| Author: | |
| Published in: | Mosby |
| Release Year: | 2016 |
| ISBN: | 978-0323-3-5482-0 |
| Pages: | 1136 |
| Edition: | Fourteenth edition |
| File Size: | 133 MB |
| File Type: | |
| Language: | English |
Description of Bailey & Scott’s Diagnostic Microbiology
This, the fourteenth edition of Bailey and Scott’s Diagnostic Microbiology is the second edition that I have had the great pleasure to edit and author with some amazing colleagues. The dynamics of infectious disease trends, along with the technical developments available for diagnosing, treating, and controlling these diseases, continues to present major challenges in the laboratory and medical care.
In meeting these challenges, the primary goal for the fourteenth edition is to provide an updated and reliable reference text for practicing clinical microbiologists and technologists, while also presenting this information in a format that supports the educational efforts of all those responsible for preparing others for a career in diagnostic microbiology.
The text retains the traditional information needed to develop a solid, basic understanding of diagnostic microbiology while integrating the dynamic expansion of molecular diagnostics and advanced techniques such as matrix-assisted laser desorption time-of-flight mass spectrometry.
In meeting these challenges, the primary goal for the fourteenth edition is to provide an updated and reliable reference text for practicing clinical microbiologists and technologists, while also presenting this information in a format that supports the educational efforts of all those responsible for preparing others for a career in diagnostic microbiology.
The text retains the traditional information needed to develop a solid, basic understanding of diagnostic microbiology while integrating the dynamic expansion of molecular diagnostics and advanced techniques such as matrix-assisted laser desorption time-of-flight mass spectrometry.
Content of Bailey & Scott’s Diagnostic Microbiology
Part I Basic Medical Microbiology, 1
1 Microbial Taxonomy, 1
Classification, 2
Nomenclature, 2
Identification, 3
2 Bacterial Genetics, Metabolism,
and Structure, 5
Bacterial Genetics, 5
Bacterial Metabolism, 17
Structure and Function of the Bacterial Cell, 20
3 Host-Microorganism Interactions, 24
The Encounter Between Host and Microorganism, 25
Microorganism Colonization of Host Surfaces, 27
Microorganism Entry, Invasion, and Dissemination, 30
Outcome and Prevention of Infectious Diseases, 39
Part II General Principles in Clinical
Microbiology, 42
Section 1 Safety and Specimen Management, 42
4 Laboratory Safety, 42
Sterilization, Disinfection, and Decontamination, 42
Chemical Safety, 45
Fire Safety, 46
Electrical Safety, 46
Handling of Compressed Gases, 46
Biosafety, 47
Exposure Control Plan, 47
Employee Education and Orientation, 48
Disposal of Hazardous Waste, 48
Standard Precautions, 48
Engineering Controls, 49
Classification of Biologic Agents Based on Hazard, 52
Mailing Biohazardous Materials, 53
5 Specimen Management, 56
General Concepts for Specimen Collection and
Handling, 56
Specimen Preservation, 57
Specimen Workup, 69
Expediting Results Reporting: Computerization, 70
Section 2 Approaches to Diagnosis of Infectious
Diseases, 72
6 Role of Microscopy, 72
Bright-Field (Light) Microscopy, 72
Phase-Contrast Microscopy, 79
Fluorescent Microscopy, 80
Dark-Field Microscopy, 83
Electron Microscopy, 84
Digital Automated Microscopy, 85
7 Traditional Cultivation and Identification, 86
Organism Identification, 86
Principles of Bacterial Cultivation, 86
Bacterial Cultivation, 96
Principles of Identification, 99
Principles of Phenotypic Identification
Schemes, 106
Commercial Identification Systems
and Automation, 111
8 Nucleic Acid-Based Analytic Methods
for Microbial Identification and
Characterization, 113
Overview of Nucleic Acid-Based Methods, 114
Post amplification and Traditional Analysis, 135
9 Overview of Immunochemical Methods Used
for Organism Detection, 144
Features of the Immune Response, 144
Production of Antibodies for Use in Laboratory
Testing, 147
IgM Clinical Significance, 149
Separating IgM from IgG for Serologic Testing, 149
Principles of Immunochemical Methods Used for
Organism Detection, 149
Section 3 Evaluation of Antimicrobial
Activity, 161
10 Principles of Antimicrobial Action and
Resistance, 161
Antimicrobial Action, 161
Mechanisms of Antibiotic Resistance, 169
11 Laboratory Methods and Strategies for
Antimicrobial Susceptibility Testing, 177
Goal and Limitations, 177
Testing Methods, 178
Laboratory Strategies for Antimicrobial Susceptibility
Testing, 197
Accuracy, 199
Communication, 203
Part III Bacteriology, 205
Section 1 Principles of Identification, 205
12 Overview of Bacterial Identification Methods
and Strategies, 205
The rationale for Approaching Organism Identification, 205
Future Trends of Organism Identification, 206
Section 2 Catalase-Positive, Gram-Positive Cocci, 248
13 Staphylococcus, Micrococcus, and Similar
Organisms, 248
General Characteristics, 248
Epidemiology, 249
Pathogenesis and Spectrum of Disease, 249
Laboratory Diagnosis, 252
Antimicrobial Susceptibility Testing and Therapy, 259
Prevention, 261
Section 3 Catalase-Negative, Gram-Positive Cocci, 264
14 Streptococcus, Enterococcus, and Similar
Organisms, 264
General Characteristics, 265
Epidemiology, 265
Pathogenesis and Spectrum of Disease, 266
Laboratory Diagnosis, 270
Antimicrobial Susceptibility Testing and Therapy, 279
Prevention, 281
Section 4 Non-Branching, Catalase-Positive,
Gram-Positive Bacilli, 283
15 Bacillus and Similar Organisms, 283
General Characteristics, 283
Laboratory Diagnosis, 287
Antimicrobial Susceptibility Testing and Therapy, 290
Prevention, 292
16 Listeria, Corynebacterium, and Similar
Organisms, 294
General Characteristics, 294
Epidemiology, 294
Pathogenesis and Spectrum of Disease, 296
Laboratory Diagnosis, 298
Antimicrobial Susceptibility Testing and Therapy, 304
Prevention, 307
Treatment, 307
Section 5 Non-Branching, Catalase-Negative,
Gram-Positive Bacilli, 309
17 Erysipelothrix, Lactobacillus, and Similar
Organisms, 309
General Characteristics, 309
Epidemiology, 309
Pathogenesis and Spectrum of Disease, 309
Laboratory Diagnosis, 311
Antimicrobial Susceptibility Testing and Therapy, 315
Prevention, 315
Section 6 Branching or Partially Acid-Fast,
Gram-Positive Bacilli, 318
18 Nocardia, Streptomyces, Rhodococcus,
and Similar Organisms, 318
General Characteristics, 319
Epidemiology and Pathogenesis, 319
The spectrum of Disease, 321
Laboratory Diagnosis, 322
Antimicrobial Susceptibility Testing and Therapy, 326
Prevention, 326
Section 7 Gram-Negative Bacilli and Coccobacilli
(MacConkey-Positive, Oxidase-Negative), 329
19 Enterobacteriaceae, 329
General Characteristics, 330
Epidemiology, 330
Pathogenesis and Spectrum of Diseases, 332
Specific Organisms, 332
Laboratory Diagnosis, 338
Antimicrobial Susceptibility Testing and Therapy, 351
Prevention, 354
20 Acinetobacter, Stenotrophomonas, and Other
Organisms, 357
General Characteristics, 357
Epidemiology, 357
Pathogenesis and Spectrum of Disease, 358
Laboratory Diagnosis, 359
Antimicrobial Resistance and Antimicrobial
Susceptibility Testing, 362
Antimicrobial Therapy, 363
Prevention, 363
Section 8 Gram-Negative Bacilli and Coccobacilli
(MacConkey-Positive, Oxidase-
Positive), 365
21 Pseudomonas, Burkholderia, and Similar
Organisms, 365
General Characteristics, 365
Epidemiology, 366
Pathogenesis and Spectrum of Disease, 367
Laboratory Diagnosis, 369
Antimicrobial Susceptibility Testing and Therapy, 375
Prevention, 375
22 Achromobacter, Rhizobium, Ochrobactrum,
and Similar Organisms, 379
General Characteristics, 379
Epidemiology, 379
Pathogenesis and Spectrum of Disease, 379
Laboratory Diagnosis, 381
Antimicrobial Susceptibility Testing and Therapy, 383
Prevention, 383
23 Chryseobacterium, Sphingobacterium,
and Similar Organisms, 385
General Characteristics, 385
Epidemiology, 385
Pathogenesis and Spectrum of Disease, 386
Laboratory Diagnosis, 386
Antimicrobial Susceptibility Testing and Therapy, 388
Prevention, 389
24 Alcaligenes, Bordetella (Nonpertussis),
Comamonas, and Similar Organisms, 391
General Characteristics, 391
Epidemiology, 392
Pathogenesis and Spectrum of Disease, 392
Laboratory Diagnosis, 394
Antimicrobial Susceptibility Testing and Therapy, 396
Prevention, 398
25 Vibrio, Aeromonas, and Similar Organisms, 399
General Characteristics, 399
Epidemiology, 399
Pathogenesis and Spectrum of Disease, 400
Laboratory Diagnosis, 402
Antimicrobial Susceptibility Testing and Therapy, 406
Prevention, 406
Section 9 Gram-Negative Bacilli and Coccobacilli
(MacConkey-Negative, Oxidase-Positive), 408
26 Sphingomonas paucimobilis and Similar
Organisms, 408
General Considerations, 408
Epidemiology, Spectrum of Disease, and
Antimicrobial Therapy, 408
Laboratory Diagnosis, 408
Prevention, 413
27 Moraxella, 415
General Characteristics, 415
Epidemiology, Spectrum of Disease, and
Antimicrobial Therapy, 415
Laboratory Diagnosis, 416
Prevention, 418
28 Eikenella corrodens and Similar Organisms, 420
General Characteristics, 420
Epidemiology, Spectrum of Disease, and
Antimicrobial Therapy, 420
Laboratory Diagnosis, 421
Serodiagnosis, 423
Prevention, 423
29 Pasteurella and Similar Organisms, 425
General Characteristics and Taxonomy, 425
Epidemiology, Spectrum of Disease, and
Antimicrobial Therapy, 425
Laboratory Diagnosis, 426
Serodiagnosis, 429
Prevention, 429
30 Actinobacillus, Kingella, Cardiobacterium,
Capnocytophaga, and Similar Organisms, 430
General Characteristics, 430
Epidemiology, Pathogenesis, and Spectrum of
Disease and Antimicrobial Therapy, 431
Laboratory Diagnosis, 433
Serodiagnosis, 436
Prevention, 436
Section 10 Gram-Negative Bacilli and Coccobacilli
(MacConkey-Negative, Oxidase-
Variable), 438
31 Haemophilus, 438
General Characteristics, 438
Epidemiology, 438
Pathogenesis and Spectrum of Disease, 438
Laboratory Diagnosis, 440
Antimicrobial Susceptibility Testing and Therapy, 443
Prevention, 445
Section 11 Gram-Negative Bacilli that are Optimally
Recovered on Special Media, 446
32 Bartonella and Afipia, 446
Bartonella, 446
Afipia felis, 450
33 Campylobacter, Arcobacter, and
Helicobacter, 452
Campylobacter and Arcobacter, 452
Helicobacter spp., 457
34 Legionella, 462
General Characteristics, 462
Pathogenesis and Spectrum of Disease, 462
Laboratory Diagnosis, 465
Antimicrobial Susceptibility Testing and Therapy, 467
Prevention, 467
35 Brucella, 470
General Characteristics, 470
Epidemiology and Pathogenesis, 470
Spectrum of Disease, 471
Laboratory Diagnosis, 471
Antimicrobial Susceptibility Testing and Therapy, 473
Prevention, 473
36 Bordetella pertussis, Bordetella
parapertussis, and Related Species, 475
General Characteristics, 475
Spectrum of Disease, 476
Laboratory Diagnosis, 477
Antimicrobial Susceptibility Testing and Therapy, 479
Prevention, 479
37 Francisella, 480
General Characteristics, 480
Epidemiology and Pathogenesis, 480
Spectrum of Disease, 481
Laboratory Diagnosis, 481
Antimicrobial Susceptibility Testing and Therapy, 483
Prevention, 483
38 Streptobacillus moniliformis and Spirillum
minus, 485
Streptobacillus moniliformis, 485
Spirillum minus, 487
Section 12 Gram-Negative Cocci, 489
39 Neisseria and Moraxella catarrhalis, 489
General Characteristics, 489
Epidemiology, 489
Pathogenesis and Spectrum of Disease, 490
Laboratory Diagnosis, 490
Antimicrobial Susceptibility Testing and Therapy, 496
Prevention, 497
Section 13 Anaerobic Bacteriology, 499
40 Overview and General Laboratory
Considerations, 499
General Characteristics, 499
Specimen Collection and Transport, 499
Macroscopic Examination of Specimens, 500
Direct Detection Methods, 500
Specimen Processing, 504
Anaerobic Media, 505
Approach to Identification, 506
Antimicrobial Susceptibility Testing and Therapy, 509
41 Overview of Anaerobic Organisms, 513
Epidemiology, 514
Pathogenesis and Spectrum of Disease, 514
Prevention, 523
Section 14 Mycobacteria and Other Bacteria with
Unusual Growth Requirements, 524
42 Mycobacteria, 524
Mycobacterium tuberculosis Complex, 525
Nontuberculous Mycobacteria, 528
Laboratory Diagnosis of Mycobacterial Infections, 534
Antimicrobial Susceptibility Testing and Therapy, 550
Prevention, 552
43 Obligate Intracellular and Nonculturable
Bacterial Agents, 555
Chlamydia, 555
Rickettsia, Orientia, Anaplasma, and Ehrlichia, 563
Coxiella, 566
Tropheryma whipplei, 566
Klebsiella granulomatis, 567
44 Cell Wall-Deficient Bacteria: Mycoplasma
and Ureaplasma, 570
General Characteristics, 570
Epidemiology and Pathogenesis, 570
Spectrum of Disease, 572
Laboratory Diagnosis, 572
Cultivation, 574
Susceptibility Testing and Therapy, 576
Prevention, 577
45 The Spirochetes, 578
Treponema, 578
Borrelia, 583
Brachyspira, 586
Leptospira, 587
Prevention, 588
Part IV Parasitology, 590
46 Overview of the Methods and Strategies
in Parasitology, 590
Epidemiology, 590
Pathogenesis and Spectrum of Disease, 593
Laboratory Diagnosis, 601
Approach to Identification, 606
Prevention, 627
47 Intestinal Protozoa, 629
Amoebae, 629
Flagellates, 649
Ciliates, 656
Sporozoa (Apicomplexa), 657
Microsporidia, 665
48 Blood and Tissue Protozoa, 670
Plasmodium spp., 670
Babesia spp., 682
Trypanosoma spp., 683
Leishmania spp., 687
49 Protozoa from Other Body Sites, 691
Free-Living Amoebae, 691
Naegleria fowleri, 691
Acanthamoeba spp., 695
Acanthamoeba Keratitis, 696
Balamuthia mandrillaris, 696
Trichomonas vaginalis, 697
Pentatrichomonas hominis, 699
Toxoplasma gondii, 699
50 Intestinal Nematodes, 703
Ascaris lumbricoides, 703
Enterobius vermicularis, 705
Strongyloides stercoralis, 707
Trichostrongylus spp., 709
Trichuris trichiura, 709
Capillaria philippinensis, 710
Hookworms, 711
Ancylostoma duodenale, 711
Necator americanus, 712
Results and Reporting, 713
51 Tissue Nematodes, 714
Trichinella spiralis, 714
Toxocara canis (Visceral Larva Migrans) and
Toxocara cati (Ocular Larva Migrans), 715
Ancylostoma braziliense or Ancylostoma caninum
(Cutaneous Larva Migrans), 716
Dracunculus medinensis, 717
Parastrongylus cantonensis (Cerebral
Angiostrongyliasis), 718
Parastrongylus costaricensis (Abdominal
Angiostrongyliasis), 719
Gnathostoma spinigerum, 719
Dirofilaria immitis and Other Species, 719
52 Blood Nematodes, 721
Wuchereria bancrofti, 721
Brugia malayi and Brugia timori, 723
Loa loa, 724
Onchocerca volvulus, 725
Mansonella spp. (M. ozzardi, M. streptocerca,
M. perstans), 726
53 Intestinal Cestodes, 728
Diphyllobothrium latum, 728
Dipylidium caninum, 733
Hymenolepis nana, 733
Hymenolepis diminuta, 735
Taenia solium, 736
Taenia saginata, 737
54 Tissue Cestodes, 739
Taenia solium, 739
Echinococcus granulosus, 740
Echinococcus multilocularis, 742
Taenia multiceps and Other Species, 743
Spirometra mansonoides, 743
55 Intestinal Trematodes, 745
Fasciolopsis buski, 745
Heterophyes and Metagonimus yokogawai, 746
56 Liver and Lung Trematodes, 748
The Liver Flukes, 748
The Lung Flukes, 750
57 Blood Trematodes, 753
General Characteristics, 753
Epidemiology, 754
Pathology and Spectrum of Disease, 755
Laboratory Diagnosis, 755
Therapy, 756
Prevention, 756
Part V Mycology, 757
58 Overview of Fungal Identification Methods
and Strategies, 757
Epidemiology, 758
General Features of the Fungi, 758
Taxonomy of the Fungi, 758
Clinical Classification of the Fungi, 759
Pathogenesis and Spectrum of Disease, 762
Laboratory Diagnosis, 762
General Considerations for the Identification of
Yeasts, 771
General Considerations for the Identification of
Molds, 772
General Morphologic Features of the Molds, 774
Clinical Relevance for Fungal Identification, 776
Laboratory Safety, 779
Prevention, 780
59 Hyaline Molds, Mucorales, Entomophthorales,
Dermatophytes, and Opportunistic and
Systemic Mycoses, 782
The Mucorales, 782
The Entomophthorales, 786
The Dermatophytes, 787
The Opportunistic Mycoses, 793
Systemic Mycoses, 798
60 Dematiaceious (Melanized) Molds, 812
General Characteristics, 812
Epidemiology and Pathogenesis, 812
Pathogenesis and Spectrum of Disease, 813
Laboratory Diagnosis, 815
61 Opportunistic Atypical Fungus: Pneumocystis
jirovecii, 822
General Characteristics, 822
Epidemiology, 822
Pathogenesis and Spectrum of Disease, 822
Laboratory Diagnosis, 823
62 The Yeasts, 825
General Characteristics, 825
Epidemiology, 826
Pathogenesis and Spectrum of Disease, 827
Laboratory Diagnosis, 830
Commercially Available Yeast Identification
Systems, 835
Conventional Yeast Identification Methods, 836
63 Antifungal Susceptibility Testing, Therapy,
and Prevention, 840
Antifungal Susceptibility Testing, 840
Antifungal Therapy and Prevention, 841
Part VI Virology, 844
64 Overview of the Methods and Strategies in
Virology, 844
General Characteristics, 845
Epidemiology, 848
Pathogenesis and Spectrum of Disease, 848
Prevention and Therapy, 849
Viruses That Cause Human Diseases, 849
Laboratory Diagnosis, 849
65 Viruses in Human Disease, 881
Viruses in Human Disease, 881
Adenoviruses, 881
Arenaviruses, 883
Bunyaviruses, 884
Caliciviruses, 885
Coronaviruses, 886
Filoviruses, 887
Flaviviruses, 888
Herpesvirus, 890
Hepadnaviruses, 891
Herpes Viruses, 892
Orthomyxoviruses, 897
Papillomaviruses, 899
Paramyxoviruses, 900
Parvoviruses, 902
Picornaviruses, 903
Polyomaviruses, 905
Poxviruses, 906
Reoviruses, 907
Retroviruses, 908
Rhabdoviruses, 910
Togaviruses, 911
Miscellaneous Viruses, 911
Interpretation of Laboratory Test Results, 911
Prions in Human Disease, 913
66 Antiviral Therapy, Susceptibility Testing,
and Prevention, 916
Antiviral Therapy, 916
Antiviral Resistance, 916
Methods of Antiviral Susceptibility Testing, 917
Prevention of Other Viral Infections, 920
Part VII Diagnosis by Organ System, 924
67 Bloodstream Infections, 924
General Considerations, 925
Detection of Bacteremia, 931
Special Considerations for Other Relevant
Organisms Isolated from Blood, 938
68 Infections of the Lower Respiratory Tract, 942
General Considerations, 942
Diseases of the Lower Respiratory Tract, 945
Laboratory Diagnosis of Lower Respiratory Tract
Infections, 950
69 Upper Respiratory Tract Infections and Other
Infections of the Oral Cavity and Neck, 957
General Considerations, 957
Diseases of the Upper Respiratory Tract, Oral Cavity,
and Neck, 957
Diagnosis of Upper Respiratory Tract Infections, 961
Diagnosis of Infections in the Oral Cavity and Neck, 963
70 Meningitis and Other Infections of the Central
Nervous System, 965
General Considerations, 965
Shunt Infections, 970
Laboratory Diagnosis of Central Nervous System
Infections, 971
71 Infections of the Eyes, Ears, and Sinuses, 976
Eyes, 976
Ears, 983
Sinuses, 984
72 Infections of the Urinary Tract, 987
General Considerations, 987
Infections of the Urinary Tract, 988
Laboratory Diagnosis of Urinary Tract Infections, 992
73 Genital Tract Infections, 999
General Considerations, 999
Genital Tract Infections, 1001
Laboratory Diagnosis of Genital Tract Infections, 1007
74 Gastrointestinal Tract Infections, 1015
Anatomy, 1015
Resident Gastrointestinal Microbiome, 1017
Gastroenteritis, 1017
Other Infections of the Gastrointestinal Tract, 1025
Laboratory Diagnosis of Gastrointestinal Tract
Infections, 1028
75 Skin, Soft Tissue, and Wound Infections, 1034
General Considerations, 1034
Skin and Soft Tissue Infections, 1035
Laboratory Diagnostic Procedures, 1042
76 Normally Sterile Body Fluids, Bone and Bone
Marrow, and Solid Tissues, 1046
Specimens from Sterile Body Sites, 1046
Laboratory Diagnostic Procedures, 1051
Part VIII Clinical Laboratory
Management, 1055
77 Quality in the Clinical Microbiology
Laboratory, 1055
Quality Program, 1056
Specimen Collection and Transport, 1056
Standard Operating Procedure Manual, 1057
Personnel, 1057
Reference Laboratories, 1057
Patient Reports, 1057
Proficiency Testing, 1057
Performance Checks, 1058
Antimicrobial Susceptibility Tests, 1058
Maintenance of Quality Control Records, 1059
Maintenance of Reference Quality Control
Stocks, 1059
Quality Assurance Program, 1060
Types of Quality Assurance Audits, 1060
Conducting a Quality Assurance Audit, 1061
Continuous Daily Monitoring, 1061
78 Infection Control, 1063
Incidence of Health Care-Associated Infections, 1064
Types of Health Care-Associated Infections, 1064
Emergence of Antibiotic-Resistant
Microorganisms, 1065
Hospital Infection Control Programs, 1065
Role of the Microbiology Laboratory, 1066
Characterizing Strains Involved in an Outbreak, 1066
Preventing Health Care-Associated Infections, 1068
Surveillance Methods, 1070
79 Sentinel Laboratory Response to
Bioterrorism, 1072
General Considerations, 1072
Government Laws and Regulations, 1072
Laboratory Response Network, 1073
Glossary, 1077
Index, 1084
1 Microbial Taxonomy, 1
Classification, 2
Nomenclature, 2
Identification, 3
2 Bacterial Genetics, Metabolism,
and Structure, 5
Bacterial Genetics, 5
Bacterial Metabolism, 17
Structure and Function of the Bacterial Cell, 20
3 Host-Microorganism Interactions, 24
The Encounter Between Host and Microorganism, 25
Microorganism Colonization of Host Surfaces, 27
Microorganism Entry, Invasion, and Dissemination, 30
Outcome and Prevention of Infectious Diseases, 39
Part II General Principles in Clinical
Microbiology, 42
Section 1 Safety and Specimen Management, 42
4 Laboratory Safety, 42
Sterilization, Disinfection, and Decontamination, 42
Chemical Safety, 45
Fire Safety, 46
Electrical Safety, 46
Handling of Compressed Gases, 46
Biosafety, 47
Exposure Control Plan, 47
Employee Education and Orientation, 48
Disposal of Hazardous Waste, 48
Standard Precautions, 48
Engineering Controls, 49
Classification of Biologic Agents Based on Hazard, 52
Mailing Biohazardous Materials, 53
5 Specimen Management, 56
General Concepts for Specimen Collection and
Handling, 56
Specimen Preservation, 57
Specimen Workup, 69
Expediting Results Reporting: Computerization, 70
Section 2 Approaches to Diagnosis of Infectious
Diseases, 72
6 Role of Microscopy, 72
Bright-Field (Light) Microscopy, 72
Phase-Contrast Microscopy, 79
Fluorescent Microscopy, 80
Dark-Field Microscopy, 83
Electron Microscopy, 84
Digital Automated Microscopy, 85
7 Traditional Cultivation and Identification, 86
Organism Identification, 86
Principles of Bacterial Cultivation, 86
Bacterial Cultivation, 96
Principles of Identification, 99
Principles of Phenotypic Identification
Schemes, 106
Commercial Identification Systems
and Automation, 111
8 Nucleic Acid-Based Analytic Methods
for Microbial Identification and
Characterization, 113
Overview of Nucleic Acid-Based Methods, 114
Post amplification and Traditional Analysis, 135
9 Overview of Immunochemical Methods Used
for Organism Detection, 144
Features of the Immune Response, 144
Production of Antibodies for Use in Laboratory
Testing, 147
IgM Clinical Significance, 149
Separating IgM from IgG for Serologic Testing, 149
Principles of Immunochemical Methods Used for
Organism Detection, 149
Section 3 Evaluation of Antimicrobial
Activity, 161
10 Principles of Antimicrobial Action and
Resistance, 161
Antimicrobial Action, 161
Mechanisms of Antibiotic Resistance, 169
11 Laboratory Methods and Strategies for
Antimicrobial Susceptibility Testing, 177
Goal and Limitations, 177
Testing Methods, 178
Laboratory Strategies for Antimicrobial Susceptibility
Testing, 197
Accuracy, 199
Communication, 203
Part III Bacteriology, 205
Section 1 Principles of Identification, 205
12 Overview of Bacterial Identification Methods
and Strategies, 205
The rationale for Approaching Organism Identification, 205
Future Trends of Organism Identification, 206
Section 2 Catalase-Positive, Gram-Positive Cocci, 248
13 Staphylococcus, Micrococcus, and Similar
Organisms, 248
General Characteristics, 248
Epidemiology, 249
Pathogenesis and Spectrum of Disease, 249
Laboratory Diagnosis, 252
Antimicrobial Susceptibility Testing and Therapy, 259
Prevention, 261
Section 3 Catalase-Negative, Gram-Positive Cocci, 264
14 Streptococcus, Enterococcus, and Similar
Organisms, 264
General Characteristics, 265
Epidemiology, 265
Pathogenesis and Spectrum of Disease, 266
Laboratory Diagnosis, 270
Antimicrobial Susceptibility Testing and Therapy, 279
Prevention, 281
Section 4 Non-Branching, Catalase-Positive,
Gram-Positive Bacilli, 283
15 Bacillus and Similar Organisms, 283
General Characteristics, 283
Laboratory Diagnosis, 287
Antimicrobial Susceptibility Testing and Therapy, 290
Prevention, 292
16 Listeria, Corynebacterium, and Similar
Organisms, 294
General Characteristics, 294
Epidemiology, 294
Pathogenesis and Spectrum of Disease, 296
Laboratory Diagnosis, 298
Antimicrobial Susceptibility Testing and Therapy, 304
Prevention, 307
Treatment, 307
Section 5 Non-Branching, Catalase-Negative,
Gram-Positive Bacilli, 309
17 Erysipelothrix, Lactobacillus, and Similar
Organisms, 309
General Characteristics, 309
Epidemiology, 309
Pathogenesis and Spectrum of Disease, 309
Laboratory Diagnosis, 311
Antimicrobial Susceptibility Testing and Therapy, 315
Prevention, 315
Section 6 Branching or Partially Acid-Fast,
Gram-Positive Bacilli, 318
18 Nocardia, Streptomyces, Rhodococcus,
and Similar Organisms, 318
General Characteristics, 319
Epidemiology and Pathogenesis, 319
The spectrum of Disease, 321
Laboratory Diagnosis, 322
Antimicrobial Susceptibility Testing and Therapy, 326
Prevention, 326
Section 7 Gram-Negative Bacilli and Coccobacilli
(MacConkey-Positive, Oxidase-Negative), 329
19 Enterobacteriaceae, 329
General Characteristics, 330
Epidemiology, 330
Pathogenesis and Spectrum of Diseases, 332
Specific Organisms, 332
Laboratory Diagnosis, 338
Antimicrobial Susceptibility Testing and Therapy, 351
Prevention, 354
20 Acinetobacter, Stenotrophomonas, and Other
Organisms, 357
General Characteristics, 357
Epidemiology, 357
Pathogenesis and Spectrum of Disease, 358
Laboratory Diagnosis, 359
Antimicrobial Resistance and Antimicrobial
Susceptibility Testing, 362
Antimicrobial Therapy, 363
Prevention, 363
Section 8 Gram-Negative Bacilli and Coccobacilli
(MacConkey-Positive, Oxidase-
Positive), 365
21 Pseudomonas, Burkholderia, and Similar
Organisms, 365
General Characteristics, 365
Epidemiology, 366
Pathogenesis and Spectrum of Disease, 367
Laboratory Diagnosis, 369
Antimicrobial Susceptibility Testing and Therapy, 375
Prevention, 375
22 Achromobacter, Rhizobium, Ochrobactrum,
and Similar Organisms, 379
General Characteristics, 379
Epidemiology, 379
Pathogenesis and Spectrum of Disease, 379
Laboratory Diagnosis, 381
Antimicrobial Susceptibility Testing and Therapy, 383
Prevention, 383
23 Chryseobacterium, Sphingobacterium,
and Similar Organisms, 385
General Characteristics, 385
Epidemiology, 385
Pathogenesis and Spectrum of Disease, 386
Laboratory Diagnosis, 386
Antimicrobial Susceptibility Testing and Therapy, 388
Prevention, 389
24 Alcaligenes, Bordetella (Nonpertussis),
Comamonas, and Similar Organisms, 391
General Characteristics, 391
Epidemiology, 392
Pathogenesis and Spectrum of Disease, 392
Laboratory Diagnosis, 394
Antimicrobial Susceptibility Testing and Therapy, 396
Prevention, 398
25 Vibrio, Aeromonas, and Similar Organisms, 399
General Characteristics, 399
Epidemiology, 399
Pathogenesis and Spectrum of Disease, 400
Laboratory Diagnosis, 402
Antimicrobial Susceptibility Testing and Therapy, 406
Prevention, 406
Section 9 Gram-Negative Bacilli and Coccobacilli
(MacConkey-Negative, Oxidase-Positive), 408
26 Sphingomonas paucimobilis and Similar
Organisms, 408
General Considerations, 408
Epidemiology, Spectrum of Disease, and
Antimicrobial Therapy, 408
Laboratory Diagnosis, 408
Prevention, 413
27 Moraxella, 415
General Characteristics, 415
Epidemiology, Spectrum of Disease, and
Antimicrobial Therapy, 415
Laboratory Diagnosis, 416
Prevention, 418
28 Eikenella corrodens and Similar Organisms, 420
General Characteristics, 420
Epidemiology, Spectrum of Disease, and
Antimicrobial Therapy, 420
Laboratory Diagnosis, 421
Serodiagnosis, 423
Prevention, 423
29 Pasteurella and Similar Organisms, 425
General Characteristics and Taxonomy, 425
Epidemiology, Spectrum of Disease, and
Antimicrobial Therapy, 425
Laboratory Diagnosis, 426
Serodiagnosis, 429
Prevention, 429
30 Actinobacillus, Kingella, Cardiobacterium,
Capnocytophaga, and Similar Organisms, 430
General Characteristics, 430
Epidemiology, Pathogenesis, and Spectrum of
Disease and Antimicrobial Therapy, 431
Laboratory Diagnosis, 433
Serodiagnosis, 436
Prevention, 436
Section 10 Gram-Negative Bacilli and Coccobacilli
(MacConkey-Negative, Oxidase-
Variable), 438
31 Haemophilus, 438
General Characteristics, 438
Epidemiology, 438
Pathogenesis and Spectrum of Disease, 438
Laboratory Diagnosis, 440
Antimicrobial Susceptibility Testing and Therapy, 443
Prevention, 445
Section 11 Gram-Negative Bacilli that are Optimally
Recovered on Special Media, 446
32 Bartonella and Afipia, 446
Bartonella, 446
Afipia felis, 450
33 Campylobacter, Arcobacter, and
Helicobacter, 452
Campylobacter and Arcobacter, 452
Helicobacter spp., 457
34 Legionella, 462
General Characteristics, 462
Pathogenesis and Spectrum of Disease, 462
Laboratory Diagnosis, 465
Antimicrobial Susceptibility Testing and Therapy, 467
Prevention, 467
35 Brucella, 470
General Characteristics, 470
Epidemiology and Pathogenesis, 470
Spectrum of Disease, 471
Laboratory Diagnosis, 471
Antimicrobial Susceptibility Testing and Therapy, 473
Prevention, 473
36 Bordetella pertussis, Bordetella
parapertussis, and Related Species, 475
General Characteristics, 475
Spectrum of Disease, 476
Laboratory Diagnosis, 477
Antimicrobial Susceptibility Testing and Therapy, 479
Prevention, 479
37 Francisella, 480
General Characteristics, 480
Epidemiology and Pathogenesis, 480
Spectrum of Disease, 481
Laboratory Diagnosis, 481
Antimicrobial Susceptibility Testing and Therapy, 483
Prevention, 483
38 Streptobacillus moniliformis and Spirillum
minus, 485
Streptobacillus moniliformis, 485
Spirillum minus, 487
Section 12 Gram-Negative Cocci, 489
39 Neisseria and Moraxella catarrhalis, 489
General Characteristics, 489
Epidemiology, 489
Pathogenesis and Spectrum of Disease, 490
Laboratory Diagnosis, 490
Antimicrobial Susceptibility Testing and Therapy, 496
Prevention, 497
Section 13 Anaerobic Bacteriology, 499
40 Overview and General Laboratory
Considerations, 499
General Characteristics, 499
Specimen Collection and Transport, 499
Macroscopic Examination of Specimens, 500
Direct Detection Methods, 500
Specimen Processing, 504
Anaerobic Media, 505
Approach to Identification, 506
Antimicrobial Susceptibility Testing and Therapy, 509
41 Overview of Anaerobic Organisms, 513
Epidemiology, 514
Pathogenesis and Spectrum of Disease, 514
Prevention, 523
Section 14 Mycobacteria and Other Bacteria with
Unusual Growth Requirements, 524
42 Mycobacteria, 524
Mycobacterium tuberculosis Complex, 525
Nontuberculous Mycobacteria, 528
Laboratory Diagnosis of Mycobacterial Infections, 534
Antimicrobial Susceptibility Testing and Therapy, 550
Prevention, 552
43 Obligate Intracellular and Nonculturable
Bacterial Agents, 555
Chlamydia, 555
Rickettsia, Orientia, Anaplasma, and Ehrlichia, 563
Coxiella, 566
Tropheryma whipplei, 566
Klebsiella granulomatis, 567
44 Cell Wall-Deficient Bacteria: Mycoplasma
and Ureaplasma, 570
General Characteristics, 570
Epidemiology and Pathogenesis, 570
Spectrum of Disease, 572
Laboratory Diagnosis, 572
Cultivation, 574
Susceptibility Testing and Therapy, 576
Prevention, 577
45 The Spirochetes, 578
Treponema, 578
Borrelia, 583
Brachyspira, 586
Leptospira, 587
Prevention, 588
Part IV Parasitology, 590
46 Overview of the Methods and Strategies
in Parasitology, 590
Epidemiology, 590
Pathogenesis and Spectrum of Disease, 593
Laboratory Diagnosis, 601
Approach to Identification, 606
Prevention, 627
47 Intestinal Protozoa, 629
Amoebae, 629
Flagellates, 649
Ciliates, 656
Sporozoa (Apicomplexa), 657
Microsporidia, 665
48 Blood and Tissue Protozoa, 670
Plasmodium spp., 670
Babesia spp., 682
Trypanosoma spp., 683
Leishmania spp., 687
49 Protozoa from Other Body Sites, 691
Free-Living Amoebae, 691
Naegleria fowleri, 691
Acanthamoeba spp., 695
Acanthamoeba Keratitis, 696
Balamuthia mandrillaris, 696
Trichomonas vaginalis, 697
Pentatrichomonas hominis, 699
Toxoplasma gondii, 699
50 Intestinal Nematodes, 703
Ascaris lumbricoides, 703
Enterobius vermicularis, 705
Strongyloides stercoralis, 707
Trichostrongylus spp., 709
Trichuris trichiura, 709
Capillaria philippinensis, 710
Hookworms, 711
Ancylostoma duodenale, 711
Necator americanus, 712
Results and Reporting, 713
51 Tissue Nematodes, 714
Trichinella spiralis, 714
Toxocara canis (Visceral Larva Migrans) and
Toxocara cati (Ocular Larva Migrans), 715
Ancylostoma braziliense or Ancylostoma caninum
(Cutaneous Larva Migrans), 716
Dracunculus medinensis, 717
Parastrongylus cantonensis (Cerebral
Angiostrongyliasis), 718
Parastrongylus costaricensis (Abdominal
Angiostrongyliasis), 719
Gnathostoma spinigerum, 719
Dirofilaria immitis and Other Species, 719
52 Blood Nematodes, 721
Wuchereria bancrofti, 721
Brugia malayi and Brugia timori, 723
Loa loa, 724
Onchocerca volvulus, 725
Mansonella spp. (M. ozzardi, M. streptocerca,
M. perstans), 726
53 Intestinal Cestodes, 728
Diphyllobothrium latum, 728
Dipylidium caninum, 733
Hymenolepis nana, 733
Hymenolepis diminuta, 735
Taenia solium, 736
Taenia saginata, 737
54 Tissue Cestodes, 739
Taenia solium, 739
Echinococcus granulosus, 740
Echinococcus multilocularis, 742
Taenia multiceps and Other Species, 743
Spirometra mansonoides, 743
55 Intestinal Trematodes, 745
Fasciolopsis buski, 745
Heterophyes and Metagonimus yokogawai, 746
56 Liver and Lung Trematodes, 748
The Liver Flukes, 748
The Lung Flukes, 750
57 Blood Trematodes, 753
General Characteristics, 753
Epidemiology, 754
Pathology and Spectrum of Disease, 755
Laboratory Diagnosis, 755
Therapy, 756
Prevention, 756
Part V Mycology, 757
58 Overview of Fungal Identification Methods
and Strategies, 757
Epidemiology, 758
General Features of the Fungi, 758
Taxonomy of the Fungi, 758
Clinical Classification of the Fungi, 759
Pathogenesis and Spectrum of Disease, 762
Laboratory Diagnosis, 762
General Considerations for the Identification of
Yeasts, 771
General Considerations for the Identification of
Molds, 772
General Morphologic Features of the Molds, 774
Clinical Relevance for Fungal Identification, 776
Laboratory Safety, 779
Prevention, 780
59 Hyaline Molds, Mucorales, Entomophthorales,
Dermatophytes, and Opportunistic and
Systemic Mycoses, 782
The Mucorales, 782
The Entomophthorales, 786
The Dermatophytes, 787
The Opportunistic Mycoses, 793
Systemic Mycoses, 798
60 Dematiaceious (Melanized) Molds, 812
General Characteristics, 812
Epidemiology and Pathogenesis, 812
Pathogenesis and Spectrum of Disease, 813
Laboratory Diagnosis, 815
61 Opportunistic Atypical Fungus: Pneumocystis
jirovecii, 822
General Characteristics, 822
Epidemiology, 822
Pathogenesis and Spectrum of Disease, 822
Laboratory Diagnosis, 823
62 The Yeasts, 825
General Characteristics, 825
Epidemiology, 826
Pathogenesis and Spectrum of Disease, 827
Laboratory Diagnosis, 830
Commercially Available Yeast Identification
Systems, 835
Conventional Yeast Identification Methods, 836
63 Antifungal Susceptibility Testing, Therapy,
and Prevention, 840
Antifungal Susceptibility Testing, 840
Antifungal Therapy and Prevention, 841
Part VI Virology, 844
64 Overview of the Methods and Strategies in
Virology, 844
General Characteristics, 845
Epidemiology, 848
Pathogenesis and Spectrum of Disease, 848
Prevention and Therapy, 849
Viruses That Cause Human Diseases, 849
Laboratory Diagnosis, 849
65 Viruses in Human Disease, 881
Viruses in Human Disease, 881
Adenoviruses, 881
Arenaviruses, 883
Bunyaviruses, 884
Caliciviruses, 885
Coronaviruses, 886
Filoviruses, 887
Flaviviruses, 888
Herpesvirus, 890
Hepadnaviruses, 891
Herpes Viruses, 892
Orthomyxoviruses, 897
Papillomaviruses, 899
Paramyxoviruses, 900
Parvoviruses, 902
Picornaviruses, 903
Polyomaviruses, 905
Poxviruses, 906
Reoviruses, 907
Retroviruses, 908
Rhabdoviruses, 910
Togaviruses, 911
Miscellaneous Viruses, 911
Interpretation of Laboratory Test Results, 911
Prions in Human Disease, 913
66 Antiviral Therapy, Susceptibility Testing,
and Prevention, 916
Antiviral Therapy, 916
Antiviral Resistance, 916
Methods of Antiviral Susceptibility Testing, 917
Prevention of Other Viral Infections, 920
Part VII Diagnosis by Organ System, 924
67 Bloodstream Infections, 924
General Considerations, 925
Detection of Bacteremia, 931
Special Considerations for Other Relevant
Organisms Isolated from Blood, 938
68 Infections of the Lower Respiratory Tract, 942
General Considerations, 942
Diseases of the Lower Respiratory Tract, 945
Laboratory Diagnosis of Lower Respiratory Tract
Infections, 950
69 Upper Respiratory Tract Infections and Other
Infections of the Oral Cavity and Neck, 957
General Considerations, 957
Diseases of the Upper Respiratory Tract, Oral Cavity,
and Neck, 957
Diagnosis of Upper Respiratory Tract Infections, 961
Diagnosis of Infections in the Oral Cavity and Neck, 963
70 Meningitis and Other Infections of the Central
Nervous System, 965
General Considerations, 965
Shunt Infections, 970
Laboratory Diagnosis of Central Nervous System
Infections, 971
71 Infections of the Eyes, Ears, and Sinuses, 976
Eyes, 976
Ears, 983
Sinuses, 984
72 Infections of the Urinary Tract, 987
General Considerations, 987
Infections of the Urinary Tract, 988
Laboratory Diagnosis of Urinary Tract Infections, 992
73 Genital Tract Infections, 999
General Considerations, 999
Genital Tract Infections, 1001
Laboratory Diagnosis of Genital Tract Infections, 1007
74 Gastrointestinal Tract Infections, 1015
Anatomy, 1015
Resident Gastrointestinal Microbiome, 1017
Gastroenteritis, 1017
Other Infections of the Gastrointestinal Tract, 1025
Laboratory Diagnosis of Gastrointestinal Tract
Infections, 1028
75 Skin, Soft Tissue, and Wound Infections, 1034
General Considerations, 1034
Skin and Soft Tissue Infections, 1035
Laboratory Diagnostic Procedures, 1042
76 Normally Sterile Body Fluids, Bone and Bone
Marrow, and Solid Tissues, 1046
Specimens from Sterile Body Sites, 1046
Laboratory Diagnostic Procedures, 1051
Part VIII Clinical Laboratory
Management, 1055
77 Quality in the Clinical Microbiology
Laboratory, 1055
Quality Program, 1056
Specimen Collection and Transport, 1056
Standard Operating Procedure Manual, 1057
Personnel, 1057
Reference Laboratories, 1057
Patient Reports, 1057
Proficiency Testing, 1057
Performance Checks, 1058
Antimicrobial Susceptibility Tests, 1058
Maintenance of Quality Control Records, 1059
Maintenance of Reference Quality Control
Stocks, 1059
Quality Assurance Program, 1060
Types of Quality Assurance Audits, 1060
Conducting a Quality Assurance Audit, 1061
Continuous Daily Monitoring, 1061
78 Infection Control, 1063
Incidence of Health Care-Associated Infections, 1064
Types of Health Care-Associated Infections, 1064
Emergence of Antibiotic-Resistant
Microorganisms, 1065
Hospital Infection Control Programs, 1065
Role of the Microbiology Laboratory, 1066
Characterizing Strains Involved in an Outbreak, 1066
Preventing Health Care-Associated Infections, 1068
Surveillance Methods, 1070
79 Sentinel Laboratory Response to
Bioterrorism, 1072
General Considerations, 1072
Government Laws and Regulations, 1072
Laboratory Response Network, 1073
Glossary, 1077
Index, 1084
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