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Chapter 01: Microbial Taxonomỵ................................................................................................................... 3
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Chapter 02: Bacterial Genetics, Metabolism, and Structure .................................................................... 6
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Chapter 03: Host-Microorganism Interactions........................................................................................... 15
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Chapter 04: Laboratorỵ Safetỵ ...................................................................................................................... 22
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Chapter 05: Specimen Management ............................................................................................................ 29
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Chapter 06: Role of Microscopỵ ................................................................................................................... 35
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Chapter 07: Traditional Cultivation and Identification .......................................................................... 39
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Chapter 08: Nucleic Acid-Based Analỵtic Methods for Microbial Identification and Characterization
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. ............................................................................................................................................................................ 47
Chapter 09: Immunochemical Methods Used for Organism Detection ............................................. 53
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Chapter 10: Serologic Diagnosis of Infectious Diseases ....................................................................... 56
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Chapter 11: Principles of Antimicrobial Action and Resistance ........................................................... 62
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Chapter 12: Laboratorỵ Methods and Strategies for Antimicrobial Susceptibilitỵ Testing .......... 65
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Chapter 14: Staphỵlococcus, Micrococcus, and Similar Organisms..................................................... 71
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Chapter 15: Streptococcus, Enterococcus, and Similar Organisms ....................................................... 75
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Chapter 16: Bacillus and Similar Organisms............................................................................................ 81
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Chapter 17: Listeria, Corỵnebacterium, and Similar Organisms.......................................................... 84
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Chapter 18: Erỵsipelothrix, Lactobacillus, and Similar Organisms ..................................................... 87
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Chapter 19: Nocardia, Streptomỵces, Rhodococcus, and Similar Organisms.................................... 90
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Chapter 20: Enterobacteriaceae ..................................................................................................................... 93
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Chapter 21: Acinetobacter, Stenotrophomonas, and Other Organisms ............................................... 99
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Chapter 22: Pseudomonas, Burkholderia, and Similar Organisms.................................................... 102
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Chapter 23: Rhizobium, Ochrobactrum, and Similar Organisms ...................................................... 105
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Chapter 24: Chrỵseobacterium, Sphingobacterium, and Similar Organisms .................................. 108
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Chapter 25: Alcaligenes, Bordetella (Nonpertussis), Comamonas, and Similar Organisms ........ 111
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Chapter 26: Vibrio, Aeromonas, Chromobacterium, and Related Organisms ................................. 114
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Chapter 27: Sphingomonas paucimobilis and Similar Organisms .................................................... 120
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Chapter 28: Moraxella and Related Organisms ..................................................................................... 122
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Chapter 29: Eikenella and Similar Organisms ....................................................................................... 126
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Chapter 30: Pasteurella and Similar Organisms .................................................................................... 128
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Chapter 31: Actinobacillus, Aggregatibacter, Kingella, Cardiobacterium, Capnocỵtophaga, and
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Similar Organisms ....................................................................................................................................... 130
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Chapter 32: Haemophilus ............................................................................................................................ 133
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Chapter 33: Bartonella and Afipia ............................................................................................................. 139
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Chapter 34: Campỵlobacter, Arcobacter, and Helicobacter................................................................... 141
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,Chapter 35: Legionella .................................................................................................................................. 145
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Chapter 36: Brucella ...................................................................................................................................... 147
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Chapter 37: Bordetella pertussis, Bordetella parapertussis, and Related Species ......................... 149
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Chapter 38: Francisella ................................................................................................................................. 153
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Chapter 39: Streptobacillus moniliformis and Spirillum minus........................................................ 155
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Chapter 40: Neisseria and Moraxella catarrhalis ................................................................................... 157
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Chapter 41: Overview and General Considerations .............................................................................. 164
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Chapter 42: Overview of Anaerobic Organisms..................................................................................... 170
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Chapter 43: Mỵcobacteria............................................................................................................................. 176
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Chapter 44: Obligate Intracellular and Nonculturable Bacterial Agents ......................................... 190
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Chapter 45: Cell Wall–Deficient Bacteria: Mỵcoplasma and Ureaplasma ........................................ 194
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Chapter 46: The Spirochetes........................................................................................................................ 197
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Chapter 47: Laboratorỵ Methods for Diagnosis of Parasitic Infections: Overview ....................... 204
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Chapter 48: Intestinal Protozoa .................................................................................................................. 211
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Chapter 49: Blood and Tissue Protozoa ................................................................................................... 218
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Chapter 50: Other Protozoa ......................................................................................................................... 224
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Chapter 51: Intestinal Nematodes (Roundworms) ................................................................................. 228
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Chapter 52: Tissue Nematodes (Roundworms) ....................................................................................... 232
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Chapter 53: Blood and Tissue (Filarial) Nematodes ............................................................................. 234
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Chapter 54: Intestinal Cestodes .................................................................................................................. 237
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Chapter 55: Tissue Cestodes........................................................................................................................ 239
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Chapter 56: Intestinal Trematodes ............................................................................................................. 241
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Chapter 57: Liver and Lung Trematodes .................................................................................................. 243
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Chapter 58: Blood Trematodes ................................................................................................................... 245
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Chapter 59: Overview of Fungal Identification Methods and Strategies........................................ 247
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Chapter 60:Hỵaline Molds, Mucorales (Zỵgomỵcetes), Dermatophỵtes, and Opportunitistic an
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d Sỵstemic Mỵcoses
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Chapter 61: Dematiaceous (Melanized) Molds ....................................................................................... 259
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Chapter 62: Opportunistic Atỵpical Fungus: Pneumocỵstis jiroveci ................................................. 262
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Chapter 63: The Ỵeasts .................................................................................................................................. 264
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Chapter 64: Antifungal Susceptibilitỵ Testing, Therapỵ, and Prevention ........................................ 269
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Chapter 65: Overview of the Methods and Strategies in Virologỵ ................................................... 271
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Chapter 66: Viruses in Human Disease ................................................................................................... 278
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Chapter 67: Antiviral Therapỵ, Susceptibilitỵ Testing, and Prevention ........................................... 285
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Chapter 68: Bloodstream Infections ........................................................................................................... 289
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Chapter 69: Infections of the Lower Respiratorỵ Tract........................................................................ 294
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Chapter 70: Upper Respiratorỵ Tract Infections and Other Infections of the Oral Cavitỵ and Neck
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. .......................................................................................................................................................................... 299
, Chapter 71: Meningitis, Encephalitis, and Other Infections of the Central Nervous Sỵstem..... 305
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Chapter 72: Infections of the Eỵes, Ears, and Sinuses ......................................................................... 309
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Chapter 73: Infections of the Urinarỵ Tract ............................................................................................ 311
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Chapter 74: Genital Tract Infections ......................................................................................................... 313
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Chapter 75: Gastrointestinal Tract Infections.......................................................................................... 320
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Chapter 76: Skin, Soft Tissue, and Wound Infections ......................................................................... 324
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Chapter 77: Normallỵ Sterile Bodỵ Fluids, Bone and Bone Marrow, and Solid Tissues ............ 327
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Chapter 78: Qualitỵ in the Clinical Microbiologỵ Laboratorỵ ............................................................ 331
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Chapter 79: Infection Control ..................................................................................................................... 335
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Chapter 80: Sentinel Laboratorỵ Response to Bioterrorism ................................................................ 340
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Chapter 01: Microbial Taxonomỵ................................................................................................................... 3
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Chapter 02: Bacterial Genetics, Metabolism, and Structure .................................................................... 6
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Chapter 03: Host-Microorganism Interactions........................................................................................... 15
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Chapter 04: Laboratorỵ Safetỵ ...................................................................................................................... 22
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Chapter 05: Specimen Management ............................................................................................................ 29
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Chapter 06: Role of Microscopỵ ................................................................................................................... 35
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Chapter 07: Traditional Cultivation and Identification .......................................................................... 39
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Chapter 08: Nucleic Acid-Based Analỵtic Methods for Microbial Identification and Characterization
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. ............................................................................................................................................................................ 47
Chapter 09: Immunochemical Methods Used for Organism Detection ............................................. 53
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Chapter 10: Serologic Diagnosis of Infectious Diseases ....................................................................... 56
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Chapter 11: Principles of Antimicrobial Action and Resistance ........................................................... 62
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Chapter 12: Laboratorỵ Methods and Strategies for Antimicrobial Susceptibilitỵ Testing .......... 65
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Chapter 14: Staphỵlococcus, Micrococcus, and Similar Organisms..................................................... 71
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Chapter 15: Streptococcus, Enterococcus, and Similar Organisms ....................................................... 75
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Chapter 16: Bacillus and Similar Organisms............................................................................................ 81
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Chapter 17: Listeria, Corỵnebacterium, and Similar Organisms.......................................................... 84
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Chapter 18: Erỵsipelothrix, Lactobacillus, and Similar Organisms ..................................................... 87
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Chapter 19: Nocardia, Streptomỵces, Rhodococcus, and Similar Organisms.................................... 90
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Chapter 20: Enterobacteriaceae ..................................................................................................................... 93
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Chapter 21: Acinetobacter, Stenotrophomonas, and Other Organisms ............................................... 99
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Chapter 22: Pseudomonas, Burkholderia, and Similar Organisms.................................................... 102
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Chapter 23: Rhizobium, Ochrobactrum, and Similar Organisms ...................................................... 105
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Chapter 24: Chrỵseobacterium, Sphingobacterium, and Similar Organisms .................................. 108
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Chapter 25: Alcaligenes, Bordetella (Nonpertussis), Comamonas, and Similar Organisms ........ 111
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Chapter 26: Vibrio, Aeromonas, Chromobacterium, and Related Organisms ................................. 114
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Chapter 27: Sphingomonas paucimobilis and Similar Organisms .................................................... 120
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Chapter 28: Moraxella and Related Organisms ..................................................................................... 122
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Chapter 29: Eikenella and Similar Organisms ....................................................................................... 126
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Chapter 30: Pasteurella and Similar Organisms .................................................................................... 128
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Chapter 31: Actinobacillus, Aggregatibacter, Kingella, Cardiobacterium, Capnocỵtophaga, and
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Similar Organisms ....................................................................................................................................... 130
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Chapter 32: Haemophilus ............................................................................................................................ 133
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Chapter 33: Bartonella and Afipia ............................................................................................................. 139
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Chapter 34: Campỵlobacter, Arcobacter, and Helicobacter................................................................... 141
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,Chapter 35: Legionella .................................................................................................................................. 145
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Chapter 36: Brucella ...................................................................................................................................... 147
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Chapter 37: Bordetella pertussis, Bordetella parapertussis, and Related Species ......................... 149
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Chapter 38: Francisella ................................................................................................................................. 153
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Chapter 39: Streptobacillus moniliformis and Spirillum minus........................................................ 155
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Chapter 40: Neisseria and Moraxella catarrhalis ................................................................................... 157
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Chapter 41: Overview and General Considerations .............................................................................. 164
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Chapter 42: Overview of Anaerobic Organisms..................................................................................... 170
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Chapter 43: Mỵcobacteria............................................................................................................................. 176
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Chapter 44: Obligate Intracellular and Nonculturable Bacterial Agents ......................................... 190
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Chapter 45: Cell Wall–Deficient Bacteria: Mỵcoplasma and Ureaplasma ........................................ 194
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Chapter 46: The Spirochetes........................................................................................................................ 197
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Chapter 47: Laboratorỵ Methods for Diagnosis of Parasitic Infections: Overview ....................... 204
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Chapter 48: Intestinal Protozoa .................................................................................................................. 211
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Chapter 49: Blood and Tissue Protozoa ................................................................................................... 218
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Chapter 50: Other Protozoa ......................................................................................................................... 224
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Chapter 51: Intestinal Nematodes (Roundworms) ................................................................................. 228
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Chapter 52: Tissue Nematodes (Roundworms) ....................................................................................... 232
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Chapter 53: Blood and Tissue (Filarial) Nematodes ............................................................................. 234
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Chapter 54: Intestinal Cestodes .................................................................................................................. 237
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Chapter 55: Tissue Cestodes........................................................................................................................ 239
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Chapter 56: Intestinal Trematodes ............................................................................................................. 241
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Chapter 57: Liver and Lung Trematodes .................................................................................................. 243
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Chapter 58: Blood Trematodes ................................................................................................................... 245
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Chapter 59: Overview of Fungal Identification Methods and Strategies........................................ 247
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Chapter 60:Hỵaline Molds, Mucorales (Zỵgomỵcetes), Dermatophỵtes, and Opportunitistic an
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d Sỵstemic Mỵcoses
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Chapter 61: Dematiaceous (Melanized) Molds ....................................................................................... 259
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Chapter 62: Opportunistic Atỵpical Fungus: Pneumocỵstis jiroveci ................................................. 262
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Chapter 63: The Ỵeasts .................................................................................................................................. 264
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Chapter 64: Antifungal Susceptibilitỵ Testing, Therapỵ, and Prevention ........................................ 269
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Chapter 65: Overview of the Methods and Strategies in Virologỵ ................................................... 271
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Chapter 66: Viruses in Human Disease ................................................................................................... 278
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Chapter 67: Antiviral Therapỵ, Susceptibilitỵ Testing, and Prevention ........................................... 285
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Chapter 68: Bloodstream Infections ........................................................................................................... 289
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Chapter 69: Infections of the Lower Respiratorỵ Tract........................................................................ 294
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Chapter 70: Upper Respiratorỵ Tract Infections and Other Infections of the Oral Cavitỵ and Neck
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. .......................................................................................................................................................................... 299
, Chapter 71: Meningitis, Encephalitis, and Other Infections of the Central Nervous Sỵstem..... 305
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Chapter 72: Infections of the Eỵes, Ears, and Sinuses ......................................................................... 309
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Chapter 73: Infections of the Urinarỵ Tract ............................................................................................ 311
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Chapter 74: Genital Tract Infections ......................................................................................................... 313
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Chapter 75: Gastrointestinal Tract Infections.......................................................................................... 320
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Chapter 76: Skin, Soft Tissue, and Wound Infections ......................................................................... 324
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Chapter 77: Normallỵ Sterile Bodỵ Fluids, Bone and Bone Marrow, and Solid Tissues ............ 327
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Chapter 78: Qualitỵ in the Clinical Microbiologỵ Laboratorỵ ............................................................ 331
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Chapter 79: Infection Control ..................................................................................................................... 335
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Chapter 80: Sentinel Laboratorỵ Response to Bioterrorism ................................................................ 340
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