User-friendly, quick clinical microbiology reference

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Preface xi
About the Authors xv

SECTION 1 Taxonomic Classification of Medically Important Microorganisms 1

General Comments 2
Taxonomic Classification of Bacteria 2
Table 1.1 Reclassification of the Former Family Enterobacteriaceae 10
Table 1.2 Newly Assigned Genera for Former Mycobacterium 11
Table 1.3 Enterobacter cloacae Complex Organisms 12
Table 1.4 Klebsiella oxytoca Complex Organisms 12
Table 1.5 Taxonomy of Citrobacter freundii Complex 12
Table 1.6 Taxonomy of Pseudomonas fluorescens Group Organisms 12
Table 1.7 Taxonomy of Pseudomonas putida Group Organisms 13
Table 1.8 Taxonomy of Pseudomonas aeruginosa Group Organisms 13
Table 1.9 Taxonomy of Acinetobacter calcoaceticus-baumannii Complex 13
Table 1.10 Taxonomy of Burkholderia cepacia Complex 13
Table 1.11 Taxonomy of Mycobacteria 14
Table 1.12 Taxonomy of the Staphylococcus aureus Complex 16
Table 1.13 Taxonomy of the Staphylococcus intermedius Group 16
Table 1.14 Taxonomy of the Viridans Group Streptococci 16
Taxonomic Classification of Human Viruses 17
Taxonomic Classification of Fungi 21
Table 1.15 Revised Species Names of Selected Clinically Relevant Fungi 22
Taxonomic Classification of Parasites 25

SECTION 2 Indigenous and Pathogenic Microbes of Humans 31

General Comments 32
Table 2.1 Human Indigenous Flora 32
Table 2.2 Summary of Notifiable Infectious Diseases: United States, 2016 and 2020 43
Table 2.3 Arthropod Vectors of Medically Important Diseases 48
Table 2.4 Fungal Pathogens and Geographic Distribution 51
Table 2.5 Parasitic Pathogens and Geographic Distribution 62
Microbes Responsible for Human Disease 70

SECTION 3 Specimen Collection and Transport 93

General Comments 94
Table 3.1 Bacteriology: Collection and Transport Guidelines 96
Table 3.2 Specimen Collection and Transport Guidelines for Infrequently Encountered Bacteria 114
Table 3.3 Guidelines for Collection of Specimens for Anaerobic Culture 115
Table 3.4 Possible Rejection Criteria for Specimens Submitted for Bacterial Culture 116
Virology: General Specimen Guidelines 117
Virology: Specific Specimen Guidelines 118
Table 3.5 Recommended Blood Volumes to Collect for Blood Cultures 121
Table 3.6 Mycology: Collection and Transport Guidelines 122
Table 3.7 Parasitology: Specimen Guidelines 127
Table 3.8 Guidelines for Processing Stool Specimens for Parasites 132

SECTION 4 Bacterial Diagnosis 135

General Comments 136
Table 4.1 Detection Methods from Clinical Specimens for Clinically Relevant Bacteria 136
Table 4.2 Recommendations for Gram Stain from Primary Specimen and Plating Media 139
Table 4.3 Screening Specimens for Routine Bacterial Culture 143
Table 4.4 Processing Specimens for Mycobacterial Identification 144
Microscopy 144
Primary Plating Media: Bacteria 146
Primary Plating Media: Mycobacteria 159
Specific Diagnostic Tests for Pathogen Detection 161
Aerobic Gram-Positive Cocci 161
Aerobic Gram-Positive Rods 162
Acid-Fast and Partially Acid-Fast Gram-Positive Rods 164
Aerobic Gram-Negative Cocci 164
Aerobic Gram-Negative Rods 165
Anaerobic Bacteria 172
Curved and Spiral-Shaped Bacteria 173
Mycoplasma spp. and Obligate Intracellular Bacteria 176
Identification Tables 178

SECTION 5 Viral Diagnosis 217

General Comments 218
Table 5.1 Detection Methods for Viruses 218
Table 5.2 Cells Used for Viral Isolation 220
RNA Viruses 221
DNA Viruses 229
Table 5.3 EBV Serologic Profiles Under Different Conditions 231
Table 5.4 Clinical Diseases of Parvovirus B19 and Method of Diagnosis 232
Table 5.5 Hepatitis B Virus Markers in Different Stages of Infection and Convalescence 233
Transmissible Spongiform Encephalopathies 235

SECTION 6 Fungal Diagnosis 237

Mycology: Specimen Collection and Transport Guidelines 238
Table 6.1 Methods for the Identification of Fungi 240
Microscopy 240
Table 6.2 Characteristic Fungal Elements Seen by Direct Examination of Clinical Specimens 243
Primary Plating Media 246
Table 6.3 Mycology Plating Guide 249
Specific Diagnostic Tests 251
Aspergillus Species 251
Blastomyces dermatitidis 251
Candida Species 252
Coccidioides Species (Coccidioidomycosis) 252
Cryptococcus neoformans and gattii (Cryptococcosis) 253
Histoplasma Species 253
Malassezia Species 254
Paracoccidioides brasiliensis 254
Talaromyces (Penicillium) marneffei 255
Pneumocystis jirovecii 255
Sporothrix schenckii 255
Mucormycetes (Zygomycetes) 255
Identification Tables 257

SECTION 7 Parasitic Diagnosis 271

General Comments 272
Microscopy 272
Table 7.1 Detection Methods for Parasites 273
Specific Diagnostic Tests 277
Free-Living Amebae 277
Intestinal and Urogenital Protozoa 277
Blood and Tissue Protozoa 280
Microsporidia 282
Helminths: Nematodes 283
Helminths: Trematodes 285
Helminths: Cestodes 286
Identification Tables and Figures 287
Table 7.2 Trophozoites of Common Intestinal Amebae 287
Table 7.3 Cysts of Common Intestinal Amebae 290
Figure 7.1 Intestinal Amebae of Humans 293
Table 7.4 Trophozoites of Flagellates 294
Table 7.5 Cysts of Flagellates 296
Figure 7.2 Intestinal and Urogenital Flagellates of Humans 297
Table 7.6 Morphological Characteristics of Ciliates, Coccidia, Microsporidia, and Tissue Protozoa 298
Table 7.7 Morphological Characteristics of Protozoa Found in Blood 300
Table 7.8 Morphological Characteristics of Blood and Tissue Nematodes 302
Table 7.9 Morphological Characteristics of Helminths 303
Figure 7.3 Relative Sizes of Helminth Eggs 305

SECTION 8 Susceptibility Testing and Methods of Organism Identification 307

General Comments 308
Susceptibility Testing Methods 308
Table 8.1 Clinical and Laboratory Standards Institute (CLSI) Documents Related to Antimicrobial Susceptibility Testing from Humans 308
Table 8.2 Summary of CLSI Antimicrobial Susceptibility Test Methods for Select Bacteria, Mycobacteria, and Fungi 311
Antimicrobial Treatment Information 315
Table 8.3 Organisms Included in CLSI and EUCAST Breakpoint Tables 315
Table 8.4 Guide to Interpretive Criteria for Select Organisms for Commonly Tested Antimicrobials 317
Table 8.5 Surrogate Antibiotic Susceptibility Prediction 330
Table 8.6 Routes of Administration and Drug Class for Select Antimicrobial Agents 334
Table 8.7 Routes of Administration and Drug Class for Select Antifungal Agents 337
Table 8.8 Routes of Administration and Drug Class for Select Antiparasitic Agents 338
Table 8.9 Antibacterial Agents for Specific Bacteria 339
Antimicrobial Resistance Mechanisms 345
Table 8.10 Intrinsic Resistance of Selected Gram-Negative Bacteria 345
Table 8.11 Intrinsic Resistance of Selected Gram-Positive Bacteria 346
Table 8.12 Important Mechanisms of Multidrug Resistance in Bacteria 346
Table 8.13 Activity Profiles of Select Beta-Lactam Antibiotics Against Commonly Encountered Gram-Negative Beta-Lactamases 350
MALDI-TOF MS and Sequencing 351
Table 8.14 Summary of MALDI-TOF MS Identification of Bacteria, Mycobacteria, and Fungi 351
Table 8.15 Gene Sequencing Targets for Organism Identification 356

Index 359