Professional Documents
Culture Documents
PART/CHAPTER Chapters/Contents
Page
28 69 172 255 374 384 402 438 502,543 632 656
Color Atlas of Medical Microbiology (Kayser, Thieme 2005) 1. Basic Principles 2. Bacteriology 3. Mycology 4. Virology 5. Parasitology 6. Organ System Infections
1. General Aspects of Medical Microbiology 2. Basic Principles of Immunology 3. General Bacteriology 4. Bacteria as Human Pathogens 5. General Mycology 6. Fungi as Human Pathogens 7. General Virology 8. Viruses as Human Pathogens 9. Protozoa, 10. Helminths 11. Arthropods 12. Etiological and Laboratory Diagnostic Summaries in Tabular Form
Encyclopedia of Microbiology, 3rd ed. 2009 APPLIED MICROBIOLOGY: AGRO/FOOD APPLIED MICROBIOLOGY: INDUSTRIAL
Agrobacterium and Plant Cell Transformation, Aquaculture Beer/Brewing, Dairy Products, Fermented Foods,Food Spoilage, Preservation and Quality Control, Forest Products: Biotechnology in Pulp and Paper Processing, Insecticides Microbial, Pesticides Microbial, Water Drinking, Wine Acetic Acid Production,Amino Acid Production,Amylases Antibiotic Production, Biodeterioration Including Cultural Heritage Bioreactors,Biotransformations,Cellulases,Corrosion, Microbial Cosmetics Microbiology,Enzymes, Industrial (overview),Ethanol Flavor Compounds,Heavy Metal Pollutants: Environmental and Biotechnological Aspects, Industrial Biotechnology, (overview) Industrial Fermentation Processes,Lactic Acid, Microbially Produced Lignin, Lignocellulose, Ligninase, Lipases, Lipids, Production Metal Extraction and Biomining, Organic and Fatty Acid Production Petroleum Microbiology, Pigments Microbial, Polyketides Polysaccharides Microbial, Proteases Production, Solvent Production Sterilization and Disinfection,Vitamins and Vitamin-like Compounds Wastewater Treatment (not infectious hazards), Water Treatment Industrial, Water Treatment- Municipal,Xylanases Archaea (overview) Actinobacteria, Bacillus Subtilis, Caulobacter, Chlamydia, Clostridia Corynebacteria (including diphtheria), Cyanobacteria, Escherichia Coli Gram-Negative Cocci- Pathogenic, Gram-Negative OpportunisticAnaerobes: Friends and Foes, Haemophilus Influenzae Helicobacter Pylori, Legionella, Bartonella, Haemophilus,Listeria Monocytogenes,Lyme Disease,Mycoplasma and Spiroplasma Myxococcus, Pseudomonas, Rhizobia, Spirochetes, Staphylococcus Streptococcus Pneumoniae, Streptomyces, Tuberculosis: Molecular -Basis of Pathogenesis Cell Membrane- Prokaryotic, Cell Structure Organization- Bacteria and Archaea, Development- Prokaryotic: Variety and Versatility, FlagellaProkaryotic, Intracellular Structures of Prokaryotes: InclusionsCompartments and Assemblages, Localization- MacromolecularIntracellular, Outer Membrane- Gram-Negative Bacteria, Peptidoglycan(Murein), Pili, Fimbriae 7, 22 28,50 59,85 100 116,144 151,164 179,196 211,264 275,300 310,326 340 354,367 378,398 412,426 448,477 487,517 534,554 567,574 592,605 618 643,703 710,741 749,761 769 779,798 815,824 836,909 920,949 956,972 990,008 1019 1040 10541085
ARCHAEA BACTERIA
1106-31 Adhesion- Microbial, Aeromicrobiology/Air Quality, Algal Blooms 1146-68 Bacteriophage Ecology, Biofilms-Microbial, Deep Sub-Surface 1184-95 Deep-Sea Hydrothermal Vents, Ecology-Microbial 1211-59 Extremophiles : Acidic Environments, Hot Environments, Cold Environments, Dry Environments (including Cryptoendoliths) 1243 Food Webs-Microbial, Freshwater Habitats, Heavy Metals Cycle (Arsenic, 1278-09 Mercury, Selenium, others), Heavy Metals, Bacterial Resistance, High1324-32 Pressure Habitats, Low-Nutrient Environments, Marine Habitats, Mats1344-82 Microbial, Methanotrophy/methane oxidation, Nitrogen Cycle,Phosphorus 1397-26 Cycle, Rhizosphere, Sediment Habitats, including Watery, Sulfur Cycle 1439-65 1474-94 Evolution, Viral, Paleontology, Microbial Aspergillus: A Multifaceted Genus, Clavicipitaceae: Free-Living and Saprotrophs to Plant Endophytes, Endophytic Microbes, Entomogenous Fungi, Fungi: Plant Pathogenic, Yeasts Chromosome Replication and Segregation, Chromosome- Bacterial Conjugation- Bacterial, DNA Mismatch Repair- Bacterial, DNA Restriction and Modification, Evolution-Theory and Experiments withMicroorganisms Genetically Modified Organisms: Guidelines and Regulations forResearch Genetics- Microbial (general), Horizontal Gene Transfer: Uptake of Extracellular DNA by Bacteria, Horizontal Transfer of Genes between Microorganisms, Metabolic Reconstruction, Metagenomics, Phylogenomics, Plasmids- Bacterial, Transduction: Host DNA Transfer by Bacteriophages, Transposable Elements AIDS- Historical, Biographies, Cholera- Historical,History of Microbiology Methods-Philosophy of, Plague-Historical, Smallpox- Historical Spontaneous Generation, Syphilis-Historical, Typhoid- Historical Typhus Fevers and Other Rickettsial Diseases-Historical Behavior Modification of Host by Microbes Endosymbionts and Intracellular Parasites, Lichens, Mycorrhizae, Rumen Airborne Infectious Microorganisms, Aminoglycosides-Bioactive Bacterial Metabolites, Antibiotic Resistance, Antifungal Agents, Antiviral Agents Bacteriophage Therapy: Past and Present Bacteriophage Therapy: Potential and Problems-Lactam Antibiotics Cyanobacterial Toxins, Diagnostic Microbiology, Emerging Infections Enteropathogenic Infections, Epidemiological Concepts and Historical Examples, Exotoxins, Food and Waterborne Illnesses, Fungal InfectionCutaneous, Fungal Infections- Systemic, Fungicides and other Chemical Approaches for use in Plant Disease Control, Gastrointestinal Microbiology in the Normal Host, Global Burden of Infectious Diseases Glycopeptides-Antimicrobial, Immune Suppression, Immunity, Infectious Waste Management, Lipopolysaccharides (Endotoxins), Macrolides Mycotoxins, Oral Microbiology, Plant Disease Resistance: Natural-Non-Host Innate or Inducible, Plant Pathogens and Disease: General-Introduction, Plant Pathogens and Disease: Newly Emerging Diseases Plant Pathogens- Bacterial, Plant Pathogens-Minor (Phytoplasmas) Prions, Quinolones, Sexually Transmitted Diseases, Skin Microbiology Subversion of Host Defences by Microbes Amino Acid Synthesis, Autotrophic CO2 Metabolism, Bacteriocins- BiologyEcology-and Evolution, Bioluminescence- Microbial, Cell Cycles and Division- Bacterial, Chemotaxis, Coenzyme and Prosthetic GroupBiosynthesis, Crystalline Cell Surface Layers (S Layers), DNA Repair DNA Replication, Energy Transduction Processes, Fermentation Glycogen Biosynthesis, Glyoxylate Cycle, Growth Kinetics- Bacterial Heme Biosynthesis, Iron Metabolism, Lipid Biosynthesis, Magnetotaxis Metabolism-Central (Intermediary), Methanogenesis, Methylation and 1505-26 1535 1547-82 1596-10 1620-41 1653 1668 1681-90 1700 1710-25 1736-69 1783 1793-22 1841-65 1872-89 1892 1914 1920-55 1968-75 1985-15 2050 2059 2067-98 2106-20 2132-58 2165-88 2198 2220 2231-76 2305-22 2352-98 2401 2439 2447-70 2481-26 2540 2623-53 266-83 2692-00 2710-20 2734-53 2766-01 2816-41 2863-08
PHYSIOLOGY
PROTISTS
PUBLIC ISSUES
TECHNIQUES
VIRUSES
other Modifications of Nucleic Acids and Proteins, Nucleotide Metabolism Nutrition- Microbial, Photosynthesis: Microbial, Posttranscriptional Regulation, Quorum-Sensing in Bacteria, Regulation of Carbon-Assimilation in Bacteria, RNA Processing, RNAs, Small etc. Secondary Endosymbiosis, Sensory Transduction in Bacteria, StressResponses: Heat, Stress Responses: pH, Stress, Bacterial: General and Specific, Transcriptional Regulation, Translational Control and FidelityTransport, Solute Amitochondriate Protists (Diplomonads, Parabasalids and Oxymonads) Amoebas- Lobose, Ciliates, Coccolithophores, Dictyostelium Dinoflagellates, Euglenozoa, Foraminifera, Leishmania, Picoeukaryotes Plant Pathogens: Oomycetes (water mold), Protozoan-Intestinal Sleeping Sickness, Stramenopiles, Toxoplasmosis, Trypanosomes Biological Warfare, Careers in Microbiology, Forensic Microbiology Patenting of Living Organisms and Natural Products Space Microbiology: Planetary Protection, Burden, Diversity and Significance of Spacecraft Associated Microbes Antibiotic Susceptibility Testing,Biodegradation Database and PredictionMicrobial, Biosensors, Collection and Handling of Clinical MicrobiologicalSpecimens, Continuous Cultures (Chemostats), DNA Sequencing and Genomics, Freeze-Drying of Microorganisms, Genome SequenceDatabases: Annotation, Genome Sequence Databases: GenomicConstruction of Libraries, Genome Sequence Databases: Sequencing and Assembly, Genome Sequence Databases: Types of Data and Bioinformatic Tools, Gnotiobiotic and Axenic Animals, Phylogenetic- Methods, Preservation-Storage and Transport: Integrity and Compliance Recombinant DNA-Basic Procedures,Stable Isotopes in Microbial Ecology Strain Improvement, Teaching Resources-Microbiology Type Culture Collections and their Databases Arboviruses, Bacteriophage (overview), Hemorrhagic Fever Viruses Hepatitis Viruses, Herpesviruses, HIV/AIDS, Influenza,Oncogenic Viruses Plant Pathogens: DNA viruses, Plant Pathogens: RNA viruses, Polio Polyomaviruses and Papillomaviruses, Rabies, Respiratory Viruses Retroviruses, Viroids/Virusoids, Virus Infection, Viruses- Environmental
2917 2930-64 2978-96 3016-30 3060-85 3099-06 3122-38 3150 3166 3179-27 3238-95 3311-17 3328-65 3380-00 3413 3430 3444-55 3465-82 3507-25 3539-51 3563 3574 3589 3616-24 3638 3648-58 3663-78 3683 3691-17 3731-98 3807-36 3846-77 3896-30
14
3 Antifungal drugs
29-77
4 Dermatophytosis
80-107
5 Supelficial candidosis
109-126
6.1 Pityriasis versicolor, 129 6.2 Other Mulusseziu infections, 133 6.2.1 Mulusseziu folliculitis, 133 6.2.2 Seborrhoeic dermatitis, 133 7.1 Definition, 142 7.2 Geographical distribution, 142 7.3 The causal organisms and their habitat, 142 7.4 Epidemiology, 142 7.5 Clinical manifestations, 143 8.1 Definition, 147 8.2 Geographical distribution, 147 8.3 The causal organisms and their habitat, 147 8.4 Epidemiology, 148 9.1 Definition, 153 9.2 Geographical distribution, 153 9.3 The causal organisms and their habitat, 153 9.4 Epidemiology, 153 9.5 Clinical manifestations, 154 10.1 Definition, 156 10.2 Geographical distribution, 156 10.3 The causal organisms and their habitat, 156 10.4 Epidemiology, 156 10.5 Clinical manifestations, 160 Acute invasive pulmonary aspergillosis, 160 Tracheobronchitis and obstructing bronchial aspergillosis, 161 Acute invasive sinusitis, 162 Cerebral aspergillosis, 163 Cutaneous aspergillosis, 163 Pulmonary aspergilloma, 164 Chronic necrotizing pulmonary aspergillosis, 164 Chronic invasive sinusitis, 165 Paranasal sinus fungus ball, 166 Endocarditis, 167 Osteomyelitis, 167 Endophthalmitis, 167 Allergic bronchopulmonary aspergillosis, 168 Allergic sinusitis, 169 10.6 Essential investigations and their interpretation, 169 10.6.1 Microscopy, 170 10.6.2 Culture, 170 10.6.3 Skin tests, 171
129-140 6.3 Piedra, 134 6.4 White piedra, 134 6.6.4 Epidemiology, 138 6.6.5 Clinical manifestations, 138 6.7 Scytultdtum infection, 139 6.8 Alternariu infection, 140 142-145 7.6 Differential diagnosis, 143 7.7 Essential investigations and their interpretation, 143 7.8 Management, 144 7.9 Prevention, 145 8.5 Clinical manifestations, 148 8.6 Essential investigations and their interpretation, 149 8.7 Management, 150 9.6 Differential diagnosis, 154 9.7 Essential investigations and their interpretation, 154 9.8 Management, 155 147-150
8 Keratomycosis
9 Otomycosis
153-155
10 Aspergillosis
156-182 10.6.4 Serological tests, 171 10.6.5 Molecular diagnostics, 172 10.7 Management, 173 Acute invasive pulmonary aspergillosis, 173 Tracheobronchitis and obstructing bronchial aspergillosis, 176 Acute invasive sinusitis, 176 Cerebral aspergillosis, 177 Cutaneous aspergillosis, 177 Pulmonary aspergilloma, 177 Chronic necrotizing pulmonary aspergillosis, 178 Chronic invasive sinusitis, 178 Paranasal sinus fungus ball, 179 Endocarditis, 179 Osteomyelitis, 179 Endophthalmitis, 180 Allergic bronchopulmonary aspergillosis, 180 Allergic sinusitis, 180 10.8 Prevention, 181 10.8.1 Environmental strategies, 10.8.2 Therapeutic strategies182
11 lnvasive candidosis
11.1 Definition, 185 11.2 Geographical distribution, 185 11.3 The causal organisms and their habitat, 185 11.4 Epidemiology, 186 11.5 Clinical manifestations, 190 candidaemia, 190 Lower urinary tract candidosis, 192 11.5.1 Acute disseminated candidosis and 11.5.2 Chronic disseminated candidosis, 192 11.5.4 Renal candidosis, 193 11.5.5 Pulmonary candidosis, 193 11.5.6 Osteomyelitis and arthritis, 194 11.5.7 Peritonitis, 194 11.5.8 Endocarditis, myocarditis, pericarditis and other vascular infections, 195 11.5.9 Meningitis, 196 11.5.10 Endophthalmitis and 11.5.11 Oesophagitis, 197 11.5.12 Gastrointestinal candidosis, 11.5.13 Intrauterine candidosis, 11.6 Candidosis in special hosts, 11.6.1 Drug abusers, 199 Definition, 215 Geographical distribution, 215 The causal organism and its habitat, 215 Epidemiology, 216 Clinical manifestations, 21 8 12.5.1 Pulmonary cryptococcosis, 12.5.2 CNS cryptococcosis, 219 12.5.3 Cutaneous cryptococcosis, 12.5.4 Osteomyelitis, 221 12.5.5 Other forms of cryptococcosis, 221 Essential investigations and their Definition, 230 Geographical distribution, 230 The causal organisms and their habitat, Epidemiology, 231 Clinical manifestations, 232 13.5.1 Rhinocerebral mucormycosis, 13.5.2 Pulmonary mucormycosis, 13.5.3 Gastrointestinal mucormycosis, 13.5.4 Cutaneous mucormycosis,
12 Cryptococcosis
11.7 Essential investigations and 185-207 their interpretation, 199 11.7.1 Microscopy, 200 11.7.2 Culture, 200 11.7.3 Serological tests, 201 11.7.4 D-arabinitol detection, 202 11.7.5 Molecular diagnostics, 202 chorioretinitis, 197 11.8 Management, 203 Acute disseminated candidosis and candidaemia, 203 Chronic disseminated candidosis, 205 Lower urinary tract candidosis, 206 Renal candidosis, 206 Pulmonary candidosis, 207 Osteomyelitis and arthritis, 207 Peritonitis, 208 Endocarditis and vascular infection, 209 Meningitis, 210 Endophthalmitis, 210 Oesophagitis, 210 11.9 Prevention, 21 1 215-228 interpretation, 222 12.6.1 Microscopy, 222 12.6.2 Culture, 222 12.6.3 Serological tests, 223 12.7 Management, 224 12.7.1 Pulmonary and non-CNS 12.7.2 CNS cryptococcosis, 225 12.7.3 Management of increased intracranial cryptococcosis, 224 pressure, 227 12.8 Prevention, 228 230-238 13.5.5 Disseminated mucormycosis, 23513.5.6 Other forms of mucormycosis, 236 Differential diagnosis, 236 Essential investigations and their interpretation, 236 13.7.1 Microscopy, 236 13.7.2 Culture, 236 13.7.3 Serological tests, 237 Management, 237 Prevention, 238
13 Mucormycosis
14 Blastomycosis
15 Coccidioidomycosis
14.1 Definition, 241 14.2 Geographical distribution, 241 14.3 The causal organism and its habitat, 241 14.4 Epidemiology, 241 14.5 Clinical manifestations, 242 14.5.1 Pulmonary blastomycosis, 14.5.2 Cutaneous blastomycosis, 14.5.3 Osteoarticular blastomycosis, 244 14.5.4 Genitourinary blastomycosis, 244 14.5.5 Other forms of disseminated blastomycosis, 244 coccidioidomycosis, 253 coccidioidomycosis, 252 coccidioidomycosis, 252 15.6 Differential diagnosis, 254 15.7 Essential investigations and their interpretation, 255 15.7.1 Microscopy, 255 15.7.2 Culture, 255 15.7.3 Skin tests, 256 15.7.4 Serological tests, 256 15.8.1 Acute pulmonary 15.8.2 Chronic pulmonary coccidioidomycosis, 259 15.8.4 Meningitis, 260 15.8 Management, 257 coccidioidomycosis, 257 coccidioidomycosis, 259 17.5 Clinical manifestations, 281 17.5.1 Chronic pulmonary paracoccidioidomycosis, 282 17.5.2 Mucocutaneous paracoccidioidomycosis, 282 17.5.3 Other forms of disseminated paracoccidioidomycosis, 283 17.6 Differential diagnosis, 283 Definition, 288 Geographical distribution, 288 The causal organisms and their habitat, 288 Epidemiology, 289 Clinical manifestations, 289 Differential diagnosis, 290 19.1 Definition, 293 19.2 Rhinofacial conidiobolomycosis, 293 19.2.1 Definition, 293 19.2.2 Geographical distribution, 19.2.3 The causal organism and its habitat, 293 19.2.4 Epidemiology, 19.2.5 Clinical manifestations, 294 19.2.6 Essential investigations and their interpretation, 294 19.2.7 Management, 295
14.6 Differential diagnosis, 245 241-248 14.7 Essential investigations and their interpretation, 245 14.7.1 Microscopy, 245 14.7.2 Culture, 246 14.7.3 Serological tests, 246 14.8.1 Pulmonary blastomycosis, 14.8.2 Disseminated blastomycosis, 14.8 Management, 246 14.9 Prevention, 248 249-273 15.9 Prevention, 261 16 Histoplasmosis, 264 16.1 Definition, 264 16.2 Geographical distribution, 264 16.5 Clinical manifestations, 266 16.5.1 Acute pulmonary histoplasmosis, 266 16.5.2 Chronic pulmonary histoplasmosis, 268 16.5.3 Disseminated histoplasmosis, 268 16.5.4 African histoplasmosis, 270 16.6 Differential diagnosis, 271 16.7.4 Serological tests, 272 16.8.1 Acute pulmonary histoplasmosis, 273 17.7 Essential investigations and 281-286 their interpretation, 284 17.7.1 Microscopy, 284 17.7.2 Culture, 284 17.7.3 Serological tests, 284 17.8 Management, 285 17.9 Prevention, 286 Essential investigations and their 288-291 interpretation, 290 18.7.1 Microscopy, 290 18.7.2 Culture, 291 18.7.3 Serological tests, 291 Management, 291 293-297 19.3 Basidiobolomycosis, 295 19.3.1 Definition, 295 19.3.2 Geographical distribution, 19.3.3 The causal organism and its habitat, 295 19.3.4 Epidemiology, 295 19.3.5 Clinical manifestations, 296 19.3.6 Essential investigations and theirinterpretation, 296 19.3.7 Management, 297
17 Paracoccidioidomyc osis
18 Chromoblastomycos is
19 Entomophthoramyc osis
20 Lobomycosis
21 Mycetoma
22 Rhinosporidiosis
23 Sporotrichosis
24 Hyalohyphomycosis
20.1 Definition, 298 20.2 Geographical distribution, 298 20.3 The causal organism and its habitat, 298 20.4 Epidemiology, 298 20.5 Clinical manifestations, 298 Definition, 300 Geographical distribution, 300 The causal organisms and their habitat, 300 Epidemiology, 301 Clinical manifestations, 301 Differential diagnosis, 303 Essential investigations and their 22.1 Definition, 308 22.2 Geographical distribution, 308 22.3 The causal organism and its habitat, 308 22.4 Epidemiology, 308 22.5 Clinical manifestations, 309 Geographical distribution, 311 The causal organism and its habitat, 311 Epidemiology, 31 1 Clinical manifestations, 312 23.5.1 Lymphocutaneous sporotrichosis, 313 23.5.2 Extracutaneous sporotrichosis, 314 Differential diagnosis, 315 24.1 Definition, 319 24.2 Fusarium infection, 319 24.2.1 Geographical distribution, 24.2.2 The causal organisms and their habitat, 319 24.2.3 Epidemiology, 320 24.2.4 Clinical manifestations, 321 24.2.5 Essential investigations and their interpretation, 322 24.2.6 Management, 322
20.6 Differential diagnosis, 299 298-299 20.7 Essential investigations and their interpretation, 299 20.8 Management, 299 interpretation, 303 21.7.1 Gross examination, 303 21.7.2 Microscopy, 303 21.7.3 Culture, 304 21.7.4 Serological tests, 305 Management, 305 300-305
22.6 Differential diagnosis, 309 308-310 22.7 Essential investigations and their interpretation, 310 22.8 Management, 310 Essential investigations and their 311-317 interpretation, 315 23.7.1 Microscopy, 315 23.7.2 Culture, 315 23.7.3 Serological tests, 316 Management, 3 16 Prevention, 317
319-328 24.2.7 Prevention, 324 24.3.1 Geographical distribution, 24.3.2 The causal organism and its habitat, 325 24.3.3 Epidemiology, 325 24.3.4 Clinical manifestations, 326 24.3 Scedosportum apiospermum infection, 324 24.3.5 Essential investigations and their interpretation, 327 24.3.6 Management, 327 24.4 Other agents of hyalohyphomycosis, 328 interpretation, 332 25.7.1 Microscopy, 332 25.7.2 Culture, 332 25.7.3 Serological tests, 333 25.8 Management, 333 25.9 Prevention, 334 330-334
25.1 Definition, 330 25.2 Geographical distribution, 330 25.3 The causal organism and its habitat, 330 25.4 Epidemiology, 330 25.5 Clinical manifestations, 331 25.6 Differential diagnosis, 332 25.7 Essential investigations and their
26 Phaeohyphomycosis
Definition, 336 Geographical distribution, 336 The causal organisms and their habitat, 336 Epidemiology, 337 Clinical manifestations, 339 26.5.1 Subcutaneous phaeohyphomycosis, 339 26.5.2 Sinusitis, 339 26.5.3 Cerebral phaeohyphomycosis, 340 26.5.4 Other forms of phaeohyphomycosis, 341 Differential diagnosis, 341 27.1 Introduction, 346 27.2 Systemic Malassezta infection, 27.2.1 Geographical distribution, 27.2.2 The causal organisms and their habitat, 346 27.2.3 Epidemiology, 347 27.2.4 Clinical manifestations, 347 27.2.5 Essential investigations and their interpretation, 348 27.2.6 Management, 349
Essential investigations and their 336-344 interpretation, 342 26.7.1 Microscopy, 342 26.7.2 Culture, 342 26.7.3 Serological tests, 342 Management, 342 26.8.1 Subcutaneous phaeohyphomycosis, 342 26.8.2 Sinusitis, 343 26.8.3 Cerebral phaeohyphomycosis, 343 26.8.4 Disseminated phaeohyphomycosis, 344 27.3.1 Geographical distribution, 346-349 27.3.2 The causal organisms and their habitat, 349 27.3.3 Epidemiology, 350 27.3.4 Clinical manifestations, 350 27.3.5 Essential investigations and their interpretation, 351 27.3.6 Management, 352 27.4 Other yeast infections, 352 27.3 Trichosporonosis, 349
83-302
Part 3: Genital, Sexually Transmitted and Birth-Related Infections Part 4: Disorders Affecting More Than One System Part 5: Special Hosts, Environments and the Community
313-344
361-517
429-517
2.1 Elemental composition 7 2.2 Importance of chemical form 8 2.2.1 Five major elements 8 2.2.2 Oxygen 9 2.2.3 Growth factors 10 2.3 Structure of microbial cells 10 2.3.1 Flagella and pili 10 2.3.2 Capsules and slime layers 12 2.3.3 S-layer, outer membrane and cell wall 12 3.1 Ionophores: models of carrier proteins 35 3.2 Diffusion 37 3.3 Active transport and role of electrochemical gradients 37 3.4 ATP-dependent transport: ATPbinding cassette (ABC) pathway 38 3.5 Group translocation 39 3.6 Precursor/product antiport 40 3.7 Ferric ion (Fe(III)) uptake 41 3.8 Export of cell surface structural components 43 3.8.1 Protein transport 43 3.8.1.1 General secretory pathway (GSP) 43
4 Glycolysis
7-30 2.3.3.2 Outer membrane 13 2.3.3.3 Cell wall and periplasm 2.3.4 Cytoplasmic membrane 21 2.3.4.1 Properties and functions 2.3.4.2 Membrane structure 22 2.3.4.3 Phospholipids 23 2.3.4.4 Proteins 26 2.3.5 Cytoplasm 27 2.3.6 Resting cells 29 Further reading 30 35-51 3.8.1.2 Twin-arginine translocation (TAT) pathway 45 3.8.1.3 ATP-binding cassette (ABC) pathway 46 3.8.2 Protein translocation across the outer membrane in Gram-negative bacteria 46 3.8.2.1 Chaperone/usher pathway 3.8.2.2 Type I pathway: ATPbinding cassette (ABC) pathway 3.8.2.3 Type II pathway 47 3.8.2.4 Type III pathway 49 3.8.2.5 Type IV pathway 50 3.8.2.6 Type V pathway: autotransporter and proteins requiring single accessory factors 51 4.1 EMP pathway 61 4.3.1 HMP pathway in thre steps 60-78 4.1.1 Phosphofructokinase (PFK): key 4.3.2 Additional functions of the enzyme of the EMP HMP pathway 70 pathway 61 4.3.2.1 Utilization of pentoses 71 4.1.2 ATP synthesis and production of 4.3.2.2 Oxidative HMP cycle 71 pyruvate 63 4.3.3 Regulation of the HMP 71 4.1.3 Modified EMP pathways 64 4.3.4 F420-dependent glucose-64.1.3.1 Methylglyoxal bypass 64 phosphate dehydrogenase 71 4.1.3.2 Modified EMP pathways in 4.4 EntnerDoudoroff (ED) 72 archaea 65 4.4.1 Glycolytic pathways in 4.1.4 Regulation of the EMP pathway 66 some Gram-negative bacteria 72 4.1.4.1 Regulation of 4.4.2 Key enzymes of the ED 72 phosphofructokinase 66 4.4.3 Modified ED pathways 72 4.1.4.2 Regulation of pyruvate kinase 4.4.3.1 Extracellular oxidation of 4.1.4.3 Global regulation 67 glucose by Gram-negative 4.2 Glucose-6-phosphate synthesis: bacteria 72 gluconeogenesis 67 4.4.3.2 Modified ED pathways in 4.2.1 PEP synthesis 67 archaea 74 4.2.2 Fructose diphosphatase 68 4.5 Phosphoketolase pathways 4.2.3 Gluconeogenesis in archaea 4.5.1 Glucose fermentation by 4.2.4 Regulation ofgluconeogenesis Leuconostoc mesenteroides 75 4.3 Hexose monophosphate (HMP) 4.5.2 Bifidum pathway 77 pathway 69 4.6 Use of radiorespirometry to determine glycolytic pathways 78
5.1 Oxidative decarboxylation of pyruvate 8 5.2 Tricarboxylic acid (TCA) cycle 86 5.2.1 Citrate synthesis and the TCA cyl 5.2.2 Regulation of the TCA cycle 88 5.3 Replenishment of TCA cycle intermediates 88 5.3.1 Anaplerotic sequence 88 5.3.2 Glyoxylate cycle 89 5.3.2.1 Regulation of the glyoxylate cy 5.4 Incomplete TCA fork and reductive TCA cycle 91 5.4.1 Incomplete TCA fork 91 5.4.2 Reductive TCA cycle 92 5.5 Energy transduction in prokaryotes 5.5.1 Free energy 93 5.5.1.1 _G00 from the free energy of formation 94 5.5.1.2 _G00 from the equilibrium con 5.5.1.3 _G from _G00 95 5.5.1.4 _G00 from _G0 95 5.5.2 Free energy of an oxidation/reduction reaction 95 5.5.2.1 Oxidation/reduction potential 95 5.5.2.2 Free energy from _E00 96 5.5.3 Free energy of osmotic pressure 5.5.4 Sum of free energy change in a series of reactions 97 5.6 Role of ATP in the biological energy transduction process 98 5.6.1 High energy phosphate bonds 99 5.6.2 Adenylate energy charge 100 5.6.3 Phosphorylation potential (_Gp) 5.6.4 Interconversion of ATP and proton motive force (_p) 101 5.6.5 Substrate-level phosphorylation 5.7 Proton motive force (_p) 102 5.7.1 Proton gradient and membrane potential 102 6.1 Molecular composition of bacterial c. 6.2 Assimilation of inorganic N2 6.2.1 Nitrogen fixation 128 6.2.1.1 N2-fixing organisms 128 6.2.1.2 Biochemistry of N2 fixation 6.2.1.3 Bioenergetics of N2 fixation 6.2.1.4 Molecular oxygen and N2 fx 6.2.1.5 Regulation of N2 fixation 6.2.2 Nitrate reduction 135 6.2.3 Ammonia assimilation 137 6.3 Sulfate assimilation 139 6.4 Amino acid biosynthesis 140 6.4.1 The pyruvate and oxaloacetate families 140 6.4.2 The phosphoglycerate family 6.4.3 The 2-ketoglutarate family 6.4.4 Aromatic amino acids 141 6.4.5 Histidine biosynthesis 145
5.7.2 Acidophilicity and alkalophilicity 5.7.3 Proton motive force in acidophiles 5.7.4 Proton motive force and sodium motive force in alkalophiles 104 5.8 Electron transport (oxidative) phosphorylation 105 5.8.1 Chemiosmotic theory 105 5.8.2 Electron carriers and the electron transport chain 105 5.8.2.1 Mitochondrial electron transport chain 105 5.8.2.2 Electron carriers 107 5.8.2.3 Diversity of electron transport chains in prokaryotes 108 5.8.2.4 Inhibitors of electron transport phosphorylation (ETP) 110 5.8.2.5 Transhydrogenase 110 5.8.3 Arrangement of electron carriers in the H-translocating membrane 111 5.8.3.1 Q-cycle and Q-loop 111 5.8.3.2 Proton pump 112 5.8.4 ATP synthesis 112 5.8.4.1 ATP synthase 112 5.8.4.2 H/O ratio 113 5.8.4.3 H/ATP stoichiometry 114 5.8.5 Uncouplers 114 5.8.6 Primary H (Na) pumps in fermentative metabolism 115 5.8.6.1 Fumarate reductase 115 5.8.6.2 Na-dependent decarboxylase 5.8.6.3 _p formation through fermentation product/H symport 116 5.9 Other biological energy transduction processes 116 5.9.1 Bacterial bioluminescence 116 5.9.2 Electricity as an energy source in microbes 117 through the membrane 167 6.9.2.2 Murein synthesis 167 6.9.2.3 Teichoic acid synthesis 167 6.9.2.4 Cell wall proteins in Gram-positive 6.9.3 Outer membrane assembly 6.9.3.1 Protein translocation 169 6.9.3.2 Lipopolysaccharide (LPS) translocation 169 6.9.3.3 Phospholipid translocation 6.9.4 Cytoplasmic membrane (CM) assembly 170 6.10 Deoxyribonucleic acid (DNA) replication 170 6.10.1 DNA replication 170 6.10.1.1 RNA primer 171 6.10.1.2 Okazaki fragment 172 6.10.1.3 DNA polymerase 172 6.10.2 Spontaneous mutation 173
6.4.6 Regulation of amino acid biosynthesis 145 6.5 Nucleotide biosynthesis 145 6.5.1 Salvage pathway 145 6.5.2 Pyrimidine nucleotide biosynthesis through a de novo pw. 6.5.3 De novo synthesis of purine nucleotides 149 6.5.4 Synthesis ofdeoxynucleotides 6.6 Lipid biosynthesis 152 6.6.1 Fatty acid biosynthesis 152 6.6.1.1 Saturated acyl-ACP 153 6.6.1.2 Branched acyl-ACP 154 6.6.1.3 Unsaturated acyl-ACP 154 6.6.1.4 Cyclopropane fatty acids 6.6.1.5 Regulation of fatty acid biosynthesis 156 6.6.2 Phospholipid biosynthesis 156 6.6.3 Isoprenoid biosynthesis 159 6.7 Heme biosynthesis 159 6.8 Synthesis of saccharides and their derivatives 161 6.8.1 Hexose phosphate and UDP-sugar 6.8.2 Monomers of murein 163 6.8.3 Monomers of teichoic acid 6.8.4 Precursor of lipopolysaccharide, O-antigen 164 6.9 Polysaccharide biosynthesis and the assembly of cell surface structures 165 6.9.1 Glycogen synthesis 165 6.9.2 Murein synthesis and cell wall assembly 167 6.9.2.1 Transport of cell wall precursor components 7.1 Hydrolysis of polymers 202 7.1.1 Starch hydrolysis 202 7.1.2 Cellulose hydrolysis 203 7.1.3 Other polysaccharide hydrolases 7.1.4 Disaccharide phosphorylases 7.1.5 Hydrolysis of proteins, nucleic acids and lipids 206 7.2 Utilization of sugars 206 7.2.1 Hexose utilization 206 7.2.2 Pentose utilization 207 7.3 Organic acid utilization 208 7.3.1 Fatty acid utilization 208 7.3.2 Organic acids more oxidized than acetate 210 7.4 Utilization of alcohols and ketones 7.5 Amino acid utilization 214 7.5.1 Oxidative deamination 215 7.5.2 Transamination 215
6.10.3 Post-replicational modification 173 6.10.4 Chromosome segregation 1 6.11 Transcription 174 6.11.1 RNA synthesis 174 6.11.2 Post-transcriptional processing 174 6.12 Translation 175 6.12.1 Amino acid activation 176 6.12.2 Synthesis of peptide: initiation, elongation and termination 176 6.12.2.1 Ribosomes 177 6.12.2.2 Initiation and elongation 6.12.2.3 Termination 178 6.12.3 Post-translational modification and protein folding 6.13 Assembly of cellular structure 6.13.1 Flagella 181 6.13.2 Capsules and slime 182 6.13.3 Nucleoid assembly 182 6.13.4 Ribosome assembly 182 6.14 Growth 182 6.14.1 Cell division 183 6.14.1.1 Binary fission 183 6.14.1.2 Multiple intracellular offspring 184 6.14.1.3 Multiple offspring by multiple fission 185 6.14.1.4 Budding 187 6.14.2 Growth yield 187 6.14.3 Theoretical maximum YATP 6.14.4 Growth yield using different electron acceptors and maintenance energy 189 6.14.5 Maintenance energy 192 7.5.3 Amino acid dehydratase 215 7.5.4 Deamination of cysteine and methionine 216 7.5.5 Deamination products of amino acids 7.6 Degradation of nucleic acid bas 7.7 Oxidation of aliphatic hydrocarbons 223 7.8 Oxidation of aromatic compounds 7.9 Utilization of methane and methanol 7.9.1 Methanotrophy and methylotrophy 7.9.2 Methanotrophy 230 7.9.3 Carbon assimilation by methylotrophs 7.9.4 Energy efficiency in C1 metabolism 7.10 Incomplete oxidation 241 7.10.1 Acetic acid bacteria 241 7.10.2 Acetoin and butanediol 242 7.10.3 Other products of aerobic metabolism 243
8 Anaerobic fermentation
9 Anaerobic respiration
8.1 Electron acceptors used in anaerobic metabolism 252 8.1.1 Fermentation and anaerobic respiration 252 8.1.2 Hydrogen in fermentation 8.2 Molecular oxygen and anaerobes 8.3 Ethanol fermentation 255 8.4 Lactate fermentation 257 8.4.1 Homolactate fermentation 8.4.2 Heterolactate fermentation 8.4.3 Biosynthesis in lactic acid bacteria 8.4.4 Oxygen metabolism in LAB 8.4.5 Lactate/H symport 260 8.4.6 LAB in fermented food 260 8.5 Butyrate and acetonebutanol ethanol fermentations 263 8.5.1 Butyrate fermentation 263 8.5.1.1 Phosphoroclastic reaction 8.5.1.2 Butyrate formation 264 8.5.1.3 Lactate fermentation by Clostridium butyricum 265 8.5.1.4 Clostridium butyricum as a probiotic 268 9.1 Denitrification 299 9.1.1 Biochemistry of denitrification 9.1.1.1 Nitrate reductase 300 9.1.1.2 Nitrite reductase 302 9.1.1.3 Nitric oxide reductase and nitrous oxide reductase 302 9.1.2 ATP synthesis in denitrification 9.1.3 Regulation of denitrification 9.1.4 Denitrifiers other than facultatively anaerobic chemoorganotrophs 304 9.1.5 Oxidation of xenobiotics under denitrifying conditions 306 9.2 Metal reduction 306 9.2.1 Fe(III) and Mn(IV) reduction 9.2.2 Microbial reduction of other metals 309 9.2.3 Metal reduction and the environment 309 9.3 Sulfidogenesis 310 9.3.1 Biochemistry of sulfidogenesis 312 9.3.1.1 Reduction of sulfate 9.3.1.2 Carbon metabolism 313 9.3.2 Electron transport and ATP yield in sulfidogens 317 9.3.2.1 Incomplete oxidizers 317 9.3.2.2 Complete oxidizers 318 9.3.3 Carbon skeleton supply in sulfidogens 318 9.3.4 Oxidation of xenobiotics under sulfidogenic conditions 320 9.4 Methanogenesis 320 9.4.1 Methanogens 320 9.4.1.1 Hydrogenotrophic methanogens 9.4.1.2 Methylotrophic methanogens
8.5.1.5 Non-butyrate clostridial fermentation 268 8.5.2 Acetonebutanolethanol fermentation 269 8.5.3 Fermentation balance 271 8.6 Mixed acid and butanediol fermentation 272 8.6.1 Mixed acid fermentation 8.6.2 Butanediol fermentation 8.6.3 Citrate fermentation by facultative anaerobes 275 8.6.4 Anaerobic enzymes 277 8.7 Propionate fermentation 278 8.7.1 Succinatepropionate pathway 278 8.7.2 Acrylate pathway 280 8.8 Fermentation of amino acids and nucleic acid bases 281 8.9 Fermentation of dicarboxylic 8.10 Hyperthermophilic archaeal fermentation 287 8.11 Degradation of xenobiotics under fermentative conditions 9.4.1.3 Aceticlastic methanogens 9.4.2 Coenzymes in methanogens 9.4.3 Methanogenic pathways 324 9.4.3 Hydrogenotrophic methanogenesis 9.4.3.2 Methylotrophic methanogenesis 9.4.3.3 Aceticlastic methanogenesis 9.4.4 Energy conservation in methanogenesis 327 9.4.5 Biosynthesis in methanogens 9.5 Homoacetogenesis 330 9.5.1 Homoacetogens 330 9.5.2 Carbon metabolism in homoacetogens 330 9.5.2.1 Sugar metabolism 330 9.5.2.2 Synthesis of carbon skeletons for biosynthesis in homoacetogens 333 9.5.3 Energy conservation in homoacetogens 334 9.6 Dehalorespiration 334 9.6.1 Dehalorespiratory organisms 9.6.2 Energy conservation in dehalorespiration 336 9.7 Miscellaneous electron acceptors 336 9.8 Syntrophic associations 337 9.8.1 Syntrophic bacteria 337 9.8.2 Carbon metabolism in syntrophic bacteria 339 9.8.3 Facultative syntrophic associations 9.9 Element cycling under anaerobic conditions 340 9.9.1 Oxidation of aromatic hydrocarbons under anaerobic conditions 341 9.9.2 Transformation of xenobiotics under anaerobic conditions 343
10 Chemolithotrophy
10.1 Reverse electron transport 10.2 Nitrification 355 10.2.1 Ammonia oxidation 356 10.2.2 Nitrite oxidation 357 10.2.3 Anaerobic nitrification 358 10.3 Sulfur bacteria and the oxidation of sulfur compounds 358 10.3.1 Sulfur bacteria 358 10.3.2 Biochemistry of sulfur compound oxidation 360 10.3.3 Carbon metabolism in colourless sulfur bacteria 362 10.4 Iron bacteria: ferrous ironoxidation 10.5 Hydrogen oxidation 364 10.5.1 Hydrogen-oxidizing bacteria 10.5.2 Hydrogenase 364 10.5.3 Anaerobic H2-oxidizers 365
11 Photosynthesis
12 Metabolic regulation
10.5.4 CO2 fixation in H2-oxidizers 10.6 Carbon monoxide oxidation: carboxydobacteria 366 10.7 Chemolithotrophs using other electron donors 367 10.8 CO2 fixation pathways in chemolithotrophs 368 10.8.1 Calvin cycle 368 10.8.1.1 Key enzymes of the Calvin cycle 10.8.1.2 Photorespiration 372 10.8.2 Reductive TCA cycle 373 10.8.3 Anaerobic CO2 fixation through the acetyl-CoA pathway 10.8.4 CO2 fixation through the 3hydroxypropionate cycle 375 10.8.5 Energy expenditure in CO2 fixation 10.9 Chemolithotrophs: what makes them unable to use organics? 377 11.1 Photosynthetic microorganisms 11.4 Light reactions 396 11.1.1 Cyanobacteria 387 11.4.1 Properties of light 397 11.1.2 Anaerobic photosynthetic bacteria 11.4.2 Excitation of antenna molecules 11.1.3 Aerobic anoxygenic phototrophic and resonance transfer 397 bacteria 388 11.4.3 Electron transport 398 11.2 Photosynthetic pigments 389 11.4.3.1 Photosystem I and II in 11.2.1 Chlorophylls 390 cyanobacteria 398 11.2.2 Carotenoids 390 11.4.3.2 Green sulfur bacteria 398 11.2.3 Phycobiliproteins 392 11.4.3.3 Purple bacteria 400 11.2.4 Pheophytin 392 11.4.3.4 Aerobic anoxygenic 11.2.5 Absorption spectra of photosynthetic bacteria 401 photosynthetic cells 393 11.5 Carbon metabolism in phototrophs 11.3 Photosynthetic apparatus 394 11.5.1 CO2 fixation 401 11.3.1 Thylakoids of cyanobacteria 394 11.5.2 Carbon metabolism in 11.3.2 Green bacteria 395 photoorgan 11.3.3 Purple bacteria 395 11.5.2.1 Purple bacteria, heliobacteria 11.3.4 Heliobacteria and aerobic and aerobic anoxygenic phototrophic anoxygenic photosynthetic bacteria 402 bacteria 395 11.5.2.2 Green sulfur bacteria 403 11.5.2.3 Cyanobacteria 403 11.6 Photophosphorylation in halophilic archaea 403 12.1 Mechanisms regulating enzyme 12.2 Global regulation: responses to synthesis 408 environmental stress 435 12.1.1 Regulation of transcription by 12.2.1 Stringent response 437 promoter structure 12.2.2 Response to ammonia limitation and sigma (_) factor activity 409 12.2.3 Response to phosphate 12.1.2 Induction of enzymes 411 limitation: the pho system 441 12.1.2.1 Inducible and constitutive 12.2.4 Regulation by molecular oxygen enzymes 411 in facultative 12.1.2.2 Enzyme induction 412 anaerobes 442 12.1.2.3 Positive and negative control 12.2.4.1 arc system 443 12.1.3 Catabolite repression 413 12.2.4.2 fnr system 444 12.1.3.1 Carbon catabolite repression by 12.2.4.3 RegB/RegA system in purple the cAMPCRP complex 414 non-sulfur photosynthetic bacteria 445 12.1.3.2 Catabolite repressor/activator 12.2.5 Oxidative stress 445 12.1.3.3 Carbon catabolite repression in 12.2.6 Heat shock response 446 Gram-positive 12.2.7 Cold shock response 448
bacteria with a low GC content 417 12.1.4 Repression and attenuation by final metabolic products 419 12.1.4.1 Repression 419 12.1.4.2 Attenuation 420 12.1.5 Regulation of gene expression by multiple end products 423 12.1.6 Termination and antitermination 12.1.6.1 Termination and antitermination aided by protein 424 12.1.6.2 Termination and antitermination aided by tRNA 426 12.1.6.3 Termination and antitermination aided by metabolites 428 12.1.7 Two-component systems with sensor-regulator proteins 428 12.1.8 Autogenous regulation 428 12.1.9 Post-transcriptional regulation of gene expression 430 12.1.9.1 RNA stability 430 12.1.9.2 mRNA structure and translational efficiency 431 12.1.9.3 Modulation of translation and stability of mRNA by protein 431 12.1.9.4 Modulation of translation and stability of mRNA by small RNA and small RNA-protein complex: riboregulation 433
13 Energy, environment 13.1 Survival and energy 482 13.2 Reserve materials in bacteria 483 and microbial survival
12.2.8 Quorum sensing 452 12.2.9 Response to changes in osmotic pressure 453 12.2.10 Other two-component systems 12.2.11 Chemotaxis 455 12.2.12 Adaptive mutation 457 12.3 Regulation through modulation of enzyme activity: fine regulation 459 12.3.1 Feedback inhibition and feedforward activation 459 12.3.2 Enzyme activity modulation through structural changes 460 12.3.2.1 Phosphorylation 461 12.3.2.2 Adenylylation 461 12.3.2.3 Acetylation 462 12.3.2.4 Other chemical modifications 12.3.2.5 Regulation through physical modification and dissociation/association 463 12.4 Metabolic regulation and growth 12.4.1 Regulation in central metabolism 12.4.2 Regulatory network 464 12.4.3 Growth rate and regulation 466 12.5 Secondary metabolites 466 12.6 Metabolic regulation and the fermentation industry 467 12.6.1 Fermentative production of antibiotics 467 12.6.2 Fermentative amino acid production 467 482-492
13.2.1 Carbohydrate reserve materials: glycogen and trehalose 483 13.2.2 Lipid reserve materials 484 13.2.2.1 Poly-_-hydroxyalkanoate (PHA) 485 13.2.2.2 Triacylglyceride (TAG) 486 13.2.2.3 Wax ester and hydrocarbons 486 13.2.3 Polypeptides as reserve materials 487 13.2.4 Polyphosphate 488 13.3 Resting cells 489 13.3.1 Sporulation in Bacillus subtilis 490 13.3.2 Cysts 490 13.3.3 Viable but non-culturable (VBNC) cells 490 13.3.4 Nanobacteria 492 13.3.5 Programmed cell death (PCD) in bacteria 492
PA RT VIII Ecology and Symbiosis PA RT IX Nonspecific Resistance the Immune Response PA RT X Microbial Diseases and Their Control
Chapter 31 Normal Microbiota and Nonspecific Host Resistance Chapter 32 Specific Immunity Chapter 33 Medical Immunology Chapter 34 Pathogenicity of Microorganisms Chapter 35 Antimicrobial Chemotherapy Chapter 36 Clinical Microbiology Chapter 37The Epidemiology of Infectious Disease Chapter 38 Human Diseases Caused by Viruses Chapter 39 Human Diseases Caused by Bacteria Chapter 40 Human Diseases Caused by Fungi and Protozoa Chapter 41 Microbiology of Food Chapter 42 Industrial Microbiology and Biotechnology
PART TWO A Survey of the Microbial World PART THREE Interaction between Microbe and Host
5.REGULATION OF PROKARYOTIC GENE EXPRESSION 194 Transcriptional Control / 194 DNA-Binding Proteins / 195 The lac Operon: A Paradigm of Gene Expression / 197 Catabolite Control: Sensing Energy Status / 201 ClassIand ClassII CRPDependentGene The Catabolite Repressor/Activator Protein Cra Catabolite Control: The GramPositive Paradigm / 206 The gal Operon: DNA Looping with a Little Help from Hu / 206 The Arabinose Operon: One Regulator, Two Functions / 208 Attenuation Controls / 211 Transcriptional Attenuation Mechanisms / 211 Translational Attenuation Control: The pyrC Strategy / 215 Membrane-Mediated Regulation: The put System / 216 Recombinational Regulation of Ge Expression (Flagellar Phase Variation) / 217 Translational Repression / 219 Anti- Regulation by Molecular Hijacking / 220 Titrating a Posttranscriptional Regulator: The CsrA/CsrB Carbon Storage Regulatory Team / 222 Global Control Networks / 223 Communication with the Environment: Two-Component Regulatory Systems Regulation of Nitrogen Assimilation and Nitrogen Fixation: Examples of Integrated Biochemical and Genetic Controls Phosphate Uptake: Communication Between Transport and Two-Component Regulatory Systems / Quorum Sensing: How Bacteria Talk to Each Other / 234 Proteolytic Control / 235 6.BACTERIOPHAGE GENETICS General Characteristics of Bacteriophages / 239 T4 Phage / 245 Structure / 245 General Pattern of T4 Gene Expression / 247 T4 Genome
Phage / 256 The Lysis-Lysogeny Decision / Transcription / 259 Function of Cro Versus CI Repressor and the Structure of OL and OR / 260 Establishment of Repressor Synthesis Control of Integration and Excision Negative Retroregulation of int by sib -Phage Replication / 264 Phage: Transposition as a Lifestyle _X174 / 271 General / 274 T4 Bacteriophage / Phage / 275 X174 / Phage / 275 7.CELL STRUCTURE AND FUNCTION 277 The Eukaryotic Nucleus / 277 Bacterial Nucleoids / 279 Nucleosomes/ Mitochondria / 287 Microbial Cell Surfaces / 288 Eukaryotic Cell Surfaces / 288 Prokaryotic Cell Surfaces / 289 Surface Layers of Bacteria / 290 Peptidoglycans of Bacterial Cell Walls Peptidoglycan (Murein) Hydrolases Peptidoglycan (Murein) Synthesis Teichoic Acids and Lipoteichoic Acids Outer Membranes of Gram-Negative Bacteria / 303 Lipopolysaccharide Biosynthesis / 308 Enterobacterial Common Antigen Cytoplasmic Membranes / 310 Permeability and Transport / 313 Periplasm / 313 Other Membranous Organelles / 314 Capsules / 315 Microbial Biofilms/ 322 Organs of Locomotion / 323 Cilia and Flagella of Eukaryotes / 323 Bacterial (Prokaryotic) Flagella / 325 Chemotaxis/ Swarming Motility / 334 Motility in Spirochetes / 337 Gliding Motility /Pili or Fimbriae / 340 Nucleus, Nucleosomes, and Nucleoids Mitochondria /Eukaryotic Cell Surface / Surface (S) layers / 344 Bacterial Cell Wall Peptidoglycan (Murein) / 345 Teichoic and Lipoteichoic Acids / 346 Outer Membrane / 346 Cytoplasmic Membrane / 346 Periplasm /Capsules / 346 Biofilms / 347 Cilia and Flagella of Eukaryotes / 347 Bacterial Flagella / 347 Chemotaxis /Swarming Motility / 348 Gliding Motility / 348 Motility in Spirochetes / 348 Pili or Fimbriae / 349
8.CENTRAL PATHWAYS OF CARBOHYDRATE METABOLISM Alternate Pathways of Carbohydrate Metabolism / 351 Fructose Bisphosphate Aldolase Pathway / 351 Alternate Pathways of Glucose Utilization / 354 Entner-Doudoroff or Ketogluconate Pathway / 354 Phosphoketolase Pathway / 356 Oxidative Pentose Phosphate Cycle Gluconeogenesis / Regulation / 360 Glycogen Synthesis /Tricarboxylic Acid Cycle / Glyoxylate Cycle / 365 9.ENERGY PRODUCTION AND METABOLITE TRANSPORT 368 Energy Production / 368 Substrate-Level Phosphorylation / 369 Oxidative Phosphorylation / 371 Measurement of PMF / 372 Electron Transport Systems / 373 Anaerobic Respiration / 376 Conversion of PMF to Energy / 377 Structure of F1F0 and the atp Operon Energy Yield / 380 Generating ATP in Alkalophiles / 380 Energetics of Chemolithotrophs / 380 pH Homeostasis / 382 Metabolite Transport / 383 Facilitated Diffusion / 383 Mechanosensitive Channels / 385 ATP-Binding Cassette Transporter Family / 385 Chemiosmotic-Driven Transport / 385 Establishing Ion Gradients / 387 Specific Transport Systems / 387 ATP-Linked Ion Motive Pumps / 387 The Histidine Permease / Iron / 389 Phosphotransferase System / 390 Energy Production / 392 Metabolite Transport / 392 10.METABOLISM OF SUBSTRATES OTHER THAN GLUCOSE 394 Utilization of Sugars other than Glucose / Lactose / 394 Galactose / Maltose / Mannitol / 396 Fucose and Rhamnose / 397 Mellibiose, Raffinose, Stachyose, Pectin and Aldohexuronate Pathways Cellulose Degradation / Starch, Glycogen, and Related Compounds, Metabolism of Aromatic Compounds Pectin Utilization ,Cellulose Utilization Utilization of Starch, Glycogen, and Related Compounds / 411 Utilization of Aromatic Hydrocarbons .
11. FERMENTATION PATHWAYS 412 Fermentation Balances / 412 Yeast Fermentation / 415 Lactic AcidProducing Fermentations / Butyric Acidand SolventProducing Fermentations / 423 Fermentations of the Mixed-Acid Type Propionic Acid Fermentation / 428 Acetic Acid Fermentation / 430 Fermentation Pathways / 431 Yeast Fermentation / 431 Lactic Acid Fermentation / 432 Butyric Acid and SolventProducing Fermentations / 432 Mixed-Acid Fermentations / 433 Propionic Acid Fermentation / 433 Acetic Acid Fermentation / 433 12.PHOTOSYNTHESIS AND INORGANIC METABOLISM Characteristics and Metabolism of Autotrophs / 434 Photosynthetic Bacteria and Cyanobacteria / 434 Autotrophic CO2 Fixation and Mechanisms of Photosynthesis / Hydrogen Bacteria / 440 Nitrifying Bacteria /Sulfur Bacteria Iron Bacteria /Methylotrophs / Methanogens / 446 13.LIPIDS AND STEROLS 450 Lipid Composition of Microorganisms Straight-Chain Fatty Acids / 451 Branched-Chain Fatty Acids / 453 Ring-Containing Fatty Acids / 454 Alk-1-enyl Ethers (Plasmalogens) Alkyl Ethers / 456 Phospholipids(Phosphoglycerides) Glycolipids / 458 Biosynthesis of Fatty Acids / 459 Biosynthesis of Phospholipids / Degradation of Fatty Acids / 466 Biosynthesis of Isoprenoids / 468 14.NITROGEN METABOLISM Biological Nitrogen Fixation / 475 The Nitrogen Fixation Process / Components of the Nitrogenase System / 480 Symbiotic Nitrogen Fixation / 483 Inorganic Nitrogen Metabolism / Assimilation of Inorganic Nitrogen General Reactions of Amino Acids Amino Acid Decarboxylases / 494 Amino Acid Deaminases / 495
Amino Acid Transaminases (Aminotransferases) / 497 Amino Acid Racemases / 498 Role of Pyridoxal-5_-Phosphate in Enzymatic Reactions with Amino Acids The Stickland Reaction / 500 Nitrogen Fixation / 501 Inorganic Nitrogen / Urease / 502 Assimilation of Inorganic Nitrogen 15.BIOSYNTHESIS AND METABOLISM OF AMINO ACIDS The Glutamate or -Ketoglutarate Family / 503 Glutamine and Glutathione Synthesis The Proline Pathway / 504 Aminolevulinate Synthesis / 504 The Arginine Pathway / 504 Polyamine Biosynthesis / 509 The -Ketoadipate Pathway to Lysine The Aspartate and Pyruvate Families Asparagine Synthesis / 513 The Aspartate Pathway / 514 The Bacterial Pathway to Lysine / 515 Threonine, Isoleucine, and Methionine Formation / Isoleucine, Valine, and Leucine Biosynthesis / 518 Regulation of the Aspartate Family The Serine-Glycine Family / 520 Aminolevulinate and the Pathway to Tetrapyrroles / 523 The Aromatic Amino Acid Pathway Phenylalanine, Tyrosine, and Tryptophan / 523 The Common Aromatic Amino Acid Pathway / 525 Pathways to Tyrosine and Phenylalanine / 526 p-Aminobenzoate and Folate Biosynthesis / 531 Enterobactin Biosynthesis / 533 The Pathway to Ubiquinone / 534 Menaquinone (Vitamin K) Biosynthesis Biosynthesis of Nicotinamide Adenine Dinucleotide (NAD) / 534 Histidine Biosynthesis,Amino Acids Glutamate (-Ketoglutarate) Family Aspartate and Pyruvate Families / 542 Serine-Glycine Family / 543 Aromatic Amino Acid Family / 543 Histidine / 544
16 PURINES AND PYRIMIDINES Biosynthesis of Purines / 545 Biosynthesis of Pyrimidines / 550 Interconversion of Nucleotides, Nucleosides, and Free Bases: Salvage Pathways / 554 Regulation of Purine and Pyrimidine Biosynthesis / 555 Purines and Pyrimidines / 559 Riboflavin Biosynthesis / 560 Thiamine Biosynthesis / 560 17.BACTERIAL CELL DIVISION Cell Division in Gram-Negative Rods / Cell Division in Gram-Positive Cocci / Cell Division in Gram-Positive Bacilli / General Reviews / 578 Cell Division in Gram-Negative Rods Cell Division in Gram-Positive Cocci Cell Division in Gram-Positive Bacilli 18.MICROBIAL STRESS RESPONSES Osmotic Stress and Osmoregulation High Osmolality / 583 Low Osmolality / 584 Osmotic Control of Gene Expression / Aerobic to Anaerobic Transitions / 587 Formate Nitrate Regulation / 589 Nitrate Response / 589 ArcAB System / Oxidative Stress / 592 Regulation of the Oxidative Stress Response / 594 pH Stress and Acid Tolerance / 596 Thermal Stress and the Heat Shock Response / 597 Nutrient Stress and the Starvation Stress Response / 601 StarvationStress Response / 601 Stringent Control / 602 Extremophiles / 605 Summary / 608 Osmotic Stress and Osmoregulation Aerobic to Anaerobic Transitions / 609 Oxidative Stress / 609 pH Stress and Acid Tolerance / 610 Thermal Stress and the Heat Shock Response / 610 Nutrient Stress and the Starvation Stress Response / 611 Stringent Control / 611 Extremophiles / 611
19.BACTERIAL DIFFERENTIATION Bacillus Endospore Formation / Life Cycle of Bacillus / 613 Stages of Sporulation / 614 Physiological and Genetic Aspects of Sporulation / 616 Sporulation Genes /Initiation /617 Transition from Stage II to Stage III Forespore Development / 620 Final Stages of Sporulation / 621 Spore Cortex Synthesis / 622 Spore Coat Protein Synthesis / Activation, Germination, and Outgrowth of Bacterial Endospores / 623 Activation / Germination / 624 Outgrowth / 627 Myxobacterial Developmental Cycle / 628
Life Cycle of Myxobacteria / 628 Aggregation and Fruiting Body Formation / 629 Genetics of Myxococcus xanthus Development / 632 Caulobacter Differentiation / 637 Life Cycle of Caulobacter crescentus / The Stalk, the Holdfast, and the Flagellum: Structure, Genetics, and Regulation / 638 Regulation and Checkpoints of the Cell Cycle of C. crescentus / 642 Endospore Formation / 644 Germination and Outgrowth of Endospores / 645 Myxobacterial Developmental Cycle / Caulobacter Differentiation / 647
20. HOSTPARASITE INTERACTIONS 648 Overview of HostParasite Relationships / 648 Structures and Functions Involved in HostParasite Interactions / 650 Adherence/Colonization / 650 Virulence Factor Secretion Systems / Exotoxins/ 658 Quorum Sensing / 664 Paradigms of Bacterial Pathogenesis Enteropathogenic Escherichia coli Salmonella Enterica Serovars / Listeria Monocytogenes / 670 Chlamydia spp / 672 Adherence/Colonization / 672 Virulence Factor Secretion Systems / Exotoxins Quorum Sensing / 674 Paradigms of Bacterial Pathogenesis / 675
12 24 36 49 62
Bacterial Diseases. Viral Diseases. Other Skin Diseases. Eye and Wound 215 Diseases. Bacterial Diseases. Viral Diseases. Fungal and Protozoal Diseases. Bacterial Diseases. Viral Diseases. Fungal and Protozoal Diseases. Bacterial Diseases. Viral Diseases. Other Microbial Diseases.
230
255
Microorganisms and Foods. Food Contamination and Preservation. Laboratory Testing. Microorganisms and Industry. Chapter 25 ENVIRONMENTAL Microbial Ecology. Biogeochemical Cycles. Wastewater Microbiology. MICROBIOLOGY
295
308
CHAPTER R 51: Introduction to Pathogenic Parasites: Pathogenesis and Chemotherapy of Parasitic Diseases CHAPTER 52: Sporozoa CHAPTER 53: Rhizopods CHAPTER 54: Flagellates CHAPTER 55: Intestinal Nematodes 691 CHAPTER 56 : Tissue Nematodes CHAPTER 57: Cestodes CHAPTER 58: Trematodes CHAPTER 59: Skin and Wound Infections CHAPTER 60: Bone and Joint Infections CHAPTER 61: Eye, Ear, and Sinus Infections CHAPTER 62: Dental and Periodontal Infections CHAPTER 63: Upper Respiratory Tract Infections and Stomatitis 815 CHAPTER 64: Middle and Lower Respiratory Tract Infections CHAPTER 65: Enteric Infections and Food Poisoning CHAPTER 66: Urinary Tract Infections CHAPTER 67: Central Nervous System Infections CHAPTER 68: Intravascular Infections, Bacteremia, and Endotoxemia CHAPTER 69: Infections of the Fetus and Newborn CHAPTER 70: Sexually Transmitted Diseases CHAPTER 71: Infections in the Immunocompromised Patient CHAPTER 72: Nosocomial Infections and Infection Control
VIRUS
EUKARYOTA
Phytogeny; General Characteristics; Cell Wall; Plasma Membrane; Metabolism; Characteristics of the Major Archaeal Groups; Halobacteria. General Characteristics; Classification, Cell Structure; Reproduction, Economic Importance; Plant Diseases-Symptoms, Transmission; Human and Animal Diseases Mollicutes; Phytoplasmas-Occurrence & Maintenance, Detection; Vectors; Spread & Transmission; Disease Symptoms; Identification; Classification; Cure & Management; Little Leaf of Brinjal-Symptoms, Control. General Characters of Cyanobacteria; Occurrence, Thallus Organization; Cell Structure, Photosynthetic Pigments and Chromatic Adaptation; Gas Vacuoles; Heterocyst-Physiology & Nature of Heterocyst, Function; Nutrition of Cyanobacteria; Reproduction-Vegetative (Fission, Fragmentation, Hormogonia); Asexual (Akinetes, Endospores, Exospores, Nannocytes, Hormospores); Genetic Recombination Spirochetes - Movement, Cell division, Diversity, Symbiosis with Invertebrates; Trepollema pallidu11l, Borrelia, Lyme diseases; Rickettsia; Chlamydia, Gliding Bacteria (The Myxobacteria); The Sheathed BacteriaSphaerotilus, Leptothrix, Halisco11le1lobacter, Chemolithotrophs; Anoxygenic Phototrophic Bacteria; Oxygenic Phototrophic Bacteria; Cyanobacteria; Nitrogen Fixing Cyanobacteria; The Purple Bacteria (Sulphur and Nonsulphur Bacteria); The Green Bacteria (Sulphur & Non-sulphur Bacteria); Budding Bacteria. Mycobacteria, Mycobacterium tuberculosis - Growth Characteristics, Pathogenicity; Endospore Forming Rods & Cocci; Anaerobic Spore Formers; Bacilllls - Anthrax, Clostridium; Actinomycetes - Biotechnological Potential of Actinomycetes; Antibiotics from Actinomycetes. Algae-General Characters, Habit & Habitat, Thallus Organization, Pigments, Reserve Food, Algal Cell-Flagella, Reproduction- Vegetative, Asexual & Sexual; Types of Life Cycle; Classification; Fungi - General Characters, Nutrition, Growth & Reproduction, Classification