Pocket Guide to Clinical Microbiology

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