded Contents XXI
ANAEROBIC SYSTEMS FOR THE
CULTIVATION OF ANAEROBIC BACTERIA 895
Anaerobic Jar Techniques 895
Use of the Anaerobic Glove Box 897
The Roll Streak System 897
Anaerobic Disposable Plastic Bags 898
Use of the Anaerobic Holding Jar 898
INCUBA TION OF CUL TURES 898
INSPECTION AND SUBCULTURE OF
COLONIES 900
AEROTOLERANCE TESTS 900
PRELIMINARY REPORTING OF RESUL TS 901
DETERMINATION OF CULTURAL AND
BIOCHEMICAL CHARACTERISTICS FOR
DIFFERENTIATION OF ANAEROBIC
ISOLATES 901
Presumptive Identification 901
Use of Differential Agar Media 901
Presumpto Plates 902
Antimicrobial Susceptibility Plates 904
Characterization of Anaerobes Using Conventional Biochemical
Tests in Large Tubes 904
Alternative Procedures 905
The Nagler Test and the CAMP Test for C. perfringens 905
Packaged Microsystems 905
Commercial Packaged Kits for Identification of Anaerobes
After 4 Hours of Incubation 905
DETERMINATION OF METABOLIC PRODUCTS
BY GAS LIQUID CHROMATOGRAPHY 906
Identification of Volatile Fatty Acids 906
Analysis of Nonvolatile Acids 908
Gas Liquid Chromatography Controls 909
IDENTIFICA TION OF ANAEROBIC BACTERIA 909
Anaerobic Gram Negative Non Spore Forming Bacilli 912
Classification and Nomenclature 912
Presumptive or Preliminary Group Identification of Bacteroides,
Prevotella, Porphyromonas, and Fusobacterium 913
Identification of the Anaerobic Cocci 924
Identification of the Anaerobic Non Spore Forming
Gram Positive Bacilli 927
Propionibacterium Species 927
Bifidobacterium Species 927
Lactobacillus Species 930
Actinomyces Species 930
Eubacterium Species 930
Mobiluncus and Bacterial Vaginosis 931
Additional Genera and Species of Anaerobic Non Spore Forming
Gram Positive Bacilli 931
Identification of Clostridium Species 931
Histotoxic Clostridia Involved in Clostridial Myonecrosis or
Gas Gangrene 932
Miscellaneous Clostridia in Other Clinical Settings 935
Clostridium Gf/ffic/fe Associated Intestinal Disease 936
Botulism 937
Tetanus 938
XXii Expanded Contents
ANTIMICROBIAL SUSCEPTIBILITY TESTING
OF ANAEROBIC BACTERIA 939
Methods for Antimicrobial Susceptibility Testing of Anaerobes 939
Chapter 17
Antimicrobial Susceptibility Testing HISTORICAL INTRODUCTION 946
BACTERIAL RESISTANCE TO ANTIMICROBIAL
AGENTS 947
Mechanistic Variables 947
Mechanisms of Resistance 949
Transport of Antimicrobial Agents Across the Cell Wall and
Cell Membranes 949
Antibiotics That Interfere With Formation of Bacterial Cell Walls:
The f Lactam and Glycopeptide Antibiotics 955
Antimicrobial Agents That Do Not Exert Their Effect on Cell Walls 961
Interactions Among Resistance Mechanisms 963
LABORATORY GUIDANCE OF ANTIMICROBIAL
THERAPY 963
TESTS FOR DETERMINING INHIBITORY
ACTIVITY OF ANTIMICROBIAL AGENTS 968
Indications 968
Choice of Test 968
Selection of Antimicrobial Agents 970
Standardization 970
Growth Medium 970
pH 970
Serum 970
Cation Concentration 975
Atmosphere 975
Temperature 975
Inoculum 975
Antimicrobial Agents 975
Quality Control 976
Quality Assurance 977
Interpretation of Results 977
Selection of Antimicrobial Agents to Be Reported 981
Macrodilution Broth Susceptibility Test 982
Agar Dilution Susceptibility Test 982
Disk Diffusion Susceptibility Test 983
Development of a Standardized Disk Diffusion Procedure 986
Interpretation of Results 987
Quality Control 989
Limitations 989
Microbroth Dilution Susceptibility Test 989
Commercial Systems 993
Vitek (BioMerieuxVitek, Hazelwood, M0) and MicroScan
(Dade International, West Sacramento, CA) 993
Epsilometer Test (Etest; AB Biodisk, Sweden) 996
SPECIAL ISSUES IN SUSCEPTIBILITY TESTING 996
(l Lactamases 996
Staphylococcus Species 1001
Haemophilus Species 1002
Neisseria gonorrhoeae 1002
Moraxella (Branhamella) catarrhalis 1002
Enterococcus Species 1002
Extended Spectrum p Lactamases 1003
Staphylococcus Species 1004
p Lactam Antibiotics (Oxacillin Resistant Staphylococcus Species) 1004
Vancomycin 1007
Macrolides, Lincosamides, and Streptogramins 1008
Fluoroquinolones 1008
Haemophilus Species 1008
Penicillin Antibiotics 1009
Chloramphenicol 1009
Cephalosporins 1009
Trimethoprim Sulfamethoxazole 1009
Streptococcus pneumoniae 1009
Penicillin and Other p Lactam Antibiotics 1009
Multiple Resistance 1010
Macrolides and Lincosamides 1010
Neisseria gonorrhoeae 1011
Neisseria meningitidis 1011
Enterococcus Species 1011
Aminoglycoside Antibiotics 1012
p Lactam Antibiotics 1012
Vancomycin 1012
Listeria monocytogenes 1013
Streptococcus pyogenes (Group A p Hemolytic Streptococcus) 1013
Penicillin 1013
Erythromycin 1013
Fluoroquinolones 1013
Streptococcus agalactiae (Group B p Hemolytic Streptococcus) 1014
Viridans Streptococci 1014
Other Gram Positive Bacteria 1014
Pseudomonas aeruginosa, Burkholderia cepacia, and
Stenotrophomonas maltophilia in Patients With Cystic Fibrosis 1014
Direct Susceptibility Testing 1014
Chapter 18
Mycoplasmas and Ureaplasmas TAXONOMY OF MYCOPLASMAS AND
UREAPLASMAS 1023
VIRULENCE FACTORS OF HUMAN
MYCOPLASMAS 1026
CLINICAL SIGNIFICANCE OF THE HUMAN
MYCOPLASMAS 1027
Mycoplasma pneumoniae 1027
Mycoplasma hominis and Ureaplasma urealyticum 1028
Mycoplasma genitalium 1033
Mycoplasma fermentans 1034
Mycoplasma penetrans 1037
Mycoplasma pirum 1038
Mycoplasma primatum 1039
Mycoplasma spermatophilum 1039
Human Infections Due to Mycoplasma Species of Animal Origin 1039
Hemotrophic Mycoplasma Species 1039
CULTURE OF HUMAN MYCOPLASMAS FROM
CLINICAL SPECIMENS 1040
General Considerations 1040
Specimen Collection 1041
Transport Media 1041
Media for Culture of Mycoplasmas 1041
Isolation and Identification of Mycoplasma pneumoniae 1042
Noncultural Detection of Mycoplasma pneumoniae 1043
Isolation and Identification of the Genital Mycoplasmas 1044
Noncultural Detection of the Genital Mycoplasmas 1045
Commercial Mycoplasma Culture Systems 1047
Isolation of Mycoplasmas on Routine Culture Media 1048
SEROLOGIC TESTS FOR DIAGNOSIS OF
MYCOPLASMA PNEUMONIAE INFECTIONS 1048
SEROLOGIC TESTS FOR GENITAL
MYCOPLASMAS 1050
ANTIMICROBIAL SUSCEPTIBILITY AND
TREATMENT OF MYCOPLASMA INFECTIONS 1051
DIAGNOSIS AND TREATMENT OF
HEMOTROPHIC MYCOPLASMA INFECTIONS
IN ANIMALS 1054
Chapter 19
Mycobacteria TRENDS IN CLINICAL TUBERCULOSIS 1065
Worldwide Increase in the Incidence of Tuberculosis 1065
Impact of Coinfection With HIV and Mycobacterium tuberculosis 1066
Persons at Risk for Tuberculosis 1066
Rapidly Progressive Disease 1066
Implementation of More Aggressive Infection Control and
Epidemiologic Measures 1067
TRENDS IN THE LABORATORY DIAGNOSIS
OF TUBERCULOSIS 1067
Use of Molecular Techniques 1067
Use of Automated Instruments 1067
Use of Broth Culture Media 1067
Inoculation of Clinical Specimens to Agar Based Culture Media 1067
Use of p nitro acetylamino hydroxypropiophenone (NAP) 1068
Applications of Gas Liquid Chromatography, High Performance
Liquid Chromatography, and Mass Spectrometry 1068
Use of the Lysis Centrifugation System Blood Culture Tube 1068
THE CLINICAL LABORA TORY 1068
Optimizing the Detection and Identification of Mycobacteria 1068
Laboratory Safety 1068
SPECIMEN COLLECTION 1069
Respiratory Specimens 1069
Blood Cultures 1069
Stool Specimens 1070
Miscellaneous Sterile Specimens 1070
LABORATORY APPROACH TO THE RECOVERY
AND IDENTIFICA TION OF MYCOBACTERIA 1071
Specimen Preparation 1072
Digestion and Decontamination 1072
Centrifugation 1074
Bone Marrow and Biopsy Specimens 1074
Miscellaneous Liquid Specimens 1075
Staining of Acid Fast Bacilli 1075
CULTURE OF SPECIMENS FOR RECOVERY
OF MYCOBACTERIA 1077
Culture Media 1077
Nonselective Culture Media for Recovery of Mycobacteria 1077
Media of Cohen and Middlebrook 1078
Selective Media 1078
Incubation 1079
Expanded Contents XXJH
RAPID METHODS FOR ESTABLISHING
A DIAGNOSIS 1079
Sensitivity of Acid Fast Smears 1079
Gas Liquid and High Performance Liquid Chromatography 1080
Use of Broth Culture Medium 1080
AUTOMA TED DETECTION SYSTEMS 1080
BACTEC AFB System 1081
Mycobacteria Growth Indicator Tube (MGIT) and MGIT 960 1081
MB/BacT Mycobacteria Detection System 1082
The ESP Culture System II 1082
The BACTEC MYCO/F Lytic 1083
MANUAL DETECTION SYSTEMS 1083
Septi Chek AFB System 1083
IDENTIFICATION OF MYCOBACTERIA USING
CONVENTIONAL METHODS 1085
Optimal Temperature for Isolation and Rates of Growth 1085
Pigment Production 1086
Niacin Accumulation 1086
Reduction of Nitrates to Nitrites 1086
Tween 80 Hydrolysis 1087
Catalase Activity 1087
Arylsulfatase Activity 1087
Urease Activity 1087
Pyrazinamidase 1087
Iron Uptake 1087
Growth Inhibition by Thiophene 2 carboxylic Acid Hydrazide 1087
Growth in 5% Sodium Chloride 1087
Growth on MacConkey Agar 1090
CLASSIFICA TION OF MYCOBACTERIA 1090
Laboratory Identification of Mycobacteria and Related Clinical
Syndromes 1091
Review of Mycobacterium Species: Laboratory Aspects and
Clinical Correlations 1091
Mycobacterium tuberculosis Complex 1091
Photochromogens 1093
Scotochromogens 1095
Nonphotochromogens 1099
Rapid Growers 1104
Other Mycobacteria 1104
THE DETECTION AND IDENTIFICATION OF
MYCOBACTERIA BY MOLECUAR METHODS 1106
Signal Amplification Methods 1107
Nucleic Acid Probes 1107
In Situ Hybridization 1107
Nucleic Acid Amplification Methods 1108
Commercially Available Applications 1108
Home Brew PCR Assays, Including Real Time PCR 1109
Postamplification Analysis 1110
Reverse Hybridization 1110
DNA Sequencing 1111
Microarray Analysis 1111
Strain Typing and DNA Fingerprinting 1111
SUSCEPTIBILITY TESTING 1113
SHORT COURSE THERAPY 1115
American Thoracic Society Recommendations 1117
SUMMARY 1117
XXIV Expanded Contents
Chapter 2O
Spirochetal Infections TAXONOMY 1126
TREPONEMA 1126
Treponema pallidum Subspecies pallidum 1126
Incubation Period 1127
Primary Syphilis 1127
Secondary Syphilis 1127
Latent Syphilis 1127
Late Syphilis 1127
Epidemiology 1128
Immunity 1129
Treponema pallidum Subspecies pertenue 1129
Treponema pallidum Subspecies endemicum 1130
Treponema carateum 1130
Laboratory Diagnosis of Treponemal Infections 1130
Serologic Tests 1131
Innovations: Provisional and Investigative Tests 1133
BORRELIA 1134
Relapsing Fever 1134
Epidemiology 1134
Clinical Disease 1135
Laboratory Diagnosis 1135
Lyme Disease 1135
Epidemiology 1137
Clinical Disease 1139
Laboratory Diagnosis 1140
LEPTOSPIRA 1143
Leptospirosis 1144
Epidemiology 1144
Clinical Disease 1144
Laboratory Diagnosis 1144
SPIRILLUM MINOR (RAT BITE FEVER) 1146
Chapter 21
Mycology PATIENTS AT RISK FOR FUNGAL INFECTIONS 1153
General Signs and Symptoms Suggesting Fungal Infection 1153
CLINICAL CATEGORIZATION OF FUNGAL
INFECTIONS 1153
Common Mycologic Terms 1155
LABORATORY APPROACH TO THE
DIAGNOSIS OF FUNGAL INFECTIONS 1156
Specimen Collection and Transport 1158
Specimen Processing 1160
Direct Examination 1160
Preparation of Mounts for Study 1162
Selection and Inoculation of Culture Media 1162
Incubation of Fungal Cultures 1165
LABORATORY APPROACH TO THE
PRESUMPTIVE IDENTIFICATION OF
FUNGAL ISOLATES 1166
Extent of Laboratory Genus/Species Identification 1166
Genus and Species Identification of the Major Groups of Fungi 1168
Zygomyces Species and Zygomycosis 1168
Histopathology of Infections Caused by the Zygomycetes 1171
HYALINE MOLDS AND
HYALOHYPHOMYCOSIS 1172
Aspergillus Species and Aspergillosis 1174
Laboratory Presentation 1174
Colony Morphology 1174
Microscopic Features 1174
Aspergillus fumigatus 1175
Aspergillus flavus 1175
Aspergillus niger 1175
Aspergillus terreus 1176
Aspergillus nidulans 1177
Histopathology 1177
Diagnosis Using Nonculture Techniques 1179
Additional Rapidly Growing Hyaline Molds 1181
Colony Characteristics 1181
Genera of Hyaline Filamentous Molds Producing
Conidia in Chains 1181
Penicillium Species 1181
Paeciliomyces Species 1182
Scopulariopsis Species 1182
Identification of Hyaline Molds Producing Conidia in Clusters 1182
Acremonium Species 1182
Fusarium species 1183
Gliocladium Species 1183
Trichoderma Species 1184
Identification of the Genera of Hyalohyphomycetes
Producing Conidia Singly 1184
Scedosporium Species 1185
Chrysosporium Species 1186
Sepedonium Species 1186
Beauveria Species 1187
IDENTIFICA TION OF THE DERMA TOPHYTES 1187
Identification of Microsporum Species 1189
Microsporum canis 1189
Microsporum gypseum 1190
Microsporum nanum 1190
Identification of Trichophyton Species 1190
Trichophyton mentagrophytes 1190
Trichophyton rubrum 1190
Trichophyton tonsurans 1191
Trichophyton verrucosum 1191
Epidermophyton floccosum 1192
Diagnosis by Nonculture Techniques 1192
THE DIMORPHIC FUNGI 1192
Blastomyces dermatitidis and Blastomycosis 1194
Laboratory Presentation 1196
Diagnosis Using Nonculture Techniques 1197
Coccidioides immitis and Coccidioidomycosis 1199
Laboratory Presentation 1199
Histoplasma capsulatum and Histoplasmosis 1199
Laboratory Presentation 1200
Diagnosis Using Nonculture Techniques 1202
Sporothrix schenckii and Sporotrichosis 1203
Laboratory Presentation 1203
Diagnosis Using Nonculture Techniques 1203
Paracoccidioides immitis and Paracoccidioidomycosis 1203
Laboratory Presentation 1206
Diagnosis Using Nonculture Techniques 1206
DEMA TIACEOUS FUNGI 1208
Agents of Phaeohyphomycosis 1208
Laboratory Presentation 1208
Macroconidia With Transverse and Longitudinal
Septa (Muriform) 1208
Alternaria Species 1209
Ulocladium Species 1209
Stemphylium Species 1210
Epicoccum Species 1210
Macroconidia With Transverse Septa 1210
Bipolaris Species 1210
Drechslera Species 1210
Curvularia Species 1210
Exsemhilum Species 1210
Macroconidia Borne Singly or Via Special Conidiation 1210
Nigrospora Species 1211
Phoma Species 1211
Chaetomium Species 1211
AGENTS OF CHROMOMYCOSIS
AND MYCETOMA 1211
Cladophialophora (Cladosporium) carrionii 1214
Phialophora verrucosum 1215
Phialophora richardsiae 1215
Fonsecaea pedrosoi 1215
Exophiala jeanselmei 1216
THE LABORATORY IDENTIFICATION
OF YEASTS 1216
Germ Tube 1216
Cornmeal Agar Preparations 1218
Growth Patterns of Yeasts on Cornmeal Agar 1219
CHROMagar 1219
Candida albicans 1219
Candida tropicalis 1220
Candida parapsilosis 1220
Candida kefyr (pseudotropicalis) 1220
Other Emerging Pathogenic Candida Species 1220
Candida Species and Candidiasis 1221
Species That Produce True Hyphae 1221
Species That Fail to Produce True Hyphae 1224
Cryptococcosis and Cryptococcus neoformans 1224
Diagnosis by Nonculture Methods 1226
Miscellaneous Non Hyphae Forming Yeasts of
Medical Importance 1226
Candida (Torulopsis) glabrata 1226
Rhodotorula Species 1226
Saccharomyces Species 1226
Hansenula anomala 1228
Malassezia furfur 1228
Laboratory Identification of Black Yeasts 1229
Aureobasidium pullulans 1229
Phaeoannellomyces werneckii 1229
Packaged Yeast Identification Systems 1230
Antifungal Susceptibility Testing 1230
SEROLOGIC DIAGNOSIS OF FUNGAL
DISEASES 1232
Chapter 22
Parasitology RISK AND PREVENTION OF PARASITIC
INFECTIONS 1247
Expanded Contents XXV
CLINICAL MANIFESTATIONS OF PARASITIC
DISEASE 1247
COLLECTION, TRANSPORT, AND
PROCESSING OF SPECIMENS 1248
Fecal Specimens 1248
Preservation of Clinical Specimens 1249
Visual Examination 1249
Processing Fresh Stool Specimens for Ova and Parasite Examination 1249
Examination of Intestinal Specimens Other Than Stool 1253
Examination of Extraintestinal Specimens 1254
Sputum 1254
Urine and Body Fluids 1254
Tissue Biopsies and Aspirates 1254
Corneal Scrapings or Biopsy 1254
Muscle Biopsy 1254
Blood 1254
IDENTIFICATION AND DIFFERENTIATION OF
PARASITES 1255
Life Cycles of Human Parasites 1256
INTESTINAL PROTOZOA 1256
The Intestinal Amoebae 1258
Amebiasis and Entamoeba histolytica 1258
Entamoeba histolytica versus Entamoeba coli 1260
Serologic Diagnosis of Amebiasis 1260
Nonpathogenic Entamoeba histolytica: Entamoeba dispar 1261
Other Intestinal Amoebae 1262
Protozoa of Uncertain Classification 1262
Intestinal Flagellates 1263
Giardia lamblia 1263
Other Intestinal Flagellates 1266
Ciliates: Balantidium coli 1267
Coccidia 1267
Cryptosporidium parvum 1267
Cyclospora cayetanensis 1270
Isospora belli 1271
Sarcocystis Species 1271
Phylum Microsporum: Microsporidium Species 1272
NEMATODES 1273
Ascariasis and Ascaris lumbricoides 1274
Trichuriasis and Trichuris trichiura (Whipworm) 1274
Enterobius vermicularis 1275
Hookworms 1276
Strongyloidiasis and Strongyloides stercoralis 1279
Trichostrongylus Species 1279
Capillaria philippinensis 1280
CESTODES 1281
Taenia solium and Taenia saginata 1282
Diphyllobothrium latum The Giant Fish Tapeworm 1284
Hymenolepis Species 1285
Dipylidium caninum 1286
TREMATODES 1286
Schistosomes 1287
Fasciola hepatica and Fasciolopsis buski 1288
Clonorchis sinensis 1290
Paragonimus westermani 1292
BLOOD AND TISSUE PARASITES 1292
Malaria 1294
Babesia 1298
Hemoflagellates: Leishmania Species and Trypanosoma Species 1298
Leishmaniasis and Leishmania Species 1299
Trypanosomiasis 1299
XXVi Expanded Contents
Filarial Nematodes and Filariasis 1303
Onchocerciasis and Onchocerca volvulus 1305
Dracunculiasis 1306
Dirofilariasis 1306
Tissue Protozoan Infections 1306
Toxoplasma gondii 1306
Pneumocystis carinii 1311
Miscellaneous Larval Tissue Parasite Infections 1311
Trichinosis 1312
Visceral Larval Migrans 1312
Cutaneous Larva Migrans—Toxocara 1314
Anisakiasis 1314
Gnathostomiasis 1315
Angiostrongyliasis 1315
Echinococcosis (Hydatid Disease) 1315
Multiceps Species—Coenurosis 1316
Sparganosis: Spirometra mansonoides 1316
SEROLOGIC DIAGNOSIS OF PARASITIC
INFECTIONS 1318
DRUGS COMMONLY USED IN THE
TREA TMENT OF PARASITIC DISEASES 1321
Chapter 23
Diagnosis of Infections Caused by Viruses,
Chlamydia, Rickettsia, and Related Organisms
INTRODUCTION 1329
Historical Review 1329
Evolution of Cell Culture Techniques 1329
Evolution of Diagnostic Virology Services 1329
Levels of Service 1330
TAXONOMY AND NOMENCLA TURE 1330
CLINICAL MANIFESTATIONS OF VIRAL
INFECTIONS 1333
Orthomyxoviruses 1335
Paramyxoviruses 1342
Parainfluenza Viruses 1342
Mumps Virus 1344
Measles Virus 1344
Respiratory Syncytial Virus 1344
Other Paramyxoviruses 1344
Picornaviruses 1344
Rhabdoviruses 1345
Arenaviruses 1346
Filoviruses 1346
Togaviruses 1347
Bunyaviruses 1348
California Encephalitis Viruses 1348
Hantaviruses 1348
Human Gastroenteritis Viruses 1349
Rotaviruses 1350
Caliciviruses 1350
Astroviruses 1350
Enteric Adenoviruses 1350
Coronaviruses 1350
Coltiviruses 1351
Retroviruses 1351
Herpesviruses 1356
Herpes Simplex Virus 1356
Cytomegalovirus 1358
Epstein Barr Virus 1359
Varicella Zoster Virus 1359
Human Herpesviruses 6 and 7 1359
Human Herpesvirus 8 1360
B Virus 1360
Adenoviruses 1360
Poxviruses 1361
Papovaviruses 1361
Papillomaviruses 1362
Polyomaviruses 1364
Parvoviruses 1364
Hepatitis Viruses 1364
Hepatitis A Virus 1365
Hepatitis B Virus 1365
Hepatitis C Virus 1365
Hepatitis D Virus 1366
Hepatitis E Virus 1366
Prion Diseases (Transmissible Spongiform Encephalopathies) 1366
CLINICAL CLASSIFICATION OF VIRAL
INFECTIONS 1367
DIAGNOSIS OF VIRAL INFECTIONS 1367
Collection of Specimens for Diagnosis 1369
Transportation and Storage of Specimens 1373
Isolation of Viruses in Culture 1373
Preparation and Maintenance of Cell Cultures 1373
Contamination of Cell Cultures 1375
Technical Aspects of Cell Culture 1377
Selection of Cell Cultures for Isolation of Viruses 1380
Inoculation and Incubation of Cell Cultures 1380
Detection of Virus and Provisional Identification 1381
Cytopathic Effect 1381
Hemagglutination and Hemadsorption 1383
Light Microscopy 1387
Electron Microscopy 1387
Biochemical Differentiation 1387
Cell Association 1389
Detection of Viral Antigens 1389
Artifacts and Non Virus Induced Changes 1389
Definitive Identification of Isolates 1390
Storage of Viral Isolates 1391
Summary of Detection and Identification of Viruses in Culture 1391
DIRECT DETECTION OF VIRUSES IN CLINICAL
SPECIMENS 1392
Light Microscopic Detection of Inclusions 1392
Electron Microscopic Detection of Viral Particles 1393
Immunologic Detection of Viral Antigen 1393
Respiratory Viruses 1393
Herpes Group Viruses 1393
Other Viruses 1394
Molecular Techniques 1394
Human Immunodeficiency Virus 1394
Hepatitis C Virus 1395
Hepatitis B Virus 1396
Human Papillomaviruses 1396
Parvovirus B19 1396
West Nile Virus 1396
Herpes Simplex Virus 1396
Cytomegalovirus 1397
Enteroviruses 1397
SARS Coronavirus 1397
Other Viral Infections 1397
Selection of Tests for Rapid Diagnosis 1397
SEROLOGIC DIAGNOSIS OF VIRAL
INFECTIONS 1397
Human Immunodeficiency Virus 1398
Hepatitis B Virus and Epstein Barr Virus 1399
Hepatitis A Virus 1401
Hepatitis C Virus 1401
Parvovirus 1402
Herpes Simplex Virus 1402
Varicella Zoster Virus 1402
Cytomegalovirus 1402
West Nile Virus 1402
Rubella 1402
SARS Coronavirus 1402
Anti IgM Antibodies 1402
Miscellaneous Serologic Procedures 1403
Diagnosis of Other Viral Infections 1403
Antiviral Susceptibility Testing 1403
INFECTIONS WITH CHLAMYDIA SPECIES 1403
Chlamydia trachomatis 1403
Clinical Features and Epidemiology 1403
Collection of Specimens 1403
Isolation of Chlamydia trachomatis in Cell Culture 1405
Direct Detection of Chlamydia trachomatis in Clinical Specimens 1405
Serologic Diagnosis 1406
Other Methods for Diagnosis 1406
Diagnosis of Sexual Abuse 1406
Chlamydia psittaci 1406
Chlamydia pneumoniae 1406
INFECTIONS WITH RICKETTSIA, COXIELLA,
EHRLICHIA, AND ANAPLASMA 1407
Rickettsia and Coxiella 1407
Clinical Features and Epidemiology 1407
Collection of Specimens 1408
Isolation of Rickettsia and Coxiella in Culture 1408
Direct Detection of Antigen and Nucleic Acid in Clinical Specimens 1409
Serologic Diagnosis 1409
Ehrlichia and Anaplasma Species 1409
Appendix I 1420
Appendix II 1437
Charts Chart 1 1 Catalase 1443
Chart 1 2 Bile Solubility Test 1443
Chart 1 3 The Slide Coagulase Test 1444
Chart 1 4 Indole Test 1445
Chart 1 5 Cytochrome Oxidase Test 1447
Chart 1 6 PYR Test 1448
Chart 3 1 Complement Fixation (CF) Test 1448
Chart 3 2 Hemagglutination Inhibition (HAI) Test 1450
Chart 6 1 o Nitrophenyl p o Galactopyranoside 1451
Chart 6 2 Nitrate Reduction: General Applications 1452
Chart 6 3 Methyl Red 1453
Chart 6 4 Voges Proskauer Test 1454
Chart 6 5 Citrate Utilization 1456
Chart 6 6 Urease: Conventional 1457
Expanded Contents XXVii
Chart 6 7 Decarboxylases 1459
Chart 6 8 Phenylalanine Deaminase 1461
Chart 7 1 Oxidative Fermentative Test (Hugh and Leifson) 1462
Chart 7 2 Flagellar Stain 1463
Chart 7 3 Fluorescence Denitrification 1465
Chart 7 4 Esculin Hydrolysis Test 1466
Chart 8 1 The CAMP Test 1468
Chart 9 1 Test for X and V Factor Requirements 1469
Chart 11 1 Rapid Carbohydrate Utilization Test for Identification of
Neisseria Species 1470
Chart 12 1 Furazolidone Disk Test 1471
Chart 12 2 Novobiocin Disk Test 1471
Chart 13 1 Bacitracin and SXT Susceptibility Tests 1472
Chart 13 2 Bile Esculin Test 1473
Chart 13 3 Optochin Susceptibility Test 1474
Chart 13 4 Salt Tolerance Test 1474
Chart 14 1 Loefflers Methylene Blue Stain 1475
Chart 14 2 Loefflers Serum Medium 1476
Chart 14 3 Tinsdales Agar (as Modified by Moore and Parsons)
1477
Chart 14 4 Cystine Tellurite Blood Agar 1478
Chart 15 1 Hydrolysis of Xanthine, Hypoxanthine, Tyrosine, and
Casein 1478
Chart 17 1 Disk Diffusion (Bauer Kirby) Susceptibility Test for
Nonfastidious Bacteria 1480
Chart 17 2 Performance of Microbroth Dilution Susceptibility Tests
with Nonfastidious Bacteria 1481
Chart 17 3 Gradient Diffusion Test (Etest) for Bacterial
Susceptibility 1482
Chart 18 1 Diene s Stain Procedure for Identification of
Mycoplasmas 1483
Chart 18 2 Hemadsorption Test for Identification of Mycoplasma
pneumoniae 1484
Chart 18 3 Manganous Chloride Urea Test for Identification of
Ureaplasma urealyticum 1484
Chart 18 4 Medium for Isolation of Mycoplasma pneumoniae 1485
Chart 18 5 Medium for Isolation of the Genital Mycoplasmas 1487
Chart 18 6 Tetrazolium Reduction Test for the Presumptive
Identification of Mycoplasma pneumoniae 1488
Chart 19 1 Digestion and Decontamination: /V Acetyl
L cysteine Sodium Hydroxide (NALC) 1489
Chart 19 2 Carbol Fuchsin Stains 1491
Chart 19 3 Fluorescent Stain: Auramine 0; Auramine Rhodamine
1492
Chart 19 4 NAP Test (p Nitro a Acetylamino
p Hydroxypropiophenone); (BACTEC) 1494
Chart 19 5 Arylsulfatase 1496
Chart 19 6 Assessment of Photoreactivity of Mycobacteria 1497
Chart 19 7 Catalase 68°C 1499
Chart 19 8 Growth on MacConkey Agar 1500
Chart 19 9 Inhibition by Thiophene 2 carboxylic Acid Hydrazide (T2H,
ijxg/mL) 1501
Chart 19 10 Iron Uptake 1502
Chart 19 11 Niacin Accumulation 1502
Chart 19 12 Nitrate Reduction: Mycobacteria 1504
Chart 19 13 Pyrazinamidase 1505
Chart 19 14 Sodium Chloride Tolerance: Mycobacteria 1506
Chart 19 15 Tween 80 Hydrolysis 1507
Chart 19 16 Urease: Mycobacteria 1508
Chart 19 17 DNA Probes for the Identification of Mycobacteria 1509
Chart 19 18 Detection, Identification, and Drug Susceptibility Testing
of M. tuberculosis by Radiometric Instrumentation 1511
XXVlii Expanded Contents
Chart 20 1 Darkfield Microscopy of Genital Lesions 1513
Chart 20 2 Venereal Disease Research Laboratory (VDRL) Slide Test
on Serum 1514
Chart 20 3 Rapid Plasma Reagin (RPR) Card Test 1517
Chart 20 4 Fluorescent Treponemal Antibody Absorption Test (FTA
ABS) 1521
Chart 22 1 Fecal Concentration Techniques for the Recovery of
Intestinal Parasites 1525
Chart 22 2 Trichrome Staining Technique for Fecal Smears 1528
Chart 22 3 Preparation of Thin and Thick Blood Smears 1529
Chart 22 4 Calibration of the Ocular Micrometer 1531
Chart 22 5 Cellulose Tape Preparation for Pinworm Examination
1533
Chart 23 1 Hemadsorption (HAD) Test 1534
Chart A 1 Formulations of Commonly Used Stool Preservatives 1535
Color Plates Index
|
| adam_txt |
Brief C
Chapter 1
Introduction to Microbiology: Part I: The
Role of the Microbiology Laboratory in the
Diagnosis of Infectious Diseases: Guidelines
to Practice and Management I
Chapter 2
Introduction to Microbiology: Part II:
Guidelines for the Collection, Transport,
Processing, Analysis, and Reporting of
Cultures From Specific Specimen Sources 67
Chapter 3 Laboratory Diagnosis by Immunologic
Methods 111
Chapter 4 Molecular Microbiology 132
Chapter 5
Medical Bacteriology: Taxonomy,
Morphology, Physiology, and Virulence 166
Chapter 6
The Enterohacteriaceae 211
Chapter 7
The Nonfermentath e (• ram Negati ve
Bacilli 303
Chapter 8
Curved Gram Negative Bacilli and
(Kidase Positive Fermenters:
Campylobaeteraceae and Yibrionaccae 392
Dntents
Chapter 9
Miscellaneous Fastidious Gram Negative
Bacilli 429
Chapter 1O
Legionella 549
Chapter 11 Neisseria Species and Moraxella
catarrhalis 566
Chapter 12 Gram Positive Cocci: Part I: Staphylococci
and Related (»ram Positive Cocci 623
Chapter 13
Gram Positive Cocci: Part II: Streptococci,
Enterococci, and the "Streptococcus Like"
Bacteria 672
Chapter 14
Aerobic and Facultative
Gram Positive Bacilli 765
Chapter 15 Aerobic Actinomycetes 858
Chapter 16 The Anaerobic Bacteria 877
Chapter 17
Antimicrobial Susceptibility Festing 945
ix
X Brief Contents
Chapter 18 Mycoplasmas and Ureapiasmas 1022
Chapter 19 Mycobacteria 1064
Chapter 2O Spirochetal Infections 1125
Chapter 21 Mycology 1151
Chapter 22 Parasitology 1244
Chapter 23 Diagnosis of Infections Caused by
Viruses, Chlamydia, Rickettsia,
and Related Organisms 1327
Appendix I Ectoparasites and Other Invertebrates In
the Clinical Laboratory: A Brief Guide 1420
Appendix II Free Living Antebae 1437
Charts 1442
Color Plates
Index i i
Expanded
Chapter 1
Introduction to Microbiology Part I: The Role of the Microbiology
Laboratory in the Diagnosis of Infectious
Diseases: Guidelines to Practice and
Management
INTRODUCTION 2
Outline of the Book 2
The World of Infectious Disease 2
THE TRIAD OF INFECTIOUS DISEASE 2
The Infectious Agent 3
Classes of Infectious Agents 3
Interactions Between Hosts and Infectious Agents 4
Purpose of Infectious Agents in Nature 4
Virulence 4
The Environment 5
The Infected Host 5
Innate Humoral (Noncellular) Defenses 6
Innate Cellular Defenses 7
Types of Inflammation 7
Adaptive Immunologic Cellular Defenses 7
Adaptive Immunologic Noncellular (Humoral) Defenses 8
Clinical Signs and Symptoms of Infection 8
Indirect Effects of Infectious Agents on Humans 9
PHASES OF THE DIAGNOSTIC CYCLE 9
Preanalytic Phase 10
Specimen Collection 10
Specimen Transport 14
Specimen Receipt and Preliminary Observations 14
Criteria for Rejection of Specimens 14
Cost Effective Approaches in the Preanalytic Phase 15
Analytic Phase 15
Microscopic Examination 15
Processing Specimens 27
Interpretation of Cultures 33
Procedures for Preliminary Identification of Bacterial Isolates 38
Identification of Organisms Other Than Bacteria 39
Testing of Susceptibility to Antimicrobial Agents 39
Cost Effective Approaches in the Analytic Phase 39
Postanalytic Phase 43
Reporting Results 43
Interactions With Epidemiologists 44
Analysis of Results 44
Maintenance of Samples and Records 44
Contents
ADMINISTRATIVE ASPECTS OF THE
MICROBIOLOGY LABORA TORY 45
Government Regulations 45
Risk Management 47
Laboratory Safety 47
General Safety Rules and Regulations 47
Routine Safety Precautions 48
Biologic Agents 50
Universal Precautions 51
Shipping of Specimens and Etiologic Agents 55
Nonbiologic Hazards 56
Bioterrorism 58
Quality Assurance 58
Quality Control 59
Components of a Quality Control Program 60
Monitoring Laboratory Equipment 60
Monitoring Culture Media, Reagents, and Supplies 61
Chapter 2
Introduction to Microbiology Part III Guidelines for the Collection,
Transport, Processing, Analysis, and
Reporting of Cultures from Specific
Specimen Sources
INFECTIONS OF THE RESPIRATORY TRACT 68
Infections of the Upper Respiratory Tract 71
Indigenous Flora 71
Pharyngitis 72
Infections of the Oral Cavity Other Than Pharyngitis 73
Infections of the Nasopharynx and Nasopharyngeal Cultures 74
Otitis Media and Sinusitis 74
Epiglottitis 74
Laryngitis 74
Other Infections of the Upper Respiratory Tract 74
Infections of the Lower Respiratory Tract 75
Tracheobronchitis 75
Bronchiolitis 75
Pneumonia 75
Chronic Pneumonia 76
Empyema 76
Pneumonia in Special Populations 76
Collection of Specimens for the Diagnosis of Lower
Respiratory Infection 76
Laboratory Diagnosis of Pneumonia 78
xi
XII Expanded Contents
INFECTIONS OF THE GASTROINTESTINAL
TRACT 79
Lower Intestinal Infections 79
Clinical Symptoms 79
Collection of Fecal Specimens 81
Epidemiologic Considerations in the Evaluation of Patients With
Gastroenteritis 81
Upper Intestinal Infections 81
Clinical Symptoms 81
Obtaining Specimens From the Upper Gastrointestinal Tract 82
URINARY TRACT INFECTIONS 82
Clinical Signs and Symptoms 82
Host Factors 83
Collection of Urine Samples for Culture 83
Midstream Urine Specimens 83
Other Voided Urine Specimens 84
Catheter Collections 85
Suprapubic Aspiration 85
Culture of Urine Specimens 85
Screening Tests for Urinary Tract Infection 86
Screening Tests for Bacteriuria 86
Screening Tests for Pyuria 86
INFECTIONS OF THE GENITAL TRACT 87
Sexually Transmitted Infections 87
Urethritis and Cervicitis 87
Genital Ulcer Disease 88
Genital Infections Transmitted by Nonsexual Means 88
Vaginitis and Vaginosis 88
Infections of the Upper Female Genital Tract 89
Systemic Complications of Genital Infections 89
Diagnosis of Genital Tract Infections 89
Diagnosis of Urethritis, Cervicitis, and Vaginitis 89
Diagnosis of Genital Ulcer Disease and Venereal Warts 90
Collection of Genital Specimens 90
INFECTIONS OF THE BONES AND JOINTS 91
Clinical Presentation 91
Diagnosis of Infections of the Bones and Joints 91
INFECTIONS OF THE CENTRAL NERVOUS
SYSTEM 92
Meningitis 92
Encephalitis and Brain Abscess 93
Diagnosis of Central Nervous System Infections 93
Collection of Specimens 93
Assessing the Inflammatory Response and Microscopic Techniques 93
Direct Detection of Antigen and Nucleic Acid 94
Serologic Diagnosis 95
Diagnosis by Culture 95
WOUNDS, ABSCESSES, AND CELLULITIS 95
Clinical Presentation 95
Diagnosis of Wound Infections, Abscesses, and Cellulitis 95
Collection of Specimens 95
Microscopic Examination of Specimens 96
Culture 96
EYE INFECTIONS 96
Clinical Presentation 96
Conjunctivitis 96
Keratitis 97
Uveitis and Endophthalmitis 97
Diagnosis of Eye Infections 97
Collection of Specimens 97
Microscopic Examination 97
Culture 97
INFECTIONS OF THE BLOOD 97
Clinical Presentation and Pathogenesis 97
Bacteremia and Septicemia 97
Types of Bacteremia 97
Intravascular Infection 98
Catheter Associated Bacteremia and Sepsis 100
Collection of Blood Cultures 100
Contamination With Skin Flora 100
Number and Timing of Cultures 101
Culture Media 101
Systems for Processing Blood Cultures 102
Manual Blood Culture Systems 102
Lysis Centrifugation Blood Culture System 103
Automated and Computerized Blood Culture Systems 103
Comparative Studies 104
Special Considerations 105
Fastidious Organisms and Endocarditis 105
Catheter Associated Bacteremia and Sepsis 105
Tissues and Biopsies 105
Chapter 3
Laboratory Diagnosis by Immunologic
Methods ANTIGENS AND ANTIBODIES: BASIC
DEFINITIONS 112
MONOCLONAL ANTIBODIES 113
TYPES OF ANTIGEN ANTIBODY REACTIONS
USED IN DIAGNOSTIC SEROLOGY 114
Precipitin Reactions 114
Complement Fixation and Hemagglutination Inhibition 116
Agglutination Reactions 116
SOLID PHASE IMMUNOASSA Y METHODS 119
Enzyme Immunoassays for Antibody Detection 119
Enzyme Immunoassay Antibody Capture Methods for
IgM Detection 122
Enzyme Immunoassays for Antigen Detection 122
IMMUNOFLUORESCENCE TECHNIQUES 125
Immunofluorescence Techniques for Antigen Detection 125
Immunofluorescence Techniques for Antibody Detection 125
Chapter 4
Molecular Microbiology NUCLEIC ACIDS—THE BASICS OF DNA
ANDRNA 133
Structure of DNA 133
Structure of RNA 134
Function of DNA—Information Storage 135
Function of RNA—Information Transfer 135
Reading (Transcription) and Interpretation (Translation)
of the Genetic Code 135
SIGNAL AMPLIFICA TION METHODS 137
Nucleic Acid Probes 137
Clinical Applications 137
Hybrid Capture 137
Clinical Applications 138
Branched DNA 139
Clinical Applications 139
In Situ Hybridization 139
Clinical Applications 140
NUCLEIC ACID AMPLIFICA TION 141
Basics of the Polymerase Chain Reaction 141
Clinical Applications 143
Other Methods of Nucleic Acid Amplification 143
Clinical Applications 144
Modifications of PCR 144
RT PCR 144
Clinical Applications 145
Broad Range PCR 145
Clinical Applications 145
Multiplex PCR 146
Clinical Applications 146
Nested PCR 146
Clinical Applications 146
POSTAMPLIFICA TION ANAL YSIS 147
Traditional Methods of Detection 147
Gel Electrophoresis/Southern Blot Analysis 147
Enzymatic Detection of Amplified Products 147
Clinical Applications 148
Reverse Hybridization 148
Clinical Applications 148
DNA Sequencing 148
Traditional DNA Sequencing 149
Clinical Applications 149
Sequencing by Synthesis (Pyrosequencing) 149
Clinical Applications 150
Microarray Analysis 150
Clinical Applications 151
REAL TIME NUCLEIC ACID AMPLIFICA TION 151
Methods of Detecting the Products of Real Time Amplification 151
SYBR Green 151
Hybridization Probes 151
Clinical Applications 154
STRAIN TYPING 156
Non Amplification Based Typing 156
Pulsed Field Gel Electrophoresis 156
Amplification Based Typing 157
PCR RFLP 157
Rep PCR 158
Clinical Applications of Microbial Typing 158
CONCLUSION 158
Chapter 5
Medical Bacteriology: Taxonomy,
Morphology, Physiology, and Virulence TAXONOMY: CLASSIFICATION,
NOMENCLATURE, AND IDENTIFICATION
OF BACTERIA 167
Expanded Contents XJH
The Naming of Bacteria 167
Phenotypic Identification of Bacteria 168
Phylogenetic Criteria for Classification of Bacteria 168
BASIC BACTERIAL ANATOMY AND
PHYSIOLOGY 177
Bacterial Size and Shape 177
Nuclear Structure, DNA Replication, Transcription,
and Translation 178
Cytoplasm 181
Cytoplasmic Membrane 182
Bacterial Cell Wall Structure 182
Gram Positive Bacterial Cell Walls 184
Gram Negative Bacterial Cell Walls 185
"Acid Fast" Bacterial Cell Walls 188
Bacterial Endospores 189
Bacterial Surface Structures 190
Capsules 190
Flagelia 190
Fimbriae (Pili) 191
Genetic Exchange and Recombination in Bacteria 192
Requirements for Bacterial Growth and Metabolism 195
Carbon 195
Carbon Dioxide 195
Oxygen 195
Nitrogen 195
Growth Factors 196
Kinetics of Bacterial Cell Growth 196
General Bacterial Metabolism and Energy Generation 196
Fermentation 196
Utilization of Pyruvate 198
BACTERIAL VIRULENCE FACTORS AND
PATHOGENICITY 200
Definitions and Concepts 200
Requirements for Pathogenicity 203
Virulence Factors of Microorganisms 204
Adhesins 204
Aggressins 204
Exotoxins and Endotoxins 205
Bacterial Superantigens 207
Chapter 6
The Enterobacteriaceae CHARACTERISTICS FOR PRESUMPTIVE
IDENTIFICATION 213
Screening Characteristics 213
Carbohydrate Utilization 213
Cytochrome Oxidase Activity 215
Nitrate Reduction 216
CULTURE MEDIA USED FOR DETECTION OF
CARBOHYDRA TE FERMENT A TION 216
Use of Kligler Iron Agar and Triple Sugar Iron Agar 216
Biochemical Principles 217
SELECTION OF PRIMARY ISOLA TION MEDIA 218
Chemicals and Compounds Used in Selective Media 219
Selective Isolation Media 221
XIV Expanded Contents
Highly Selective Isolation Media Used Primarily for
Gastrointestinal Specimens 222
Enrichment Media 222
Guidelines for Choosing Selective Isolation Media 222
DIFFERENTIAL IDENTIFICATION
CHARACTERISTICS 223
Indole Production 224
Methyl Red Test 224
Voges Proskauer Test 225
Citrate Utilization 225
Urease Production 225
Decarboxylation of Lysine, Ornithine, and Arginine 225
Phenylalanine Deaminase Production 226
Hydrogen Sulfide Production 226
Motility 227
TAXONOMY OF THE ENTEROBACTERIACEAE 228
Classification of Enterobacteriaceae by Tribes 228
Key Identification Characteristics for the Most Common Species 228
Tribe Escherichieae 235
Tribe Edwardsielleae 250
Tribe Salmonelleae 251
Tribe Citrobactereae 258
Tribe Klebsielleae 259
Tribe Proteeae 267
Tribe Yersinieae 269
Tribe Erwinieae 274
Miscellaneous New Genera of Enterobacteriaceae 274
Identification Characteristics of Newer Enterobacteriaceae Til
Clinical Significance of Newer Enterobacteriaceae Til
QUICK SCREENING METHODS FOR RAPID
IDENTIFICATION 282
Commercial Screening Kits 282
Chromogenic Agar Media 283
CLASSIC IDENTIFICA TION SYSTEMS 284
Checkerboard Matrix 284
Branching Flow Diagrams 284
Computer Aided Schemes 285
NUMERIC CODING SYSTEMS 285
Reading Octal Codes in Numeric Code Registers 286
Estimated Frequency of Occurrence 287
Calculation of Likelihood 287
Resolving Discrepancies 287
PACKAGED KIT IDENTIFICA TION SYSTEMS 287
Overview of Packaged Systems 287
Specific Identification Systems 289
API 20E 289
BBL Crystal Entenc Noi.fernienter ID System 289
RapID onE System 289
Enterotube ii 290
Micro ID 291
Bioiog GN2 Micropiate 291
MicroScan System 291
Sensititre System 291
SEMIAUTOMATED AND AUTOMATED
IDENTIFICATION SYSTEMS 292
MicroScan Walkaway 292
Vitek System 292
Sensititre Gram Negative Autoldentification System 293
The Phoenix System 293
The OmniLog ID System 293
Chapter 7
The Nonfermentative Gram Negative Bacilli
Part I: Metabolism of the Nonfermenters
FERMENTATIVE AND OXIDATIVE
METABOLISM 309
The Embden Meyerhof Parnas Pathway 309
The Entner Doudoroff Pathway 311
The Warburg Dickens Hexose Monophosphate Pathway 312
INITIAL CLUES THAT AN UNKNOWN
ISOLA TE IS A NONFERMENTER 312
Lack of Evidence for Glucose Fermentation 312
Positive Cytochrome Oxidase Reaction 312
Failure to Grow on MacConkey Agar 313
TESTS USED IN THE IDENTIFICATION OF
NONFERMENTERS 313
Utilization of Glucose 313
Motility 313
Pigment Production 314
Hydrolysis of Urea 314
Nitrate Reduction 315
Denitrification of Nitrates and Nitrites 315
Indole Production 315
Decarboxylation 315
Esculin Hydrolysis 315
Flagella Stains 315
Leifson Method 315
Ryu Method 316
Wet Mount Technique 316
Flagellar Morphology 316
Part III Taxonomy, Biochemical
Characteristics, and Clinical Significance of
Medically Important Genera of
Nonfermenters
ORGANISMS THAT ARE MOTILE WITH
POLAR FLAGELLA 316
Pseudomonads 316
Family Pseudomonadaceae 317
Genus Pseudomonas—rRNA Group I 317
Family Burkholderiaceae 323
rRNA Group II 323
Genus Burkholderia—Pseudomallei Group 323
Genus Ralstonia and Genus Cupriavidus 328
Genus Pandoraea 329
Genus Inquilinus 331
Genua Lautropia 331
Family Comamonadaceae 331
rRNA Group III 331
Acidovorans Group 331
Facilis Delafieldii Group 332
Family Caulobacteraceae 332
rRNA Group IV 332
Brevundimonas Diminuta Group 332
Family Xanthomonadaceae 332
rRNA Group V 332
Genus Stenotrophomonas 332
Family Sphingomonadaceae 334
Genus Sphingomonas 334
Family Oceanospirillaceae 334
Genus Balneatrix 334
Family Oxalobacteraceae 334
Genus Massilia 334
Genus Herbaspirillum 334
Family Alteromonadaceae 336
Genus Shewanella—Hydrogen Sulfide Producing Group 336
Genus Alishewanella—Halophilic Group 337
Family Halomonadaceae 337
Genus Halomonas 337
Family Methylobacteriaceae 337
Genus Methylobacterium 337
Genus Roseomonas 338
Unnamed Species 339
Laribacter hongkongensis 339
ORGANISMS THAT ARE MOTILE WITH
PERITRICHOUS FLAGELLA 340
Family Alcaligenaceae 340
Genus Alcaligenes 340
Genus Achromobacter 340
Genus Bordetella 343
Genus Kerstersia 344
Genus 0/#e//a 344
Family Rhizobiaceae 344
Genus Rhizobium (Formerly Agrobacterium) 344
Family Brucellaceae 345
Genus Ochrobactrum 345
ORGANISMS THAT ARE NONMOTILE AND
OXIDASE POSITIVE 345
Family Flavobacteriaceae 345
Chryseobacterium, Empedobacter, and Unnamed CDC Groups 346
Weeksella and Bergeyella 348
Genus Myroides 348
Family Sphingobacteriaceae 348
Sphingobacterium and Pedobacter 348
Family Moraxellaceae 349
Genus Moraxella 349
Genus Psychrobacter and CDC EO Groups 350
Family Neisseriaceae 353
Genus Neisseria 353
Gilardi Rod Group 1 353
ORGANISMS THAT ARE NONMOTILE AND
OXIDASE NEGATIVE 353
Genus Acinetobacter 353
CDC Group NO 1 355
Bordetella holmesii (CDC Group NO 2) 355
CDC Group EO 5 355
Expanded Contents XV
Part III: Approach to Recovery and
Identification of Nonfermenters
LEVELS OF SERVICE IN IDENTIFICATION OF
NONFERMENTERS 355
GUIDELINES FOR RECOVERY OF
NONFERMENTERS 356
IDENTIFICATION OF MOST COMMON SPECIES 356
Pseudomonas aeruginosa 356
Acinetobacter baumannii 357
Stenotrophomonas maltophilia 357
METHODS FOR IDENTIFICATION USING
CONVENTIONAL TESTS 357
Weyant (CDC), Gilardi, and Pickett Identification Schemes 358
Practical Approach to Identification of Nonfermenters 358
Computer Aided Schemes 359
COMMERCIAL KIT SYSTEMS 359
The Oxi/Ferm Tube 359
The API 20E System 362
The API 20NE System 362
The Remel N/F System 362
The Crystal Enteric/Nonfermenter System 367
The RapID NF Plus System 367
The Biolog System 373
AUTOMA TED IDENTIFICA TION SYSTEMS 373
The Vitek Legacy System 373
The Vitek 2 System 374
The Microscan Walkaway 96, Walkaway 40, and
Autoscan 4 Systems 375
The Sensititre AP80 System 375
The Phoenix System 375
SELECTION OF A SYSTEM 375
Chapter 8
Curved Gram Negative Bacilli and Oxidase
Positive Fermenters: Campylobacteraceae and
Vibrionaceae Part I: Curved Rods: Campylobacter,
Wolinella, Arcobacter Helicobacter, and
Related Bacteria
HISTORICAL BACKGROUND 393
CLASSIFICATION OF CAMPYLOBACTER AND
RELATED TAXA 393
Campylobacter Species 395
Campylobacter jejuni Subsp. jejuni 395
Other Campylobacter Species 398
Former Wolinella and Bacteroides Species Included in the Family
Campylobacteraceae 402
Genus Arcobacter 403
Genus Helicobacter 403
H. pylori 404
Other Medically Important Helicobacter Species 404
Nonhuman Helicobacter Species 405
Other Microaerophilic Gram Negative Bacilli 405
XVi Expanded Contents
DEFINITIVE IDENTIFICATION OF
CAMPYLOBACTERS AND RELATED
BACTERIA 406
Rapid Identification of Campylobacters From Colonies and
From Stool Specimens 406
Nonculture Tests 406
Direct Detection Methods 407
Culture and Isolation of Helicobacter pylori 407
Specimens for Recovery of H. pylori 407
Isolation Procedure 407
Identification of H. pylori 407
Biopsy Urease Test (CLO Test) 408
Noninvasive Tests To Diagnose H. pylori Infection 408
Accuracy of Invasive and Noninvasive Tests To Diagnose
H. pylori Infection 408
Enterohepatic Helicobacters 408
Part II: The Families Vibrionaceae and
Aeromonadaceae
PHYLOGENY OF THE VIBRIONACEAE 408
Genus Vibrio 408
Taxonomy 409
Description and Associated Clinical Syndromes of Vibrio
Species of Human Importance 409
Methods for Laboratory Isolation of Vibrios 414
Biochemical Characterization and Laboratory Identification
of Vibrio Species 416
GENERA LISTONELLA, PHOTOBACTERIUM AND
SHEWANELLA 417
AEROMONAS AND PLESIOMONAS 417
Genus Aeromonas 417
Taxonomy 419
Clinical Significance 419
Aeromonas Species in Medicinal Leeches 420
Laboratory Recovery of Aeromonas Species From Clinical Specimens 420
Laboratory Identification of Aeromonas Species 420
Genus Plesiomonas 422
Laboratory Isolation and Identification 422
GENUS CHROMOBACTERIUM 422
Chapter 9
Miscellaneous Fastidious Gram Negative
Bacilli HAEMOPHILUS SPECIES 431
Taxonomy of Haemophilus and Related Organisms 431
Haemophilus influenzae 433
Haemophilus influenzae Type B Vaccines 433
Infections Caused by Haemophilus Species 435
Meningitis 435
Epiglottitis 439
Otitis Media 439
Sinusitis 440
Bronchitis and Chronic Obstructive Pulmonary Disease 440
Pneumonia 440
Bacteremia and Infectious Complications of Bacteremia 441
Endocarditis 441
Urogenital, Maternal, and Perinatal Infections 441
Ocular Infections 442
Brazilian Purpuric Fever 442
Miscellaneous Haemophilus influenzae Infections 443
Haemophilus parainfluenzae 443
Haemophilus aphrophilus and Haemophilus paraphrophilus 444
Other Haemophilus Species 444
Haemophilus ducreyi 444
Laboratory Diagnosis of Haemophilus Infections 444
Direct Examination of Clinical Specimens 444
Culture of Haemophilus Species 445
Identification of Haemophilus Species 446
Laboratory Diagnosis of Haemophilus ducreyi Infection 449
Antimicrobial Susceptibility of Haemophilus Species 451
ACTINOBACILLUS SPECIES 452
Actinobacillus actinomycetemcomitans 452
Clinical Significance 452
Cultural Characteristics and Identification 453
Antimicrobial Susceptibility 455
Actinobacillus ureae 455
Actinobacillus hominis 458
Animal Species in the Genus Actinobacillus 458
PASTEURELLA AND MANNHEIMIA
SPECIES 458
Taxonomy and Characteristics of the Genus Pasteurella 458
Pasteurella multocida 459
Clinical Significance and Virulence 459
Cultural Characteristics and Identification 462
Antimicrobial Susceptibility 464
Other Pasteurella Species Isolated From Human Infections 465
Pasteurella pneumotropica ["Actinobacillus pneumotropica") 465
Pasteurella aerogenes {"Actinobacillus aerogenes") 465
Pasteurella dagmatis 465
Pasteurella canis and Pasteurella stomatis 466
Pasteurella bettyae 466
Pasteurella caballi 466
Pasteurella gallinarum 466
Mannheimia Species (Formerly the "Pasteurella
haemolyticalPasteurella granulomatis" Complex) 467
CARDIOBACTERIUM HOMINIS 467
Taxonomy 467
Clinical Significance 468
Cultural Characteristics and Identification 468
Antimicrobial Susceptibility 468
EIKENELLA CORRODENS 470
Taxonomy and Virulence 470
Clinical Significance 470
Cultural Characteristics and Identification 471
Antimicrobial Susceptibility 471
KINGELLA AND SUTTONELLA SPECIES 472
Taxonomy 472
Clinical Significance 472
Cultural Characteristics and Identification 473
Antimicrobial Susceptibility 474
HUMAN CAPNOCYTOPHAGA SPECIES 474
Taxonomy 474
Clinical Significance 474
Cultural Characteristics and Identification 475
Antimicrobial Susceptibility 475
CANINE CAPNOCYTOPHAGA SPECIES 477
Taxonomy 477
Clinical Significance 477
Cultural Characteristics and Identification 477
Antimicrobial Susceptibility 478
DYSGONOMONAS SPECIES 479
CDC GROUPS EF 4A AND EF 4B 479
SIMONSIELLA SPECIES 481
STREPTOBACILLUS MONIUFORMIS 481
Taxonomy 481
Clinical Significance 481
Cultural Characteristics and Identification 481
Antimicrobial Susceptibility 482
BRUCELLA SPECIES 482
Epidemiology of Brucellosis 482
Taxonomy of Brucella Species 484
Virulence of Brucella Species 484
Clinical Spectrum of Brucellosis 486
Serologic Diagnosis of Brucellosis 486
Isolation and Cultural Characteristics 488
Identification of Brucella Species 488
Treatment of Brucellosis 490
FRANCISELLA TULARENSIS 491
Epidemiology of Tularemia 491
History and Taxonomy 491
Virulence of F. tularensis 492
Clinical Spectrum of Tularemia 493
Isolation and Cultural Characteristics 494
Serologic Diagnosis of Tularemia 495
Treatment of Tularemia 495
BARTONELLA SPECIES 497
Taxonomy and Epidemiology of Bartonella Species 497
Clinical Significance of Bartonella Species 499
Oroya Fever and Verruga Peruana 500
"Classical" and "Urban" Trench Fever 500
Bacillary Angiomatosis 501
Peliosis 501
Fever and Bacteremia 502
Endocarditis 502
Cat Scratch Disease (CSD) 503
Miscellaneous Infections 504
Detection, Isolation, and Identification of Bartonella Species 505
Specimen Types 505
Culture 505
Gram Stain and Colony Morphology 505
Identification Methods 505
Serologic Diagnosis of Bartonella Infections 507
In Vitro Antimicrobial Susceptibility 509
AFIPIA SPECIES 510
Taxonomy and Clinical Significance 510
Isolation and Identification 510
Antimicrobial Susceptibility 510
BORDETELLA SPECIES 510
Background and Taxonomy of Bordetella Species 510
Epidemiology of Pertussis 512
Clinical Significance of Bordetella pertussis 512
Pertussis Vaccines 513
Clinical Significance of Other Bordetella Species 516
Bordetella parapertussis 516
Bordetella bronchiseptica 516
Bordetella hinzii 517
Bordetella holmesii 517
Bordetella trematum 517
Expanded Contents XVH
Isolation and Identification of Bordetella Species 517
Specimens and Culture Media 517
Direct Fluorescent Antibody Test 518
Cultural Characteristics and Identification 519
New Technologies for Detection and Identification
of Bordetella pertussis 519
Serologic Tests for Diagnosis of Pertussis 521
Treatment of Pertussis 522
Antimicrobial Susceptibility Testing of Bordetella Species 522
Chapter 1O
Legionella TAXONOMY AND CHARACTERISTICS OF THE
GENUS LEGIONELLA 550
CLINICAL AND PATHOLOGIC SPECTRUM OF
LEGIONELLOSIS 551
Predisposing Factors 552
Pathology and Pathogenesis 552
EPIDEMIOLOGIC AND ECOLOGIC ASPECTS OF
LEGIONELLOSIS 553
Incidence 553
Legionellaceae in the Environment 553
Natural Habitats 553
Man Made (Artificial) Aquatic Habitats 554
Legionellosis in Travelers 554
Nosocomial Outbreaks of Legionellosis 555
LABORATORY DIAGNOSIS 555
Selection, Collection, and Transport of Clinical Specimens 555
Direct Examination of Clinical Specimens 556
Gross Examination and Microscopic Examination of Stained Materials 556
Microscopic Examination of Stained Materials 556
Direct Fluorescent Antibody (DFA) Procedure 556
Antigen Detection in Urine and Body Fluids 557
DETECTION OF LEGIONELLA
IN CLINICAL SPECIMENS 557
Isolation of Legionella Species From Clinical Specimens 557
Biopsy, Surgical Removal, and Autopsy Tissue 557
Pleural Fluid and Transtracheal Aspirates 557
Acid Wash Decontamination Procedure for Sputum and Other
Contaminated Specimens 557
Blood Cultures 557
Identification of Legionella Species 558
Antimicrobial Susceptibility and Treatment 558
Serum Indirect Immunofluorescent Antibody Test 560
Molecular Diagnosis 560
ENVIRONMENTAL MICROBIOLOGY STUDIES 561
Isolation of Legionella From Environmental Samples 561
Typing of Legionella Isolates 561
Chapter 11
Neisseria Species and Moraxella catarrhalis
TAXONOMY OF THE FAMILY NEISSERIACEAE
AND THE FAMIL Y MORAXELLACEAE 568
GENERAL CHARACTERISTICS OF THE GENUS
NEISSERIA 569
XViM Expanded Contents
CLINICAL SIGNIFICANCE OF NEISSERIA
SPECIES 570
Neisseria gonorrhoeae 570
Epidemiology 570
Infections Caused by N. gonorrhoeae 573
Neisseria meningitidis 578
Epidemiology 578
Infections Caused by N. meningitidis 580
Meningococcal Prophylaxis and Meningococcal Vaccines 582
Other Neisseria Species 584
CLINICAL SIGNIFICANCE OF MORAXELLA
CATARRHALIS 585
ISOLA TION OF NEISSERIA SPECIES 588
Neisseria gonorrhoeae 588
Direct Gram Stained Smears 588
Specimen Collection 588
Specimen Transport 589
Selective Culture Media: Inoculation and Incubation 590
Neisseria meningitidis 591
Laboratory Safety 591
Direct Gram Stained Smears and Direct Capsular Antigen Tests 591
Specimen Collection and Transport 591
Isolation and Incubation 591
IDENTIFICATION OF NEISSERIA SPECIES 592
Colony Morphology 592
Gram Stain and Oxidase Test 593
Superoxol Test 593
Differentiation of Other Organisms on Selective Media 593
Presumptive Criteria for Identification of N. gonorrhoeae 593
Identification Tests for Neisseria Species 593
Carbohydrate Utilization Tests 594
Conventional CTA Carbohydrates 594
Rapid Carbohydrate Utilization Test 594
RIM Neisseria Test (Rapid Identification Method Neisseria) 594
Other Carbohydrate Utilization Methods. 594
Chromogenic Enzyme Substrate Tests 594
Gonochek II 595
BactiCard Neisseria 595
Immunologic Methods for Culture Confirmation of N. gonorrhoeae 596
Direct Fluorescent Monoclonal Antibody Test 596
Coagglutination Tests 596
GonoGen II Test 596
Multitest Identification Systems 597
DNA Probe Test for Culture Confirmation of N. gonorrhoeae 597
Nucleic Acid Hybridization and Amplification Tests for
N. gonorrhoeae 597
Molecular Methods for Detection of N. meningitidis 599
CULTURAL CHARACTERISTICS OF NEISSERIA
SPECIES 600
Neisseria gonorrhoeae 600
Neisseria meningitidis 602
Other Neisseria Species 603
Neisseria lactamica 603
Neisseria cinerea 603
Neisseria flavescens 603
Neisseria subflava Biovars, Neisseria mucosa. and Neisseria sicca 603
Neisseria polysaccharea 604
Neisseria eiongata Subspecies 604
Neisseria gonorrhoeae Subspecies kochii (¦¦Neisseria kochii') 604
Atypical and Non Human Neisseria Species 604
CULTURAL CHARACTERISTICS AND
IDENTIFICATION OF MORAXELLA
CATARRHALIS 604
ANTIMICROBIAL SUSCEPTIBILITY OF
NEISSERIA SPECIES 605
Neisseria gonorrhoeae 605
Neisseria meningitidis 607
ANTIMICROBIAL SUSCEPTIBILITY OF
MORAXELLA CATARRHALIS 608
Chapter 12
Gram Positive Cocci Part I: Staphylococd and Related Gram
Positive Cocci
TAXONOMY OF STAPHYLOCOCCI AND
RELA TED GRAM POSITIVE COCCI 624
CLINICAL SIGNIFICANCE OF STAPHYLOCOCCI
AND RELA TED GRAM POSITIVE COCCI 625
Staphylococcus aureus Subsp. aureus 625
Coagulase Negative Staphylococci 638
Staphylococcus epidermidis 638
Staphylococcus saprophyticus Subsp. saprophyticus 641
Other Coagulase Negative Staphylococci 642
Micrococcus Species and Related Genera 642
Rothia mucilaginosa 642
ISOLATION AND PRELIMINARY
DIFFERENTIATION OF STAPHYLOCOCCI
AND RELA TED GRAM POSITIVE COCCI 643
Direct Gram Stained Smears 643
Isolation From Clinical Specimens 643
Colony Morphology 643
The Catalase Test 644
Methods for Differentiating Micrococci and Staphylococci 644
Fermentation of Glucose 644
Susceptibility to Lysostaphin 645
Production of Acid From Glycerol in the Presence of Erythromycin 645
Susceptibility to Furazolidone 645
Modified Oxidase Test 645
Susceptibility to Bacitracin 645
IDENTIFICATION OF STAPHYLOCOCCUS
AUREUS 645
Slide Coagulase Test 645
Tube Coagulase Test 646
Alternative Coagulase Test Procedures 646
Latex Agglutination 646
Passive Hemagglutination 646
Additional Confirmatory Tests 647
Deoxyribonuclease (DNase) Test 647
Thermostable Endonuclease Test 648
Mannitol Fermentation 648
Other Methods for Identification of Staphylococcus aureus 648
Rapid Tests for Detection of Methicillin Resistance 648
Differentiation of Coagulase Positive Staphylococci
of Veterinary Origin 648
IDENTIFICATION OF COAGULASE NEGATIVE
STAPHYLOCOCCI 649
Conventional Identification Methods 649
Production of Phosphatase for Identification of
Staphylococcus epidermidis 650
Pyrrolidonyl Arylamidase Activity 650
Susceptibility to Polymyxin B 652
Omithine Decarboxylase Test (ODC) 652
Urease Production 655
Acetoin Production 655
Susceptibility to Deferoxamine 655
Susceptibility to Novobiocin for Identification of Staphylococcus
saprophyticus 655
Commercial Identification Systems 655
RapiDEC Staph 656
API Staph IDENT 656
API Staph 656
API ID32 Staph 656
Vitek Gram Positive Identification (GPI) Card 657
MicroScan Rapid Pos Combo Panel 657
MicroScan Pos ID Panel 657
BBL Crystal Gram Positive (GP) Identification System 657
Staf Sistem 18 R 658
Staph Zym 658
Microbact Staphylococcal 12S 658
Microbial Identification System 658
Biolog Microplate Identification System 658
Molecular Identification and Typing Methods for Staphylococci 658
Identification of Micmcoccus and Related Species 661
Identification of Rothia mucilaginosa 661
LABORATORY APPROACH TO THE
IDENTIFICATION OF STAPHYLOCOCCI 661
Chapter 13
Gram Positive Cocci Part III Streptococci, Enterococci, and the
"Streptococcus Like" Bacteria
GENERAL CHARACTERISTICS OF THE
STREPTOCOCCI 674
GROUP A p HEMOLYTIC STREPTOCOCCI
(STREPTOCOCCUS PYOGENES) 676
Virulence Factors 676
Clinical Significance 679
GROUP B p HEMOLYTIC STREPTOCOCCI
(STREPTOCOCCUS AGALACTIAE) 683
Virulence Factors 683
Clinical Significance 684
GROUP C AND GROUP G /3 HEMOLYTIC
STREPTOCOCCI 688
GROUP F p HEMOL YTIC STREPTOCOCCI 689
OTHER STREPTOCOCCI IN THE "PYOGENIC
COCCI" GROUP 689
STREPTOCOCCUS PNEUMONIAE 689
Virulence Factors 689
Pneumococcal Vaccines 690
Clinical Significance 691
Expanded Contents XJX
VIRIDANS STREPTOCOCCI 693
THEANGINOSUS GROUP: STREPTOCOCCUS
ANGINOSUS, STREPTOCOCCUS
CONSTELLATUS, AND STREPTOCOCCUS
INTERMEDIUS 695
GROUP D STREPTOCOCCI: THE
"STREPTOCOCCUS BOVIS/STREPTOCOCCUS
EQUINUS COMPLEX" AND RELATED
SPECIES 697
STREPTOCOCCUS SUIS 698
OTHER VIRIDANS STREPTOCOCCI ISOLATED
FROM ANIMALS 700
MISCELLANEOUS STREPTOCOCCI 700
ENTEROCOCCUS SPECIES 700
Taxonomy 700
Virulence Factors 701
Clinical Significance 701
Genus Melissococcus 704
THE "STREPTOCOCCUS LIKE" BACTERIA 704
Abiotrophia and Granulicatella Species 704
Aerococcus and Helcococcus Species 705
Leuconostoc Species 706
Pediococcus and Tetragenococcus Species 706
Gemella Species 707
Vagococcus Species 707
Alloiococcus Species 708
Globicatella Species 708
Facklamia Species 708
Dolosigranulum, Ignavigranum, and Dolosicoccus Species 709
Eremococcus Species 709
Genus Lactococcus 709
ISOLATION AND IDENTIFICATION OF
STREPTOCOCCI AND
"STREPTOCOCCUS LIKE" BACTERIA 709
Direct Gram Stained Smears 709
Culture Media 710
Hemolysis on Blood Agar 710
Nonculture, Direct Detection Techniques for Group A
|5 Hemolytic Streptococci in Pharyngeal Specimens 711
Nonculture, Direct Detection Techniques for Group B
fj Hemolytic Streptococci and Streptococcus pneumoniae 712
Colony Morphology and Catalase Testing 713
Recognition and Preliminary Characterization of Streptococci
and the "Streptococcus Like" Bacteria 713
Presumptive Identification of Streptococci 715
Susceptibility to Bacitracin 715
Susceptibility to Sulfamethoxazole Trimethoprim (SXT) 715
CAMP Test and Pigment Production 717
Hydrolysis of Sodium Hippurate 717
Bile Esculin Test 717
Sait Tolerance Test (6.5% NaCI Broth) 717
Leucine Aminopeptidase (LAP) Test 718
Pyrrolidonyl Arylamidase (PYR) Test 718
Susceptibility to Optochin 718
Bile Solubility Test 718
Commercial Presumptive Identification Tests 718
XX Expanded Contents
Serologic Identification of [1 Hemolytic Streptococci 718
Capillary Precipitin Test 718
Coagglutination 718
Latex Agglutination 719
Serologic Identification of Streptococcus pneumoniae 719
Biochemical Characteristics for Identification of
Groupable Streptococci 719
Identification of the Viridans Streptococci 719
Sanguis Group 722
Mitis Group 722
Mutans Group 722
Salivarius Group 722
Anginosus Group 725
Bovis Group 726
Identification of Streptococcus suis and Other Streptococci
Isolated From Animals 726
Identification of Enterococcus Species 726
Identification of Abiotrophia and Granulicatella Species 731
Identification of Aerococcus and Helcococcus Species 731
Identification of Leuconostoc, Pediococcus, and
Tetragenococcus Species 734
Identification of Gemella Species 736
Identification of Vagococcus Species 736
Identification of Alloiococcus, Globicatella, Facklamia,
Dolosigranulum, Ignavigranum, and Dolosicoccus Species 738
Identification of Lactococcus Species 742
Commercially Available Systems for Identification of Streptococci,
Enterococci, and Selected "Streptococcus Like" Bacteria 742
API Rapid Strep 743
BBL Crystal Gram Positive Identification System 743
Rapid ID 32 Strep 744
RapID STR 744
Vitek Gram Positive Identification (GPI) Card 744
Microscan Gram Positive Breakpoint Combo Panel 745
Chapter 14
Aerobic and Facultative Gram Positive
Bacilli LISTERIA SPECIES AND LISTERIA
MONOCYTOGENES 766
Taxonomy of the Genus Listeria 766
Virulence Factors of L monocytogenes 768
Epidemiology of L monocytogenes 768
Clinical Significance of L. monocytogenes 768
Isolation of L monocytogenes From Clinical Specimens 770
Identification of Listeria Species 770
Antimicrobial Susceptibility and Treatment of Listeria Infections 773
Pathogenicity of Other Listeria Species 773
ERYSIPELOTHRIX SPECIES: ERYSIPELOTHRIX
RHUSIOPATHIAE AND ERYSIPELOTHRIX
TONSILLARUM 773
Taxonomy of the Genus Erysipelothrix 773
Virulence Factors of £ rhusiopathiae 774
Clinical Significance of £ rhusiopathiae 774
Isolation and Identification of £ rhusiopathiae 775
Antimicrobial Susceptibility of £ rhusiopathiae 775
BACILLUS SPECIES AND RELA TED GENERA 775
Taxonomy and the Taxonomic Dissection of the Genus Bacillus 775
Bacillus anthracis 776
Epidemiology of Anthrax 776
Virulence Factors of B. anthracis 111
Clinical Presentations of Anthrax 777
Treatment of Anthrax 778
Prevention of Anthrax 778
Bacillus cereus 778
Virulence Factors of B. cereus 778
B. cereus Gastroenteritis 779
Opportunistic Bacillus Species Infections 779
Bacteremia and Endocarditis 779
Infections in Compromised Hosts 780
Ocular Infections 780
Musculoskeletal Infections 780
Nosocomial Infections 780
Laboratory Safety, Specimen Collection, and Processing 781
Isolation and Identification of Bacillus Species: The
"Bacillus cereus Group": B. anthracis, B. cereus,
B. thuringiensis, and B. mycoides 781
Antimicrobial Susceptibility of Bacillus Species 783
CORYNEBACTERIUM SPECIES 783
Introduction and Taxonomy 783
Identification of Corynebacterium Species and the
Coryneform Bacteria 785
Antimicrobial Susceptibility Testing of Corynebacterium
Species and the Coryneform Bacteria 797
Members of the Genus Corynebacterium Isolated From Humans 797
Corynebacterium amycolatuin 798
Corynebacterium diphtheriae 803
Corynebacterium jeikeium 807
Corynebacterium pseudodiphtheriticum 808
Corynebacterium striatum 808
Corynebacterium urealyticum 808
Corynebacterium Species Associated With Animals 809
Corynebacterium Species Isolated From Foods and
the Environment 810
OTHER CORYNEFORM BACTERIA 810
Actinobaculum Species 810
Actinomyces Species Isolated From Humans 811
Actinomyces Species Isolated From Animals 817
Arcanobacterium Species 817
Arthrobacter Species 823
Brevibacterium Species 823
Cellulomonas, Cellulosimicrobium, and Oerskovia Species 826
Dermabacter Species 828
Exiguobacterium Species 828
Leifsonia Species 830
Microbacterium (Aureobacteriuni) Species 830
Rothia and "Rothia Like" Species (CDC Group 4) 832
Turicella Species 834
GARDNERELLA VAGINAL IS 834
Taxonomy and Cellular Morphology 834
Virulence Factors of 6. vaginalis 835
Clinical Significance of G. vaginalis 835
Isolation and Identification 836
Antimicrobial Susceptibility 838
LACTOBACILLUS SPECIES 838
Taxonomy and Epidemiology 838
Clinical Significance 839
Isolation and Identification 840
Antimicrobial Susceptibility 840
Chapter 15
Aerobic Actinomycetes INTRODUCTION, CLASSIFICATION, AND
TAXONOMY 858
THE NOCARDIOFORM GROUP 860
Nocardia 860
Epidemiology, Pathology, and Pathogenesis 861
Clinical Disease 862
Rhodococcus 863
Epidemiology, Pathology, and Pathogenesis 863
Clinical Disease 863
Other Nocardioform Bacteria 863
THE MADUROMYCETES AND
THERMOMONOSPORAS 864
Actinomadura 864
Epidemiology 864
Clinical Disease and Pathology 864
Nocardiopsis 864
THE STREPTOMYCETES 865
Streptomyces 865
THERMOPHILIC ACTINOMYCETES 865
MISCELLANEOUS ACTINOMYCETES 865
Oerskovia 865
Dermatophilus 865
Tropheryma whipplei 865
History and Taxonomy 865
Ecology 866
Clinical Disease and Pathology 866
LABORATORY DIAGNOSIS OF INFECTIONS
CAUSED BY AEROBIC ACTINOMYCETES 866
Primary Isolation 866
Differentiation of Nocardia From Other Genera of
Aerobic Actinomycetes 867
Identification of Thermophilic Actinomycetes 871
Identification of Tropheryma whipplei 871
In Vitro Susceptibility of Nocardia and Related Bacteria to
Antimicrobial Agents and Therapy of Infections 871
Chapter 16
The Anaerobic Bacteria RELATIONSHIPS OF BACTERIA TO OXYGEN 878
Oxygen Tolerance 879
Oxidation Reduction Potential 879
HABITATS 880
TAXONOMIC CLASSIFICATION AND
NOMENCLATURE 880
HUMAN INFECTIONS 887
ISOLA TION OF ANAEROBIC BACTERIA 890
Selection of Specimens for Culture 890
Collection and Transport of Specimens 891
Anaerobic Blood Culture (Summary of Guidelines for
Traditional Broth and Instrumented Systems) 891
Direct Examination of Clinical Materials 892
Selection and Use of Media 893
Expanded Contents XXI
ANAEROBIC SYSTEMS FOR THE
CULTIVATION OF ANAEROBIC BACTERIA 895
Anaerobic Jar Techniques 895
Use of the Anaerobic Glove Box 897
The Roll Streak System 897
Anaerobic Disposable Plastic Bags 898
Use of the Anaerobic Holding Jar 898
INCUBA TION OF CUL TURES 898
INSPECTION AND SUBCULTURE OF
COLONIES 900
AEROTOLERANCE TESTS 900
PRELIMINARY REPORTING OF RESUL TS 901
DETERMINATION OF CULTURAL AND
BIOCHEMICAL CHARACTERISTICS FOR
DIFFERENTIATION OF ANAEROBIC
ISOLATES 901
Presumptive Identification 901
Use of Differential Agar Media 901
Presumpto Plates 902
Antimicrobial Susceptibility Plates 904
Characterization of Anaerobes Using Conventional Biochemical
Tests in Large Tubes 904
Alternative Procedures 905
The Nagler Test and the CAMP Test for C. perfringens 905
Packaged Microsystems 905
Commercial Packaged Kits for Identification of Anaerobes
After 4 Hours of Incubation 905
DETERMINATION OF METABOLIC PRODUCTS
BY GAS LIQUID CHROMATOGRAPHY 906
Identification of Volatile Fatty Acids 906
Analysis of Nonvolatile Acids 908
Gas Liquid Chromatography Controls 909
IDENTIFICA TION OF ANAEROBIC BACTERIA 909
Anaerobic Gram Negative Non Spore Forming Bacilli 912
Classification and Nomenclature 912
Presumptive or Preliminary Group Identification of Bacteroides,
Prevotella, Porphyromonas, and Fusobacterium 913
Identification of the Anaerobic Cocci 924
Identification of the Anaerobic Non Spore Forming
Gram Positive Bacilli 927
Propionibacterium Species 927
Bifidobacterium Species 927
Lactobacillus Species 930
Actinomyces Species 930
Eubacterium Species 930
Mobiluncus and Bacterial Vaginosis 931
Additional Genera and Species of Anaerobic Non Spore Forming
Gram Positive Bacilli 931
Identification of Clostridium Species 931
Histotoxic Clostridia Involved in Clostridial Myonecrosis or
Gas Gangrene 932
Miscellaneous Clostridia in Other Clinical Settings 935
Clostridium Gf/ffic/fe Associated Intestinal Disease 936
Botulism 937
Tetanus 938
XXii Expanded Contents
ANTIMICROBIAL SUSCEPTIBILITY TESTING
OF ANAEROBIC BACTERIA 939
Methods for Antimicrobial Susceptibility Testing of Anaerobes 939
Chapter 17
Antimicrobial Susceptibility Testing HISTORICAL INTRODUCTION 946
BACTERIAL RESISTANCE TO ANTIMICROBIAL
AGENTS 947
Mechanistic Variables 947
Mechanisms of Resistance 949
Transport of Antimicrobial Agents Across the Cell Wall and
Cell Membranes 949
Antibiotics That Interfere With Formation of Bacterial Cell Walls:
The f Lactam and Glycopeptide Antibiotics 955
Antimicrobial Agents That Do Not Exert Their Effect on Cell Walls 961
Interactions Among Resistance Mechanisms 963
LABORATORY GUIDANCE OF ANTIMICROBIAL
THERAPY 963
TESTS FOR DETERMINING INHIBITORY
ACTIVITY OF ANTIMICROBIAL AGENTS 968
Indications 968
Choice of Test 968
Selection of Antimicrobial Agents 970
Standardization 970
Growth Medium 970
pH 970
Serum 970
Cation Concentration 975
Atmosphere 975
Temperature 975
Inoculum 975
Antimicrobial Agents 975
Quality Control 976
Quality Assurance 977
Interpretation of Results 977
Selection of Antimicrobial Agents to Be Reported 981
Macrodilution Broth Susceptibility Test 982
Agar Dilution Susceptibility Test 982
Disk Diffusion Susceptibility Test 983
Development of a Standardized Disk Diffusion Procedure 986
Interpretation of Results 987
Quality Control 989
Limitations 989
Microbroth Dilution Susceptibility Test 989
Commercial Systems 993
Vitek (BioMerieuxVitek, Hazelwood, M0) and MicroScan
(Dade International, West Sacramento, CA) 993
Epsilometer Test (Etest; AB Biodisk, Sweden) 996
SPECIAL ISSUES IN SUSCEPTIBILITY TESTING 996
(l Lactamases 996
Staphylococcus Species 1001
Haemophilus Species 1002
Neisseria gonorrhoeae 1002
Moraxella (Branhamella) catarrhalis 1002
Enterococcus Species 1002
Extended Spectrum p Lactamases 1003
Staphylococcus Species 1004
p Lactam Antibiotics (Oxacillin Resistant Staphylococcus Species) 1004
Vancomycin 1007
Macrolides, Lincosamides, and Streptogramins 1008
Fluoroquinolones 1008
Haemophilus Species 1008
Penicillin Antibiotics 1009
Chloramphenicol 1009
Cephalosporins 1009
Trimethoprim Sulfamethoxazole 1009
Streptococcus pneumoniae 1009
Penicillin and Other p Lactam Antibiotics 1009
Multiple Resistance 1010
Macrolides and Lincosamides 1010
Neisseria gonorrhoeae 1011
Neisseria meningitidis 1011
Enterococcus Species 1011
Aminoglycoside Antibiotics 1012
p Lactam Antibiotics 1012
Vancomycin 1012
Listeria monocytogenes 1013
Streptococcus pyogenes (Group A p Hemolytic Streptococcus) 1013
Penicillin 1013
Erythromycin 1013
Fluoroquinolones 1013
Streptococcus agalactiae (Group B p Hemolytic Streptococcus) 1014
Viridans Streptococci 1014
Other Gram Positive Bacteria 1014
Pseudomonas aeruginosa, Burkholderia cepacia, and
Stenotrophomonas maltophilia in Patients With Cystic Fibrosis 1014
Direct Susceptibility Testing 1014
Chapter 18
Mycoplasmas and Ureaplasmas TAXONOMY OF MYCOPLASMAS AND
UREAPLASMAS 1023
VIRULENCE FACTORS OF HUMAN
MYCOPLASMAS 1026
CLINICAL SIGNIFICANCE OF THE HUMAN
MYCOPLASMAS 1027
Mycoplasma pneumoniae 1027
Mycoplasma hominis and Ureaplasma urealyticum 1028
Mycoplasma genitalium 1033
Mycoplasma fermentans 1034
Mycoplasma penetrans 1037
Mycoplasma pirum 1038
Mycoplasma primatum 1039
Mycoplasma spermatophilum 1039
Human Infections Due to Mycoplasma Species of Animal Origin 1039
Hemotrophic Mycoplasma Species 1039
CULTURE OF HUMAN MYCOPLASMAS FROM
CLINICAL SPECIMENS 1040
General Considerations 1040
Specimen Collection 1041
Transport Media 1041
Media for Culture of Mycoplasmas 1041
Isolation and Identification of Mycoplasma pneumoniae 1042
Noncultural Detection of Mycoplasma pneumoniae 1043
Isolation and Identification of the Genital Mycoplasmas 1044
Noncultural Detection of the Genital Mycoplasmas 1045
Commercial Mycoplasma Culture Systems 1047
Isolation of Mycoplasmas on Routine Culture Media 1048
SEROLOGIC TESTS FOR DIAGNOSIS OF
MYCOPLASMA PNEUMONIAE INFECTIONS 1048
SEROLOGIC TESTS FOR GENITAL
MYCOPLASMAS 1050
ANTIMICROBIAL SUSCEPTIBILITY AND
TREATMENT OF MYCOPLASMA INFECTIONS 1051
DIAGNOSIS AND TREATMENT OF
HEMOTROPHIC MYCOPLASMA INFECTIONS
IN ANIMALS 1054
Chapter 19
Mycobacteria TRENDS IN CLINICAL TUBERCULOSIS 1065
Worldwide Increase in the Incidence of Tuberculosis 1065
Impact of Coinfection With HIV and Mycobacterium tuberculosis 1066
Persons at Risk for Tuberculosis 1066
Rapidly Progressive Disease 1066
Implementation of More Aggressive Infection Control and
Epidemiologic Measures 1067
TRENDS IN THE LABORATORY DIAGNOSIS
OF TUBERCULOSIS 1067
Use of Molecular Techniques 1067
Use of Automated Instruments 1067
Use of Broth Culture Media 1067
Inoculation of Clinical Specimens to Agar Based Culture Media 1067
Use of p nitro acetylamino hydroxypropiophenone (NAP) 1068
Applications of Gas Liquid Chromatography, High Performance
Liquid Chromatography, and Mass Spectrometry 1068
Use of the Lysis Centrifugation System Blood Culture Tube 1068
THE CLINICAL LABORA TORY 1068
Optimizing the Detection and Identification of Mycobacteria 1068
Laboratory Safety 1068
SPECIMEN COLLECTION 1069
Respiratory Specimens 1069
Blood Cultures 1069
Stool Specimens 1070
Miscellaneous "Sterile" Specimens 1070
LABORATORY APPROACH TO THE RECOVERY
AND IDENTIFICA TION OF MYCOBACTERIA 1071
Specimen Preparation 1072
Digestion and Decontamination 1072
Centrifugation 1074
Bone Marrow and Biopsy Specimens 1074
Miscellaneous Liquid Specimens 1075
Staining of Acid Fast Bacilli 1075
CULTURE OF SPECIMENS FOR RECOVERY
OF MYCOBACTERIA 1077
Culture Media 1077
Nonselective Culture Media for Recovery of Mycobacteria 1077
Media of Cohen and Middlebrook 1078
Selective Media 1078
Incubation 1079
Expanded Contents XXJH
RAPID METHODS FOR ESTABLISHING
A DIAGNOSIS 1079
Sensitivity of Acid Fast Smears 1079
Gas Liquid and High Performance Liquid Chromatography 1080
Use of Broth Culture Medium 1080
AUTOMA TED DETECTION SYSTEMS 1080
BACTEC AFB System 1081
Mycobacteria Growth Indicator Tube (MGIT) and MGIT 960 1081
MB/BacT Mycobacteria Detection System 1082
The ESP Culture System II 1082
The BACTEC MYCO/F Lytic 1083
MANUAL DETECTION SYSTEMS 1083
Septi Chek AFB System 1083
IDENTIFICATION OF MYCOBACTERIA USING
CONVENTIONAL METHODS 1085
Optimal Temperature for Isolation and Rates of Growth 1085
Pigment Production 1086
Niacin Accumulation 1086
Reduction of Nitrates to Nitrites 1086
Tween 80 Hydrolysis 1087
Catalase Activity 1087
Arylsulfatase Activity 1087
Urease Activity 1087
Pyrazinamidase 1087
Iron Uptake 1087
Growth Inhibition by Thiophene 2 carboxylic Acid Hydrazide 1087
Growth in 5% Sodium Chloride 1087
Growth on MacConkey Agar 1090
CLASSIFICA TION OF MYCOBACTERIA 1090
Laboratory Identification of Mycobacteria and Related Clinical
Syndromes 1091
Review of Mycobacterium Species: Laboratory Aspects and
Clinical Correlations 1091
Mycobacterium tuberculosis Complex 1091
Photochromogens 1093
Scotochromogens 1095
Nonphotochromogens 1099
Rapid Growers 1104
Other Mycobacteria 1104
THE DETECTION AND IDENTIFICATION OF
MYCOBACTERIA BY MOLECUAR METHODS 1106
Signal Amplification Methods 1107
Nucleic Acid Probes 1107
In Situ Hybridization 1107
Nucleic Acid Amplification Methods 1108
Commercially Available Applications 1108
Home Brew PCR Assays, Including Real Time PCR 1109
Postamplification Analysis 1110
Reverse Hybridization 1110
DNA Sequencing 1111
Microarray Analysis 1111
Strain Typing and DNA Fingerprinting 1111
SUSCEPTIBILITY TESTING 1113
SHORT COURSE THERAPY 1115
American Thoracic Society Recommendations 1117
SUMMARY 1117
XXIV Expanded Contents
Chapter 2O
Spirochetal Infections TAXONOMY 1126
TREPONEMA 1126
Treponema pallidum Subspecies pallidum 1126
Incubation Period 1127
Primary Syphilis 1127
Secondary Syphilis 1127
Latent Syphilis 1127
Late Syphilis 1127
Epidemiology 1128
Immunity 1129
Treponema pallidum Subspecies pertenue 1129
Treponema pallidum Subspecies endemicum 1130
Treponema carateum 1130
Laboratory Diagnosis of Treponemal Infections 1130
Serologic Tests 1131
Innovations: Provisional and Investigative Tests 1133
BORRELIA 1134
Relapsing Fever 1134
Epidemiology 1134
Clinical Disease 1135
Laboratory Diagnosis 1135
Lyme Disease 1135
Epidemiology 1137
Clinical Disease 1139
Laboratory Diagnosis 1140
LEPTOSPIRA 1143
Leptospirosis 1144
Epidemiology 1144
Clinical Disease 1144
Laboratory Diagnosis 1144
SPIRILLUM MINOR (RAT BITE FEVER) 1146
Chapter 21
Mycology PATIENTS AT RISK FOR FUNGAL INFECTIONS 1153
General Signs and Symptoms Suggesting Fungal Infection 1153
CLINICAL CATEGORIZATION OF FUNGAL
INFECTIONS 1153
Common Mycologic Terms 1155
LABORATORY APPROACH TO THE
DIAGNOSIS OF FUNGAL INFECTIONS 1156
Specimen Collection and Transport 1158
Specimen Processing 1160
Direct Examination 1160
Preparation of Mounts for Study 1162
Selection and Inoculation of Culture Media 1162
Incubation of Fungal Cultures 1165
LABORATORY APPROACH TO THE
PRESUMPTIVE IDENTIFICATION OF
FUNGAL ISOLATES 1166
Extent of Laboratory Genus/Species Identification 1166
Genus and Species Identification of the Major Groups of Fungi 1168
Zygomyces Species and Zygomycosis 1168
Histopathology of Infections Caused by the Zygomycetes 1171
HYALINE MOLDS AND
HYALOHYPHOMYCOSIS 1172
Aspergillus Species and Aspergillosis 1174
Laboratory Presentation 1174
Colony Morphology 1174
Microscopic Features 1174
Aspergillus fumigatus 1175
Aspergillus flavus 1175
Aspergillus niger 1175
Aspergillus terreus 1176
Aspergillus nidulans 1177
Histopathology 1177
Diagnosis Using Nonculture Techniques 1179
Additional Rapidly Growing Hyaline Molds 1181
Colony Characteristics 1181
Genera of Hyaline Filamentous Molds Producing
Conidia in Chains 1181
Penicillium Species 1181
Paeciliomyces Species 1182
Scopulariopsis Species 1182
Identification of Hyaline Molds Producing Conidia in Clusters 1182
Acremonium Species 1182
Fusarium species 1183
Gliocladium Species 1183
Trichoderma Species 1184
Identification of the Genera of Hyalohyphomycetes
Producing Conidia Singly 1184
Scedosporium Species 1185
Chrysosporium Species 1186
Sepedonium Species 1186
Beauveria Species 1187
IDENTIFICA TION OF THE DERMA TOPHYTES 1187
Identification of Microsporum Species 1189
Microsporum canis 1189
Microsporum gypseum 1190
Microsporum nanum 1190
Identification of Trichophyton Species 1190
Trichophyton mentagrophytes 1190
Trichophyton rubrum 1190
Trichophyton tonsurans 1191
Trichophyton verrucosum 1191
Epidermophyton floccosum 1192
Diagnosis by Nonculture Techniques 1192
THE DIMORPHIC FUNGI 1192
Blastomyces dermatitidis and Blastomycosis 1194
Laboratory Presentation 1196
Diagnosis Using Nonculture Techniques 1197
Coccidioides immitis and Coccidioidomycosis 1199
Laboratory Presentation 1199
Histoplasma capsulatum and Histoplasmosis 1199
Laboratory Presentation 1200
Diagnosis Using Nonculture Techniques 1202
Sporothrix schenckii and Sporotrichosis 1203
Laboratory Presentation 1203
Diagnosis Using Nonculture Techniques 1203
Paracoccidioides immitis and Paracoccidioidomycosis 1203
Laboratory Presentation 1206
Diagnosis Using Nonculture Techniques 1206
DEMA TIACEOUS FUNGI 1208
Agents of Phaeohyphomycosis 1208
Laboratory Presentation 1208
Macroconidia With Transverse and Longitudinal
Septa (Muriform) 1208
Alternaria Species 1209
Ulocladium Species 1209
Stemphylium Species 1210
Epicoccum Species 1210
Macroconidia With Transverse Septa 1210
Bipolaris Species 1210
Drechslera Species 1210
Curvularia Species 1210
Exsemhilum Species 1210
Macroconidia Borne Singly or Via Special Conidiation 1210
Nigrospora Species 1211
Phoma Species 1211
Chaetomium Species 1211
AGENTS OF CHROMOMYCOSIS
AND MYCETOMA 1211
Cladophialophora (Cladosporium) carrionii 1214
Phialophora verrucosum 1215
Phialophora richardsiae 1215
Fonsecaea pedrosoi 1215
Exophiala jeanselmei 1216
THE LABORATORY IDENTIFICATION
OF YEASTS 1216
Germ Tube 1216
Cornmeal Agar Preparations 1218
Growth Patterns of Yeasts on Cornmeal Agar 1219
CHROMagar 1219
Candida albicans 1219
Candida tropicalis 1220
Candida parapsilosis 1220
Candida kefyr (pseudotropicalis) 1220
Other Emerging Pathogenic Candida Species 1220
Candida Species and Candidiasis 1221
Species That Produce True Hyphae 1221
Species That Fail to Produce True Hyphae 1224
Cryptococcosis and Cryptococcus neoformans 1224
Diagnosis by Nonculture Methods 1226
Miscellaneous Non Hyphae Forming Yeasts of
Medical Importance 1226
Candida (Torulopsis) glabrata 1226
Rhodotorula Species 1226
Saccharomyces Species 1226
Hansenula anomala 1228
Malassezia furfur 1228
Laboratory Identification of "Black Yeasts" 1229
Aureobasidium pullulans 1229
Phaeoannellomyces werneckii 1229
Packaged Yeast Identification Systems 1230
Antifungal Susceptibility Testing 1230
SEROLOGIC DIAGNOSIS OF FUNGAL
DISEASES 1232
Chapter 22
Parasitology RISK AND PREVENTION OF PARASITIC
INFECTIONS 1247
Expanded Contents XXV
CLINICAL MANIFESTATIONS OF PARASITIC
DISEASE 1247
COLLECTION, TRANSPORT, AND
PROCESSING OF SPECIMENS 1248
Fecal Specimens 1248
Preservation of Clinical Specimens 1249
Visual Examination 1249
Processing Fresh Stool Specimens for Ova and Parasite Examination 1249
Examination of Intestinal Specimens Other Than Stool 1253
Examination of Extraintestinal Specimens 1254
Sputum 1254
Urine and Body Fluids 1254
Tissue Biopsies and Aspirates 1254
Corneal Scrapings or Biopsy 1254
Muscle Biopsy 1254
Blood 1254
IDENTIFICATION AND DIFFERENTIATION OF
PARASITES 1255
Life Cycles of Human Parasites 1256
INTESTINAL PROTOZOA 1256
The Intestinal Amoebae 1258
Amebiasis and Entamoeba histolytica 1258
Entamoeba histolytica versus Entamoeba coli 1260
Serologic Diagnosis of Amebiasis 1260
Nonpathogenic Entamoeba histolytica: Entamoeba dispar 1261
Other Intestinal Amoebae 1262
Protozoa of Uncertain Classification 1262
Intestinal Flagellates 1263
Giardia lamblia 1263
Other Intestinal Flagellates 1266
Ciliates: Balantidium coli 1267
Coccidia 1267
Cryptosporidium parvum 1267
Cyclospora cayetanensis 1270
Isospora belli 1271
Sarcocystis Species 1271
Phylum Microsporum: Microsporidium Species 1272
NEMATODES 1273
Ascariasis and Ascaris lumbricoides 1274
Trichuriasis and Trichuris trichiura (Whipworm) 1274
Enterobius vermicularis 1275
Hookworms 1276
Strongyloidiasis and Strongyloides stercoralis 1279
Trichostrongylus Species 1279
Capillaria philippinensis 1280
CESTODES 1281
Taenia solium and Taenia saginata 1282
Diphyllobothrium latum The Giant Fish Tapeworm 1284
Hymenolepis Species 1285
Dipylidium caninum 1286
TREMATODES 1286
Schistosomes 1287
Fasciola hepatica and Fasciolopsis buski 1288
Clonorchis sinensis 1290
Paragonimus westermani 1292
BLOOD AND TISSUE PARASITES 1292
Malaria 1294
Babesia 1298
Hemoflagellates: Leishmania Species and Trypanosoma Species 1298
Leishmaniasis and Leishmania Species 1299
Trypanosomiasis 1299
XXVi Expanded Contents
Filarial Nematodes and Filariasis 1303
Onchocerciasis and Onchocerca volvulus 1305
Dracunculiasis 1306
Dirofilariasis 1306
Tissue Protozoan Infections 1306
Toxoplasma gondii 1306
Pneumocystis carinii 1311
Miscellaneous Larval Tissue Parasite Infections 1311
Trichinosis 1312
Visceral Larval Migrans 1312
Cutaneous Larva Migrans—Toxocara 1314
Anisakiasis 1314
Gnathostomiasis 1315
Angiostrongyliasis 1315
Echinococcosis (Hydatid Disease) 1315
Multiceps Species—Coenurosis 1316
Sparganosis: Spirometra mansonoides 1316
SEROLOGIC DIAGNOSIS OF PARASITIC
INFECTIONS 1318
DRUGS COMMONLY USED IN THE
TREA TMENT OF PARASITIC DISEASES 1321
Chapter 23
Diagnosis of Infections Caused by Viruses,
Chlamydia, Rickettsia, and Related Organisms
INTRODUCTION 1329
Historical Review 1329
Evolution of Cell Culture Techniques 1329
Evolution of Diagnostic Virology Services 1329
Levels of Service 1330
TAXONOMY AND NOMENCLA TURE 1330
CLINICAL MANIFESTATIONS OF VIRAL
INFECTIONS 1333
Orthomyxoviruses 1335
Paramyxoviruses 1342
Parainfluenza Viruses 1342
Mumps Virus 1344
Measles Virus 1344
Respiratory Syncytial Virus 1344
Other Paramyxoviruses 1344
Picornaviruses 1344
Rhabdoviruses 1345
Arenaviruses 1346
Filoviruses 1346
Togaviruses 1347
Bunyaviruses 1348
California Encephalitis Viruses 1348
Hantaviruses 1348
Human Gastroenteritis Viruses 1349
Rotaviruses 1350
Caliciviruses 1350
Astroviruses 1350
Enteric Adenoviruses 1350
Coronaviruses 1350
Coltiviruses 1351
Retroviruses 1351
Herpesviruses 1356
Herpes Simplex Virus 1356
Cytomegalovirus 1358
Epstein Barr Virus 1359
Varicella Zoster Virus 1359
Human Herpesviruses 6 and 7 1359
Human Herpesvirus 8 1360
B Virus 1360
Adenoviruses 1360
Poxviruses 1361
Papovaviruses 1361
Papillomaviruses 1362
Polyomaviruses 1364
Parvoviruses 1364
Hepatitis Viruses 1364
Hepatitis A Virus 1365
Hepatitis B Virus 1365
Hepatitis C Virus 1365
Hepatitis D Virus 1366
Hepatitis E Virus 1366
Prion Diseases (Transmissible Spongiform Encephalopathies) 1366
CLINICAL CLASSIFICATION OF VIRAL
INFECTIONS 1367
DIAGNOSIS OF VIRAL INFECTIONS 1367
Collection of Specimens for Diagnosis 1369
Transportation and Storage of Specimens 1373
Isolation of Viruses in Culture 1373
Preparation and Maintenance of Cell Cultures 1373
Contamination of Cell Cultures 1375
Technical Aspects of Cell Culture 1377
Selection of Cell Cultures for Isolation of Viruses 1380
Inoculation and Incubation of Cell Cultures 1380
Detection of Virus and Provisional Identification 1381
Cytopathic Effect 1381
Hemagglutination and Hemadsorption 1383
Light Microscopy 1387
Electron Microscopy 1387
Biochemical Differentiation 1387
Cell Association 1389
Detection of Viral Antigens 1389
Artifacts and Non Virus Induced Changes 1389
Definitive Identification of Isolates 1390
Storage of Viral Isolates 1391
Summary of Detection and Identification of Viruses in Culture 1391
DIRECT DETECTION OF VIRUSES IN CLINICAL
SPECIMENS 1392
Light Microscopic Detection of Inclusions 1392
Electron Microscopic Detection of Viral Particles 1393
Immunologic Detection of Viral Antigen 1393
Respiratory Viruses 1393
Herpes Group Viruses 1393
Other Viruses 1394
Molecular Techniques 1394
Human Immunodeficiency Virus 1394
Hepatitis C Virus 1395
Hepatitis B Virus 1396
Human Papillomaviruses 1396
Parvovirus B19 1396
West Nile Virus 1396
Herpes Simplex Virus 1396
Cytomegalovirus 1397
Enteroviruses 1397
SARS Coronavirus 1397
Other Viral Infections 1397
Selection of Tests for Rapid Diagnosis 1397
SEROLOGIC DIAGNOSIS OF VIRAL
INFECTIONS 1397
Human Immunodeficiency Virus 1398
Hepatitis B Virus and Epstein Barr Virus 1399
Hepatitis A Virus 1401
Hepatitis C Virus 1401
Parvovirus 1402
Herpes Simplex Virus 1402
Varicella Zoster Virus 1402
Cytomegalovirus 1402
West Nile Virus 1402
Rubella 1402
SARS Coronavirus 1402
Anti IgM Antibodies 1402
Miscellaneous Serologic Procedures 1403
Diagnosis of Other Viral Infections 1403
Antiviral Susceptibility Testing 1403
INFECTIONS WITH CHLAMYDIA SPECIES 1403
Chlamydia trachomatis 1403
Clinical Features and Epidemiology 1403
Collection of Specimens 1403
Isolation of Chlamydia trachomatis in Cell Culture 1405
Direct Detection of Chlamydia trachomatis in Clinical Specimens 1405
Serologic Diagnosis 1406
Other Methods for Diagnosis 1406
Diagnosis of Sexual Abuse 1406
Chlamydia psittaci 1406
Chlamydia pneumoniae 1406
INFECTIONS WITH RICKETTSIA, COXIELLA,
EHRLICHIA, AND ANAPLASMA 1407
Rickettsia and Coxiella 1407
Clinical Features and Epidemiology 1407
Collection of Specimens 1408
Isolation of Rickettsia and Coxiella in Culture 1408
Direct Detection of Antigen and Nucleic Acid in Clinical Specimens 1409
Serologic Diagnosis 1409
Ehrlichia and Anaplasma Species 1409
Appendix I 1420
Appendix II 1437
Charts Chart 1 1 Catalase 1443
Chart 1 2 Bile Solubility Test 1443
Chart 1 3 The Slide Coagulase Test 1444
Chart 1 4 Indole Test 1445
Chart 1 5 Cytochrome Oxidase Test 1447
Chart 1 6 PYR Test 1448
Chart 3 1 Complement Fixation (CF) Test 1448
Chart 3 2 Hemagglutination Inhibition (HAI) Test 1450
Chart 6 1 o Nitrophenyl p o Galactopyranoside 1451
Chart 6 2 Nitrate Reduction: General Applications 1452
Chart 6 3 Methyl Red 1453
Chart 6 4 Voges Proskauer Test 1454
Chart 6 5 Citrate Utilization 1456
Chart 6 6 Urease: Conventional 1457
Expanded Contents XXVii
Chart 6 7 Decarboxylases 1459
Chart 6 8 Phenylalanine Deaminase 1461
Chart 7 1 Oxidative Fermentative Test (Hugh and Leifson) 1462
Chart 7 2 Flagellar Stain 1463
Chart 7 3 Fluorescence Denitrification 1465
Chart 7 4 Esculin Hydrolysis Test 1466
Chart 8 1 The CAMP Test 1468
Chart 9 1 Test for X and V Factor Requirements 1469
Chart 11 1 Rapid Carbohydrate Utilization Test for Identification of
Neisseria Species 1470
Chart 12 1 Furazolidone Disk Test 1471
Chart 12 2 Novobiocin Disk Test 1471
Chart 13 1 Bacitracin and SXT Susceptibility Tests 1472
Chart 13 2 Bile Esculin Test 1473
Chart 13 3 Optochin Susceptibility Test 1474
Chart 13 4 Salt Tolerance Test 1474
Chart 14 1 Loefflers'Methylene Blue Stain 1475
Chart 14 2 Loefflers'Serum Medium 1476
Chart 14 3 Tinsdales' Agar (as Modified by Moore and Parsons)
1477
Chart 14 4 Cystine Tellurite Blood Agar 1478
Chart 15 1 Hydrolysis of Xanthine, Hypoxanthine, Tyrosine, and
Casein 1478
Chart 17 1 Disk Diffusion (Bauer Kirby) Susceptibility Test for
Nonfastidious Bacteria 1480
Chart 17 2 Performance of Microbroth Dilution Susceptibility Tests
with Nonfastidious Bacteria 1481
Chart 17 3 Gradient Diffusion Test (Etest) for Bacterial
Susceptibility 1482
Chart 18 1 Diene's Stain Procedure for Identification of
Mycoplasmas 1483
Chart 18 2 Hemadsorption Test for Identification of Mycoplasma
pneumoniae 1484
Chart 18 3 Manganous Chloride Urea Test for Identification of
Ureaplasma urealyticum 1484
Chart 18 4 Medium for Isolation of Mycoplasma pneumoniae 1485
Chart 18 5 Medium for Isolation of the Genital Mycoplasmas 1487
Chart 18 6 Tetrazolium Reduction Test for the Presumptive
Identification of Mycoplasma pneumoniae 1488
Chart 19 1 Digestion and Decontamination: /V Acetyl
L cysteine Sodium Hydroxide (NALC) 1489
Chart 19 2 Carbol Fuchsin Stains 1491
Chart 19 3 Fluorescent Stain: Auramine 0; Auramine Rhodamine
1492
Chart 19 4 NAP Test (p Nitro a Acetylamino
p Hydroxypropiophenone); (BACTEC) 1494
Chart 19 5 Arylsulfatase 1496
Chart 19 6 Assessment of Photoreactivity of Mycobacteria 1497
Chart 19 7 Catalase 68°C 1499
Chart 19 8 Growth on MacConkey Agar 1500
Chart 19 9 Inhibition by Thiophene 2 carboxylic Acid Hydrazide (T2H,
ijxg/mL) 1501
Chart 19 10 Iron Uptake 1502
Chart 19 11 Niacin Accumulation 1502
Chart 19 12 Nitrate Reduction: Mycobacteria 1504
Chart 19 13 Pyrazinamidase 1505
Chart 19 14 Sodium Chloride Tolerance: Mycobacteria 1506
Chart 19 15 Tween 80 Hydrolysis 1507
Chart 19 16 Urease: Mycobacteria 1508
Chart 19 17 DNA Probes for the Identification of Mycobacteria 1509
Chart 19 18 Detection, Identification, and Drug Susceptibility Testing
of M. tuberculosis by Radiometric Instrumentation 1511
XXVlii Expanded Contents
Chart 20 1 Darkfield Microscopy of Genital Lesions 1513
Chart 20 2 Venereal Disease Research Laboratory (VDRL) Slide Test
on Serum 1514
Chart 20 3 Rapid Plasma Reagin (RPR) Card Test 1517
Chart 20 4 Fluorescent Treponemal Antibody Absorption Test (FTA
ABS) 1521
Chart 22 1 Fecal Concentration Techniques for the Recovery of
Intestinal Parasites 1525
Chart 22 2 Trichrome Staining Technique for Fecal Smears 1528
Chart 22 3 Preparation of Thin and Thick Blood Smears 1529
Chart 22 4 Calibration of the Ocular Micrometer 1531
Chart 22 5 Cellulose Tape Preparation for Pinworm Examination
1533
Chart 23 1 Hemadsorption (HAD) Test 1534
Chart A 1 Formulations of Commonly Used Stool Preservatives 1535
Color Plates Index |
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| id | DE-604.BV022492428 |
| illustrated | Illustrated |
| index_date | 2024-07-02T17:52:24Z |
| indexdate | 2024-07-09T20:58:47Z |
| institution | BVB |
| isbn | 0781730147 9780781730143 |
| language | English |
| lccn | 2005008049 |
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| physical | XXXI, 1535, 30 S. Ill. |
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| spelling | Koneman's Color atlas and textbook of diagnostic microbiology Washington C. Winn ... Color atlas and textbook of diagnostic microbiology 6. ed. Philadelphia [u.a.] Lippincott Williams & Wilkins 2006 XXXI, 1535, 30 S. Ill. txt rdacontent n rdamedia nc rdacarrier 5. Aufl. u.d.T.: Color atlas and textbook of diagnostic microbiology Microbiologie clinique - Atlas Techniques et procédures de laboratoire Diagnostic microbiology Atlases Microbiology Laboratory Manuals Laboratory Techniques and Procedures Mikrobiologische Diagnostik (DE-588)4194941-9 gnd rswk-swf Mikrobiologische Diagnostik (DE-588)4194941-9 s DE-604 Winn, Washington C. Sonstige oth Koneman, Elmer W. 1932- Sonstige (DE-588)125010613 oth http://www.loc.gov/catdir/enhancements/fy0712/2005008049-d.html Publisher description HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=015699617&sequence=000008&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Koneman's Color atlas and textbook of diagnostic microbiology Microbiologie clinique - Atlas Techniques et procédures de laboratoire Diagnostic microbiology Atlases Microbiology Laboratory Manuals Laboratory Techniques and Procedures Mikrobiologische Diagnostik (DE-588)4194941-9 gnd |
| subject_GND | (DE-588)4194941-9 |
| title | Koneman's Color atlas and textbook of diagnostic microbiology |
| title_alt | Color atlas and textbook of diagnostic microbiology |
| title_auth | Koneman's Color atlas and textbook of diagnostic microbiology |
| title_exact_search | Koneman's Color atlas and textbook of diagnostic microbiology |
| title_exact_search_txtP | Koneman's Color atlas and textbook of diagnostic microbiology |
| title_full | Koneman's Color atlas and textbook of diagnostic microbiology Washington C. Winn ... |
| title_fullStr | Koneman's Color atlas and textbook of diagnostic microbiology Washington C. Winn ... |
| title_full_unstemmed | Koneman's Color atlas and textbook of diagnostic microbiology Washington C. Winn ... |
| title_short | Koneman's Color atlas and textbook of diagnostic microbiology |
| title_sort | koneman s color atlas and textbook of diagnostic microbiology |
| topic | Microbiologie clinique - Atlas Techniques et procédures de laboratoire Diagnostic microbiology Atlases Microbiology Laboratory Manuals Laboratory Techniques and Procedures Mikrobiologische Diagnostik (DE-588)4194941-9 gnd |
| topic_facet | Microbiologie clinique - Atlas Techniques et procédures de laboratoire Diagnostic microbiology Atlases Microbiology Laboratory Manuals Laboratory Techniques and Procedures Mikrobiologische Diagnostik |
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