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Tables of Contents for Essentials of Diagnostic Microbiology
Chapter/Section Title
Page #
Page Count
Preface
ix
Section I / General Topics in Microbiology
3
84
Chapter 1: Introduction to the Study of Microorganisms
3
20
Lisa Shimeld, MS
Introduction
5
1
A Brief History of Microbiology
5
5
Taxonomy and Nomenclature of Microorganisms
10
2
Prokaryotic and Eucaryotic Microorganisms
12
1
Prokaryotic Microorganisms
12
3
The Eucaryotic Microorganisms
15
8
Chapter 2: The Infectious Disease Process
23
15
Judith A. Kjelstrom, MT (ASCP), PhD
Introduction
24
1
Host Resistance Factors
25
4
Microbial Mechanisms of Pathogenicity
29
4
Pathologic Mechanisms in the Host
33
5
Chapter 3: Safety in the Clinical Microbiology Laboratory
38
16
Lynn L. Russell, MA, CLS (NCA)
Anne T. Rodgers, MT (ASCP), PhD
Introduction
39
1
Methods of Sterilization
39
2
Infectious Waste Management
41
1
Legislative and Regulatory Controls
42
3
Environmental Controls
45
1
Classification of Biohazardous Agents
45
2
Creating a Safe Laboratory Environment
47
2
Transportation of Infectious Agents
49
1
Special Precautions in the Clinical Microbiology Laboratory
50
4
Chapter 4: Immunologic and Molecular Techniques
54
8
Helen Viscount, PhD
Introduction
55
1
General Features of the Immune Response
55
2
Serologic Diagnosis of Infectious Disease
57
1
Principles and Methodologies of Immunologic Tests
57
2
Identification of Bacteria by by Immunologic Methods
59
3
Chapter 5: Quality Assurance in the Clinical Microbiology Laboratory
62
6
Kathy Nollar, MT (ASCP)
Introduction
63
1
Components of a Quality Assurance Program in Microbiology
63
1
Reporting and Use of Quality Assurance Data
64
4
Chapter 6: Automation in the Clinical Microbiology Laboratory
68
8
Steve Mahlen, MS, M (ASCP), RM (AAM)
Introduction
69
1
History of Automation in Clinical Laboratory
70
1
Principles of Growth Detection in Automated Instruments
70
1
Automated Instrument Applications in Clinical Microbiology
71
3
The Future of Automation in Microbiology
74
2
Chapter 7: Antimicrobial Agents and Antimicrobial Susceptibility Testing
76
11
James T. Griffith, PhD, CLS (NCA)
Anne T. Rodgers, PhD, MT (ASCP)
Introduction
77
1
Basic Pharmacokinetics of Antimicrobial Agents
78
2
Bacterial Resistance to Antimicrobial Agents
80
1
Susceptibility Testing Techniques
80
1
Special Considerations in Antimicrobial Susceptibility Testing
81
6
Section II / Bacteriology
87
378
Part 1 General Methods for Identification of Bacteria
Chapter 8: Microscopic, Cultural, and other Techniques for Bacterial Identification
87
16
Sheryl A. Whitlock, MA, MT (ASCP), BB
Introduction
88
1
Microscopic Morphology
88
1
Microscopic Methods
88
4
Aseptic and Pure Culture Techniques
92
6
Methods for Bacterial Identification
98
5
Chapter 9: Staphylococcus and Related Aerobic Gram-Positive Cocci
103
14
Linda S. Harrison, MS, MT (ASCP)
Introduction
104
1
Staphylococcus Aureus
105
4
Staphylococcus Epidermidis and Other Coagulase-Negative Staphylococci
109
2
Staphylococcus Saprophyticus
111
1
Micrococci
111
1
Special Considerations for Immunocompromised Hosts
112
5
Chapter 10: Streptococcus and Related Aerobic Gram-Positive Cocci
117
14
Helen Viscount, PhD
Introduction
118
1
Streptococcus pneumoniae
119
1
Streptococcus pyogenes
120
1
Streptococcus agalactiae
121
1
Enterococci
122
2
Other Group D Streptococci
124
1
Viridans Streptococci
124
2
Obscure or Rarely Isolated Organisms
126
1
Special Considerations for the Immunocompromised Hosts
126
5
Chapter 11: Aerobic Gram-Positive Bacilli, Coccobacilli, and Coryneform Bacilli
131
11
Vivian Chantakrivat, MBA, MT (ASCP)
Introduction
132
1
Bacillus Species
132
3
Listeria Species
135
1
Erysipelothrix Species
136
1
Lactobacillus Species
136
1
Corynebacterium Species
137
2
Obscure or Rarely Isolated Species
139
3
Chapter 12: Aerobic Actinomycetes
142
6
Bardwell J. Eberly, MT (ASCP), SM
Introduction
143
1
Nocardia
143
1
Actinomadura
144
1
Rhodococcus
145
3
Chapter 13: Neisseria and Other Aerobic Gram-Negative Cocci
148
11
Judith S. Heelan, PhD
Introduction
149
1
Neisseria gonorrhoeae
149
5
Neisseria meningitidis
154
1
Branhamella (Moraxella) catarrhalis
155
1
Other Neisseria Species
156
3
Chapter 14: Haemophilus
159
13
Daila S. Gridley, PhD
Introduction
160
1
Haemophilus influenzae
160
6
Other Haemophilus Species
166
1
Obscure or Rarely Isolated Organisms
167
1
Special Considerations for Immunocompromised Hosts
168
4
Chapter 15: Miscellaneous Fastidious Aerobic and Facultative Gram-Negative Bacilli and Coccobacilli
172
14
James E. Daly, MEd, MT (ASCP)
Introduction
173
1
Pasteurella
174
1
Francisella
175
1
Brucella
176
1
Bordetella
177
1
Gardnerella vaginalis
178
1
Legionella
179
1
Obscure or Rarely Isolated Organisms
180
6
Chapter 16: Gram-Negative Enteric Bacilli
186
20
Daila S. Gridley, PhD
Introduction
187
2
Escherichia
189
2
Klebsiella--Enterobacter--Serratia
191
2
Proteus--Providencia--Morganella
193
1
Citrobacter
194
1
Yersinia
194
2
Salmonella
196
3
Shigella
199
1
Other Enterobacteriaceae
200
1
Special Considerations for Immunocompromised Hosts
200
6
Chapter 17: Nonfermenting Aerobic Gram-Negative Bacilli
206
16
Daila S. Gridley, PhD
Introduction
207
1
Pseudomonas
207
7
Acnetobacter
214
1
Flavobacterium
215
1
Alcaligenes
215
1
Moraxella
216
1
Xanthomonas (Stenotrophomonas)
217
1
Special Considerations for Immunocompromised Hosts
217
5
Chapter 18: Vibrio and Other Curved Aerobic Gram-Negative Bacilli
222
16
Daila S. Gridley, PhD
Introduction
223
1
Vibrio (Cholerae, Parahemolyticus, Vulnificus)
224
3
Helicobacter
227
2
Campylobacter
229
2
Aeromonas
231
1
Plesiomonas
231
1
Chromobacterium
232
1
Special Considerations for Immunocompromised Hosts
233
5
Chapter 19: Gram-Negative Anaerobic Bacteria
238
17
Gloria T. Anderson, MT (ASCP)
David W. Craft, PhD
A. Christian Whelen, PhD, D (ABMM)
Introduction
239
2
Bacteroides fragilis Group
241
2
Bacteroides ureolyticus Group
243
4
Prevotella
247
3
Porphyromonas
250
1
Fusobacterium
250
5
Chapter 20: Gram-Positive Anaerobic Bacteria
255
12
Gloria T. Anderson, MT (ASCP)
David W. Craft, PhD
A. Christian Whelen, PhD, D (ABMM)
Introduction
256
1
Anaerobic Gram-Positive Cocci and Nonspore-Forming Bacilli
256
1
Peptostreptococcus
256
1
Propionibacterium acnes
257
1
Actinomyces
258
1
Bifidobacterium dentium
259
1
Anaerobic Gram-Positive, Spore-Forming Bacilli
259
1
Clostridium perfringens
260
1
Clostridium botulinum
261
1
Clostridium tetani
262
1
Clostridium difficile
262
5
Chapter 21: Mycobacteria
267
23
Geneva M. Burch, BS, MT (ASCP, CLS, NCA), MLT (ASCP)
Introduction
268
1
Genus Characteristics
268
1
Nutritional and Growth Requirements
268
1
Growth Rate
268
1
Colony Appearance and Pigment Production
269
1
Mycobacterium tuberculosis
269
6
Mycobacterium leprae
275
1
MOTT--Mycobacteria Other than Tuberculosis
276
1
Laboratory Studies
277
1
Identification Process
278
12
Chapter 22: Spirochetes
290
13
Lisa Shimeld, MS
Introduction
291
1
Treponema
292
3
Borrelia
295
3
Leptospira
298
1
Special Considerations for Immunocompromised Hosts
299
4
Chapter 23: Chlamydia, Mycoplasma, and Rickettsia
303
14
James D. Kettering, PhD
Daila S. Gridley, PhD
Introduction
304
1
Chlamydia
304
3
Mycoplasma
307
3
Rickettsia
310
7
Part 2 Isolation and Interpretation of Bacteria from Clinical Specimens
Chapter 24: Processing and Interpretation of Cultures from Clinical Specimens
317
22
Susan Barber, BS, MT (ASCP), SM
Introduction
318
1
Microscopic Examination of Specimens
318
3
Considerations in Choosing a Culture Protocol
321
1
Resident and Normal Flora
322
1
Presumptive and Definitive Identification
323
1
Interpretation of Cultures from Clinical Sites ("Reading Plates")
324
11
Reporting Culture Results
335
4
Chapter 25: Cerebrospinal Fluid and Other Body Fluids
339
17
Diane K. Tamanaha, MS, MT (ASCP)
Introduction
340
1
Basic Anatomy of the System
340
2
Resident Flora
342
1
Specimen Types and Collection
342
3
Opportunistic and Pathogenic Bacteria
345
5
Bacterial Diseases
350
6
Chapter 26: Blood Cultures
356
19
James O. Murray, SM (AAM), CLS (NCA), MS
Introduction
357
1
Basic Anatomy of the Blood and Lymphatic Circulatory Systems
358
1
Resident Flora
358
1
General Concepts of Bloodstream Infections
358
2
Specimen Collection
360
4
Specimen Processing
364
5
Microbial Pathogens
369
6
Chapter 27: The Respiratory Tract
375
12
Mark Shapiro, MS (ASCP), BS
Lisa Shimeld, MS
Introduction
376
1
Organisms Encountered in the Respiratory Tract
376
1
Anatomy of the Respiratory Tract
377
1
The Upper Respiratory Tract
377
4
Identification of Potential Pathogens
381
1
The Lower Respiratory Tract
382
5
Chapter 28: Ear, Eye, and Sinus Tracts
387
16
Lynn L. Russell, MA, CLS (NCA)
Introduction
388
1
Basic Anatomy of the Ear, Eye, and Sinus Tracts
388
2
Resident Flora
390
1
Specimen Types and Collection
390
4
Opportunistic or Pathogenic Microorganisms
394
1
Microbial Diseases of the Ear, Eye, and Sinus Tracts
395
8
Chapter 29: The Urinary Tract
403
10
William Nauschvetz, PhD
Introduction
404
1
Urine
405
1
Basic Anatomy of the Urinary Tract System
405
1
Resident Flora
405
1
Specimen Types and Collection
406
1
Bacterial Diseases of the Urinary Tract
407
1
Specimen Processing, Culture, and Interpretation
408
5
Chapter 30: The Genital Tract
413
9
Judith S. Heelan, PhD
Introduction
414
1
Basic Anatomy of the Genital Tract
414
1
Resident Flora
415
1
Specimen Types and Collection
416
1
Opportunistic or Pathogenic Bacteria
416
1
Bacterial Diseases of the Genital Tract
417
5
Chapter 31: The Gastrointestinal Tract
422
10
Anne T. Rodgers, MT (ASCP), PhD
Geneva M. Burch, BS, MT (ASCP), CLS (NCA), MLT (ASCP)
Introduction
423
1
Basic Anatomy of the Digestive System
423
1
Resident Flora of the Gastrointestinal Tract
424
1
Clinical Specimens
425
1
Specimen Processing
425
2
Examination of Cultures
427
1
Gastrointestinal Pathogens and Diseases
428
4
Chapter 32: Skin Infections
432
14
S. Vern Juchau, PhD, MPH, MA
Introduction
433
1
Basic Anatomy of the Skin
434
1
Resident Flora
435
1
Specimen Types and Collection
435
1
Opportunistic or Pathogenic Bacteria
436
1
Bacterial Diseases of Wounds and Other Superficial Sites
436
5
Systemic Infections with Skin Involvement
441
5
Chapter 33: Deep Tissues and Internal Organ Sites
446
19
Susan Fraser, MD
Introduction
447
1
Basic Anatomy
447
1
Resident Flora
448
2
Specimen Types and Collection
450
2
Opportunistic or Pathogenic Organisms
452
1
Diseases of These Systems and Organs
453
12
Section III / Mycology
465
82
Chapter 34: Basic Concepts and Techniques in Mycology
465
9
Anne T. Rodgers, MT (ASCP), PhD
James A. Miller, MD
Introduction
466
1
General Characteristics of Fungi
466
1
Reproduction of Fungi
467
2
Classification of Fungi
469
1
General Approach to the Identification of Fungi
470
1
Antifungal Agents and Susceptibility Testing
471
3
Chapter 35: Collection and Processing of Fungal Specimens
474
11
Anne T. Rodgers, MT (ASCP), PhD
James A. Miller, MD
Introduction
475
1
Collection and Transport of Specimens for Fungus Culture
475
1
Culture Media and Incubation Requirements
475
2
Direct Examination of Specimens
477
1
Identification Procedures
478
4
Reporting Culture Results
482
3
Chapter 36: Dermatophytes and Other Agents of Superficial Mycoses
485
10
James A. Miller, MD
Anne T. Rodgers, MT (ASCP), PhD
Introduction
486
1
Superficial Mycoses
486
2
Dermatophytes
488
7
Chapter 37: Agents of Subcutaneous Mycoses
495
8
James A. Miller, MD
Anne T. Rodgers, MT (ASCP), PhD
Introduction
496
1
Clinical Diseases
496
1
Laboratory Evaluation and Diagnosis of Subcutaneous Mycoses
497
6
Chapter 38: Systemic Dimorphic Fungi
503
12
James A. Miller, MD
Anne T. Rodgers, MT (ASCP), PhD
Introduction
504
1
Histoplasma capsulatum
505
2
Coccidioides immitis
507
2
Blastomyces dermatitidis
509
2
Paracoccidioides brasiliensis
511
4
Chapter 39: Opportunistic Fungi
515
12
James A. Miller, MD
Anne T. Rodgers, MT (ASCP), PhD
Introduction
516
1
Cryptococcosis
516
2
Candidiasis
518
1
Aspergillosis
519
2
Zygomycosis
521
1
Less Common Opportunistic Fungi
522
5
Chapter 40: Saprobic Fungi Encountered in Clinical Specimens
527
8
James A. Miller, MD
Anne T. Rodgers, MT (ASCP), PhD
Introduction
528
1
Zygomycetes
528
2
Dematiaceous Hyphomycetes
530
1
Hyaline Hyphomycetes
531
4
Chapter 41: Yeasts
535
12
Anne T. Rodgers, MT (ASCP), PhD
James A. Miller, MD
Introduction
536
1
Clinical Significance of Yeasts
536
1
Identification Procedures for Yeasts
536
4
Candida
540
2
Cryptococcus
542
1
Other Opportunistic Yeasts
542
5
Section IV / Parasitology
547
88
Chapter 42: Basic Concepts and Techniques in Parasitology
547
13
Lisa Shimeld, MS
Introduction
548
1
Symbiotic Relationships
549
1
Hosts
549
1
Parasitic Adaptations
549
2
Transmission of Parasitic Diseases
551
1
Reproduction of Parasites
552
1
Parasitic Life Cycles
552
1
Host-Parasite Relations
553
1
The Immunology of Parasitic Infection
554
1
An Overview of Some Important Parasites
554
1
Techniques for Parasitic Examination
555
5
Chapter 43: Specimen Collection and Processing for Parasite Examinations
560
12
Bardwell J. Eberly, MT (ASCAP), SM
Introduction
561
1
Specimen Collection and Processing
561
2
Direct Examination
563
3
Concentration Techniques for Detection of Parasites
565
2
Stains
567
5
Chapter 44: Intestinal and Atrial Protozoans
572
18
Lisa Shimeld, MS
Introduction
573
1
Ameba
573
7
Flagellates
580
3
Ciliates
583
1
Coccidia and Microsporidia
584
2
Artifacts That Resemble Protozoans Found in Feces
586
4
Chapter 45: Plasmodia and Other Blood and Tissue Protozoans
590
13
Lisa Shimeld, MS
Introduction
591
1
Ameba
591
1
Mastigophora, or the Hemoflagellates
592
2
Sporozoa
594
3
Coccidia
597
1
Unconventional Protozoans found in Blood and Tissue Specimens
598
5
Chapter 46: Intestinal Helminths
603
13
Lisa Shimeld, MS
Introduction
604
1
Nematodes
604
5
Cestodes
609
3
Trematodes
612
4
Chapter 47: Blood and Tissue Helminths
616
19
Jeffrey J. Adamovicz, PhD
Introduction
617
1
Nematodes
617
5
Cestodes
622
1
Trematodes
623
2
Uncommon Helminths
625
10
Section V / Virology
635
Chapter 48: Basic Concepts and Techniques in Virology
635
12
James D. Kettering, PhD
Introduction
636
1
General Characteristics of Viruses
636
4
General Approaches to Viral Diagnosis
640
7
Chapter 49: Specimen Collection and Processing of Viral Specimens
647
8
James D. Kettering, PhD
Introduction
648
1
Specimen Collection and Handling
648
3
Transport
651
1
Storage
651
1
Preparing Specimens for Inoculation
651
4
Chapter 50: Clinically Significant Viruses and Their Identification
655
26
James D. Kettering, PhD
Introduction
656
1
Viruses Commonly Isolated in a Clinical Laboratory
657
7
Occasional or Difficult Viruses Isolated in the Clinical Laboratory
664
5
Viruses Not Isolated in the Clinical Laboratory
669
12
Chapter 51: Emerging Viral Infections
681
Anne Delaney, MT (ASCP)
Introduction
682
1
Emerging Viruses
682
Glossary
G1
Index
I1