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BOOKS OF MICROBIOLOGY

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

CELL STRUCTURE CHEMICAL COMPOSITION

ENVIRONMENTAL MICROBIOLOGY AND ECOLOGY

EVOLUTION AND SYSTEMATICS FUNGI GENETICS, GENOMICS

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

HISTORY AND CULTURE, (AND BIOGRAPHIES) MUTUALISM AND COMMENSALISM PATHOGENESIS

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

Fungal Infection Diagnosis and Management 3rd 2003


1 Introduction
The nature of fungi, Classification and nomenclature of fungi and fungal Diseases, Fungi as human pathogens ,The superficial mycoses , The subcutaneous mycoses, The systemic mycoses, The changing pattern of fungal infection, New directions in diagnosis, New directions in treatment and prevention, 10 Introduction, 14 Collection of specimens, 15 Mucous membranes, Ear, Eye, Blood, Cerebrospinal fluid, Urine, Other fluids, Pus, Bone marrow, Tissue, Specimens for serological tests, Specimens for antifungal drug level determinations, Transport of specimens, Interpretation of laboratory test results, Direct microscopic examination, Histopathological examination, Culture, Skin, nails and hair, Lower respiratory tract specimens, Serological tests, Molecular diagnosis of fungal infection, 27 3.1 Introduction, 29 3.10.1 Naftifine, 64 3.2 Amphotericin 29 3.11 Caspofungin, 64 3.3 Other polyene compounds for 3.12 Flucytosine, 66 topical administration, 40 13.13 Griseofulvin, 70 3.3.1 Natamycin, 40 3.14 Other miscellaneous 3.3.2 Nystatin, 41 compounds for topical 3.4 Fluconazole, 41 administration, 72 3.5 Itraconazole, 46 3.14.1 Amorolfine hydrochloride 3.6 Ketoconazole, 51 3.14.2 Butenafine hydrochloride 3.7 Voriconazole, 54 3.14.3 Ciclopirox, 72 3.8 Other imidazole compounds for 3.14.4 Haloprogin, 73 topical administration, 59 3.14.5 Tolnaftate, 73 3.8.1 Bifonazole, 59 3.15 Empirical treatment of 3.8.2 Butoconazole, 59 suspected fungal infection in the 3.8.3 Clotrimazole, 59 neutropenic patient, 73 3.8.4 Econazole nitrate, 60 3.16 Prophylactic treatment for 3.8.5 Fenticonazole nitrate, 60 prevention 3.8.6 Isoconazole nitrate, 60 of fungal infection, 74 3.8.7 Miconazole nitrate, 60 3.17 Laboratory monitoring, 76 3.8.8 Oxiconazole, 60 3.17.1 Antifungal drug 3.8.9 Sulconazole nitrate, 61 susceptibility testing, 76 3.8.10 Terconazole, 61 3.17.2 Monitoring of blood 3.8.11 Tioconazole, 61 concentrations of antifungal 3.9 Terbinafine, 61. drugs 4.1 Introduction, 80 4.7 Tinea pedis, 95 4.2 The causal organisms and their 4.8 Tinea manuum, 99 habitat, 80 4.9 Tinea unguium, 102 4.3 Laboratory diagnosis of =(Definition, Geographical dermatophytosis, 82 distribution, Epidemiology, 4.4 Tinea capitis, 83 Clinical manifestations, 4.5 Tinea corporis, 90 Differential diagnosis, Essential 4.6 Tinea cruris, 93 investigations and their 3.10 Other allylamine compounds for interpretation, Management, topical administration, 64 Prevention)= =(Definition, Geographical distribution, Epidemiology, Clinical manifestations, Differential diagnosis, Essential investigations and their interpretation, Management, Prevention)= Candidosis: Oropharyngeal , Vaginal, Penile, Cutaneous, Cundidu nail infection, Chronic mucocutaneous, Essential investigations. Management: Oropharyngeal, Vaginal, Penile, Cutaneous,Cundidu nail infection, Chronic mucocutaneous, Prevention 1

2 Laboratory diagnosis of fungal infection, 14

14

3 Antifungal drugs

29-77

4 Dermatophytosis

80-107

5 Supelficial candidosis

109-126

6 Other cutaneous fungal infections

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

7 Mould infections of nails

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 Penici//ium marneffei infection

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

27 Other invasive yeast infections

Infection; Microbiology and Management, 3rd ed. 2006


Part 1: Infection, Pathogens and Antimicrobial Agents Part 2: Systematic Infectious Diseases
1 The Nature and Pathogenesis of Infection, 3 2 Structure and Classifi cation of Pathogens, 26 3 Laboratory Techniques in the Diagnosis of Infection, 38 4 Antimicrobial Chemotherapy, 53 5 Infections with Skin, Mucosal and Soft-tissue Disorders, 85 6 Upper Respiratory Tract Infections, 117 7 Lower Respiratory Tract Infections, 138 8 Gastrointestinal Infections and Food Poisoning, 167 9 Infections of the Liver, 202 10 Infections of the Urinary Tract, 226 11 Childhood Infections, 238 12 Infections of the Cardiovascular System, 256 13 Infections of the Central Nervous System, 268 14 Bone and Joint Infections, 302 15 Genital and Sexually Transmitted Diseases, 315 16 HIV Infection and Retroviral Diseases, 331 17 Congenital and Perinatal Infections, 344 18 Tuberculosis and Other Mycobacterial Diseases, 363 19 Bacteraemia and Sepsis, 389 20 Pyrexia of Unknown Origin, 406 21 Post-infectious Disorders, 418 22 Infections in Immunocompromised Patients, 431 23 Hospital Infections, 443 24 Travel-associated and Exotic Diseases, 460 25 Control of Infection in the Community, 502 26 Emerging and Re-emerging Infections, 517 1-53

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

Kim - Bacterial Physiology and Metabolism (Cambridge, 2008)


1 Introduction to bacterial physiology and metabolism 2 Composition and structure of prokaryotic cells
1-7

3 Membrane transport nutrient uptake and protein excretion

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 Tricarboxylic acid (TCA) cycle, electron transport and oxidative phosphorylation

6 Biosynthesis and microbial growth

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

7 Heterotrophic metabolism on substrates other than glucose

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

Microbiology 5th Ed. - L. Prescott (McGrawHill, 2002)


PA RT I Introduction to Microbiology PA RT II Microbial Nutrition, Growth, and Control PA RT III Microbial Metabolism PA RT IV Microbial Molecular Biology and Genetics PA RT V DNA Technology and Genomics PA RT VI The Viruses PA RT VII The Diversity of the Microbial World
Chapter 1 The History and Scope of Microbiology Chapter 2 The Study of Microbial Structure: Microscopy and Specimen Preparation Chapter 3 Procaryotic Cell Structure and Function Chapter 4 Eucaryotic Cell Structure and Function Chapter 5 Microbial Nutrition Chapter 6 Microbial Growth Chapter 7 Control of Microorganisms by Physical and Chemical Agents Chapter 8 Metabolism: Energy, Enzymes, and Regulation Chapter 9 Metabolism: Energy Release and Conservation Chapter 10 Metabolism:The Use of Energy in Biosynthesis Chapter 11 Genes: Structure, Replication, and Mutation Chapter 12 Genes: Expression and Regulation Chapter 13 Microbial Recombination and Plasmids Chapter 14 Recombinant DNA Technology Chapter 15 Microbial Genomics Chapter 16 Chapter 17 Chapter 18 Chapter 19 Chapter 20 Chapter 21 Chapter 22 Chapter 23 Chapter 24 Chapter 25 Chapter 26 Chapter 27 Chapter 28 Chapter 29 Chapter 30 The Viruses: Introduction and General Characteristics The Viruses: Bacteriophages The Viruses:Viruses of Eucaryotes Microbial Taxonomy The Archaea Bacteria:The Deinococci and Nonproteobacteria Gram (-)ve Bacteria:The Proteobacteria Bacteria:The Low G _ C Gram Positives Bacteria:The High G _ C Gram Positives The Fungi (Eumycota), Slime Molds, and Water Molds The Algae The Protozoa Microorganism Interactions and Microbial Ecology Microorganisms in Aquatic Environments Microorganisms in Terrestrial Environments

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

PA RT XI Food and Industrial Microbiology

Microbiology 10th edition by Tortora


PART ONE Fundamentals of Microbiology
1 The Microbial World and You I 2 Chemical Principles 26 3 Observing Microorganisms through a Microscope 54 4 Functional Anatomy of Prokaryotic and Eukaryotic Cells 76 5 Microbial Metabolism 113 6 Microbial Growth 156 7 The Control of Microbial Growth 184 8 Microbial Genetics 210 9 Biotechnology and Recombinant DNA 246 10 Classification of Microorganisms 273 11 The Prokaryotes: Domains Bacteria and Archaea 299 12 The Eukaryotes: Fungi, Algae, Protozoa, and Helminths 329 13 Viruses, Viroids, and Prions 367 14 Principles of Disease and Epidemiology 399 15 Microbial Mechanisms of Pathogenicity 428 16 Innate Immunity: Nonspecific Defenses of the Host 449 17 Adaptive Immunity: Specific Defenses of the Host 476 18 Practical Applications of Immunology 500 19 Disorders Associated with the Immune System 522 20 Antimicrobial Drugs 553 21 Microbial Diseases of the Skin and Eyes 584 22 Microbial Diseases of the Nervous System 610 23 Microbial Diseases of the Cardiovascular and Lymphatic Systems 637 24 Microbial Diseases of the Respiratory System 674 25 Microbial Diseases of the Digestive System 705 26 Microbial Diseases of the Urinary and Reproductive Systems 743 27 Environmental Microbiology 766 28 Applied and Industrial Microbiology 793

PART TWO A Survey of the Microbial World PART THREE Interaction between Microbe and Host

PART FOUR Microorganisms and Human Disease

PART FIVE Environmental and Applied Microbiology

Microbiology A Human Perspective 6th 2009


PART I LIFE AND DEATH OF MICROORGANISMS
1 Humans and the Microbial World 1 2 The Molecules of Life 18 3 Microscopy and Cell Structure 40 4 Dynamics of Prokaryotic Growth 83 5 Control of Microbial Growth 107 6 Metabolism: Fueling Cell Growth 126 7 The Blueprint of Life, from DNA to Protein 161 8 Bacterial Genetics 185 9 Biotechnology and Recombinant DNA 212 10 Identification and Classification of Prokaryotic Organisms 232 11 The Diversity of Prokaryotic Organisms 251 12 The Eukaryotic Members of the Microbial World 280 13 Viruses of Bacteria 302 14 Viruses, Prions,and Viroids:Infectious Agents of Animals and Plants 320 15 The Innate Immune Response 346 16 The Adaptive Immune Response 366 17 Host-Microbe Interactions 391 18 Immunologic Disorders 414 19 Applications of Immune Responses 431 20 Epidemiology 450 21 Antimicrobial Medications 469 22 Respiratory System Infections 495 23 Skin Infections 531 24 Wound Infections 559 25 Digestive System Infections 581 26 Genitourinary Infections 618 27 Nervous System Infections 647 28 Blood and Lymphatic Infections 674 29 HIV Disease and Complications of Immunodeficiency 697 30 Microbial Ecology 721 31 Environmental Microbiology: Treatment of Water,Wastes, and Polluted Habitats 738 32 Food Microbiology 753

PART II THE MICROBIAL WORLD PART III MICROORGANISMS AND HUMANS

PART IV INFECTIOUS DISEASES

PART V APPLIED MICROBIOLOGY

Moat - Microbial Physiology 4e (Wiley, 2002)


1.INTRODUCTION TO MICROBIAL PHYSIOLOGY Coupled Transcription and Translation Protein Folding and Chaperones / 74 Folding Stages / 75 The Escherichia coli Paradigm / 1 Protein Folding and Chaperone Cell Structure / 1 Mechanisms Outside the The Cell Surface / 1 Cytoplasm / 76 Synthesis of DNA, RNA, and Quality Control /Protein Trafficking/77 Protein 7 Insertion of Integral Membrane Metabolic and Genetic Regulation Proteins and Export of Periplasmic Microbial Genetics / 11 Proteins / 77 Chemical Synthesis / 12 Secretion of Proteins Across the Outer Chemical Composition / 12 Membrane / 81 Energy / 13 Protein Degradation / 83 OxidationReduction Versus Degradation of Abnormal Proteins Fermentation / 15 Energy-Dependent Proteases / 86 Nitrogen Assimilation / 18 Antibiotics that affect Nucleic Acid and Special Topics / 19 Protein Synthesis / 88 Endospores / Growth / 19 Agents Affecting DNA Metabolism / 88 Continuous Culture / 22 Agents Affecting Transcription / 91 Factors Affecting Growth / 22 Agents Affecting Translation / 92 Nutrition /Oxygen / 24 Nucleoids /DNA Replication / 98 Carbon Dioxide / 24 Transcription and Translation / 98 Extremophiles / 25 Protein Folding, Trafficking, and Microbial Stress Responses / 26 Degradation / Antibiotics / 100 General Recombination / 128 Genetics of Recombination / 131 Restriction and Modification / 133 Insertion Sequences and Transposable Elements / 138 Transposon Tn10 / 140 Transposon Tn3 / 143 Conjugative Transposition / 144 Evolutionary Consideration / 144 Integrons / 145 Mutagenesis / 145 Spontaneous Mutations / 147 The Nature of Mutational Events / 147 Suppressor Mutations / 149 DNA Repair Systems / 152 Photoreactivation / 152 Nucleotide Excision Repair / 152 Transcription-Coupled Repair / 155 Methyl-Directed Mismatch Repair /156 Very Short-Patch Mismatch Repair 158 DNA Glycosylases and Base Excision Repair / 158 Adaptive Response to Methylating and Ethylating Agents / 160 Postreplication Daughter Strand Gap 2.MACROMOLECULAR 3.BACTERIAL GENETICS: DNA Repair /SOS-Inducible Repair / 162 SYNTHESIS AND EXCHANGE, Replication Restart / 165 PROCESSING: RECOMBINATION, Adaptive Mutations / 166 DNA, RNA, AND PROTEIN MUTAGENESIS, AND REPAIR 101 Plasmids /Transformation / 167 SYNTHESIS 27 Conjugation / Recombination / 168 Transfer of Genetic Information in Restriction Modification / 169 Structure of DNA / 28 Prokaryotes / 101 Transposition / Mutagenesis / 169 Bacterial Nucleoids / 31 Plasmids / 102 Repair Mechanisms / 170 REP Elements / 35 Partitioning / 102 4.MICROBIAL PHYSIOLOGY IN DNA Replication / 36 Incompatibility / 103 THE GENOMIC ERA: DNA Replication is Bidirectional Nonconjugative, Mobilizable Plasmids A REVOLUTIONARY TALE 171 and Semiconservative / 36 Resistance Plasmids / 104 Genomic and Proteomic Tools / 172 DNA Polymerase Functions as a Plasmids in Other Bacterial Genera Cloning a Genome/ DNA Sequencing Dimer /Model of DNA Replication Plasmid Replication / 104 Web Science: Internet Tools for DNA Initiation of DNA Replication / 42 Addiction Modules: Plasmid Sequence Analysis / 173 Termination of DNA Replication Maintenance by Host Killing: Gene Replacement /Gene Arrays / 177 and Chromosome Partitioning /46 The ccd Genes / 108 Proteomics /Traditional Tools181 RNA Synthesis: Transcription / 47 Conjugation / 108 Mutant Hunts / 181 RNA Synthesis / 47 F Factor / 108 Transcriptional Gene Fusions RNA Turnover ,RNA Processing,54 cis/trans complementation Test / 115 (Reporter Genes) / 182 Protein Synthesis: Translation Conjugation and Pheromones in Polymerase Chain Reaction / 183 Transfer RNA / 59 Enterococci / 116 DNA Mobility Shifts (Gel Shifts and Charging of tRNA / 62 Conjugation, CellCell Signaling, and Supershifts) / 185 Ribosome Structure and Synthesis Bacterial-Induced Tumors / 117 Finding Transcriptional Starts by Initiation of Polypeptide Synthesis Transformation / 118 Primer Extension / 186 Elongation / 69 Gram-Positive Transformation / 119 Detecting DNA, RNA, Protein, and Peptide Bond Formation / 71 Gram-Negative Transformation / 123 DNA-Binding Proteins by Translocation / Termination / 72 Transfection and Forced Competence Southern, Northern, Western, and Posttranslational Processing / 73 Transduction / 124 Southwestern Blots / 187 When Nonsense Makes Sense /74 Recombination / 127 Two-Hybrid Analysis / 190

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

Molecular Methods for Virus Detection 1995


1. Nucleic Acid Detection Methods I. IntroductionII. Specimen Processing III. Target Amplification 4 IV. Probe Amplification 8 V. Detection Systems 11 VI. Potential Applications 19 VII. Difficulties and Disadvantages 2. Quality Assurance in the Molecular Virology Laboratory I. Introduction 25 II. Specimen Quality 26 III. Facilities and Equipment 27 IV. Pipettes and Pipetting 29 V. Biochemical Methods of Preventing Amplicon Carryover 30 VI. Protective Clothing 32 VII. Reagents and Glassware 32 VIII. Procedural Controls 34 IX. Proficiency Testing 34 3. Nucleic Acid Blotting Techniques for Virus Detection I. Introduction 4 II. Sample Preparation 40 III. Nucleic Acid Quantification 44 IV. Southern Blotting 45 V. Northern Blotting 51 VI. Dot/Slot Blotting DNA and RNA VII. Hybridization Theory 55 VIII. Hybridization Probes 57 IX. Filter Hybridization 62 X. Methods of Detection and Quantification 64 XI. Examples of Blotting Technology XII. Southern Blotting and the Polymerase Chain Reaction 71 4. In Situ Hybridization I. Introduction 75 II. General Procedures 76 III. Instrumentation 85 IV. Detection of Human Papillomavirus by in Situ Hybridization V. Selected Studies 94 VI. In Situ Hybridization in Conjunction with Other Techniques VII. Vendors 96 VIII. Conclusion 5. Antiviral Susceptibility Testing Using DNA-DNA Hybridization I. Introduction 103 II. Principle of the Test 110 III. Collection and Preparation of Herpes Simplex virus Isolates 110 IV. Preliminary Considerations 111 V. Antiviral Susceptibility Assay 117 VI. Conclusions 125 6. Quantification of Viral Nucleic Acids Using Branched DNA Signal Amplification I. Introduction 131 II. Description of the Procedure 132 III. Components of the bDNA Assay IV. Uses of bDNA Assays 140 V. Sample Collection and Stability 142 7. Detection Methods Using Chemiluminescence I. General Introduction 147 II. Chemiluminescence Methods 148 III. Instrumentation for Chemiluminescence Assays 153 IV. Chemiluminescence Assays for Virus Detection 154 V. Chemiluminescence Detection Protocols 159 VI. Conclusion 166 8. Detection of Viral Pathogens Using PCR Amplification I. Overview of PCR Amplification 175 II. Considerations for Diagnostic Assay Design i 81 III. PCR Amplification for the Qualitative Detection of HIV-1 Proviral DNA 183 9. Quantitation of RNA Targets Using the Polymerase Chain Reaction I. Introduction 193 II. PCR Methods for Viral RNA Quantification 194 III. Development and Validation of an RT-PCR Assay for the Precise Quantification of HIV-1 RNA in the Peripheral Blood Mononuclear Cells of Infected Individuals 205 IV. General Conclusion 214 10. Multiplex Polymerase Chain Reaction I. Introduction 219 II. Methodology III. Developing a Multiplex PCR Assay IV. Quality Assurance 231 11. PCR in Situ Hybridization I. Introduction 237 II. Methods 240 III. Applications 249 12. Nucleic Acid Sequence-Based Amplification I. Background 261 II. Application for the Detection of HIV-1 RNA in Plasma or Serum 271 III. Required Materials and Solutions 13. The Self-Sustained Sequence Replication Reaction and Its Application in Clinical Diagnostics and MolecularBiology I. Introduction 287 II. Characteristics of the 3SR Reaction III. Hybridization and Detection of 3SR Products 295 IV. Sterilization of 3SR Reactions 297 V. Applications of the 3SR Reaction VI. Experimental Procedures for Detection of HIV-1 301 VII. Conclusions 311 14. Ligase Chain Reaction for the Detection of Infectious Aget I. Introduction 315 II. Principle of the Ligase Chain Reaction 316 III. Application for Detection of Infectious Agents 318 IV. Methodology 321 15. A Chemiluminescent DNA Probe Test Based on Strand Displacement Amplification I. Introduction 330 II. Description of StrandDisplacement Amplification III. Detection of SDA Reactions 334 IV. Performance of SDA with Clinical Mycobacterium tuberculosis Specimens 335 V. Processing Clinical Specimens prior to SDA 349 VI. Protocol for Chemiluminescent Detection 341 VII. Conclusion 347 16. Ligation-Activated Transcription Amplification: Amplification and Detection of Human Papillomaviruses I. Introduction 351 II. Principle of Ligation-Activated Transcription Amplification 352 III. Antibody-Capture Solution Hybridization 353 IV. Protocols 354 V. Characteristics of the LAT Amplification System VI. Chemiluminescence Detection of Amplified Products VII. Amplification and Detection of

Schaums Outline of Microbiology, 2nd ed, 2010


Chapter 1 INTRODUCTION TO MICROBIOLOGY Chapter 2 THE CHEMICAL BASIS OF MICROBIOLOGY Chapter 3 MICROBIAL SIZE AND MICROSCOPY Chapter 4 PROKARYOTES AND EUKARYOTES Chapter 5 MICROBIAL GROWTH & CULTIVATION Chapter 6 METABOLISM OF MICROORGANISMS Chapter 7 DNA AND GENE EXPRESSION Chapter 8 MICROBIAL GENETICS Chapter 9 CONTROL OF MICROORGANISMS Chapter 10 THE MAJOR GROUPS OF BACTERIA Chapter 13 THE UNICELLULAR ALGAE Chapter 14 THE VIRUSES Chapter 15 THE HOSTPARASITE RELATIONSHIP Chapter 16 HOST RESISTANCE AND THE IMMUNE SYSTEM Chapter 17 IMMUNE TESTS AND DISORDERS Chapter 18 MICROBIAL DISEASES OF THE SKIN AND EYES Chapter 19 MICROBIAL DISEASES OF THE NERVOUS SYSTEM Chapter 20 MICROBIAL DISEASES OF THE RESPIRATORY SYSTEM Chapter 21 MICROBIAL DISEASES OF THE DIGESTIVE SYSTEM Chapter 22 MICROBIAL DISEASES OF THE BLOOD AND VISCERA Chapter 24 FOOD AND INDUSTRIALMICROBIOLOGY Development of Microbiology. Characteristics of Microorganisms. Chemical Principles. Organic Compounds of Microorganisms. Size Relationships. Microscopy. Prokaryotes. Eukaryotes. Cell Duplication and Population Growth. Quantifying Microorganisms. Environmental Growth Conditions. Laboratory Cultivation Methods. Enzymes. Energy and ATP. Glycolysis and Fermentation. The Krebs Cycle. Electron Transport and Chemiosmosis. Other Aspects of Catabolism. Photosynthesis. Structure and Physiology of DNA. Protein Synthesis. Regulation of Gene Expression. Mutations. Recombination. Genetic Engineering. Physical Agents. Chemical Agents. Antibiotics. Characteristics of Protozoa. Physiology and Reproduction of Protozoa. Classification of Protozoa. Characteristics of Unicellular Algae. Classification of Unicellular Algae. Viral Structure. Viral Replication. Viral Pathology. The Normal Flora. Pathogenicity. Types of Diseases. Phagocytosis. Types of Immunity. The Immune System. AntibodyMediated Immunity. Cell- Mediated Immunity Serological Tests. Immune Disorders. 1

12 24 36 49 62

80 94 106 120 155 162 176 187 201

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

Bacterial Diseases. Rickettsial Diseases. Viral Diseases. Other Diseases. 269

Microorganisms and Foods. Food Contamination and Preservation. Laboratory Testing. Microorganisms and Industry. Chapter 25 ENVIRONMENTAL Microbial Ecology. Biogeochemical Cycles. Wastewater Microbiology. MICROBIOLOGY

295
308

Sherris Medical Microbiology


Part I The Bacterial Cell Part II The Biology of Virus Part III Host Parasite Interactions Part IV Spread Control Of Infections
CHAPTER CHAPTER CHAPTER CHAPTER CHAPTER CHAPTER CHAPTER CHAPTER CHAPTER CHAPTER CHAPTER CHAPTER CHAPTER CHAPTER CHAPTER CHAPTER CHAPTER CHAPTER 2: Bacterial Structures 3: Bacterial Processes 4: Bacterial Genetics 5: Viral Structure 6: Viral Multiplication 7: Viral Genetics 8: Immune Response to Infection 9: Normal Microbial Flora 10: Host-Parasite Relationships 11: Sterilization and Disinfection 12: Epidemiology of Infectious Diseases 13: Antibacterial and Antiviral Agents 14: Antimicrobial Resistance 15: Principles of Laboratory Diagnosis of Infectious Diseases 16: Staphylococci 17: Streptococci and Enterococci 18: Corynebacteria, Listeria, and Bacillus 19: Clostridium, Peptostreptococcus, Bacteroides, and Other Anaerobes CHAPTER 20: Neisseria CHAPTER 21: Enterobacteriaceae CHAPTER 22:Vibrio, Campylobacter, and Helicobacter 259 CHAPTER 23: Pseudomonas and Other Opportunistic Gram-negative Bacilli CHAPTER 24: Haemophilus and Bordetella CHAPTER 25: Mycoplasma and Ureaplasma CHAPTER 26: Legionella CHAPTER 27: Spirochetes CHAPTER 28: Mycobacteria CHAPTER 29: Actinomyces and Nocardia CHAPTER 30: Chlamydia CHAPTER 31: Rickettsia, Coxiella, Ehrlichia, and Bartonella CHAPTER 32: Plague and Other Bacterial Zoonotic Diseases CHAPTER 33: Influenza, Respiratory Syncytial Virus, Adenovirus, and Other Respiratory Viruses CHAPTER 34: Mumps Virus,Measles, Rubella, and Other Childhood Exanthems CHAPTER 35: Poxviruses CHAPTER 36: Enteroviruses 493 CHAPTER 37: Hepatitis Viruses CHAPTER 38: Herpesviruses CHAPTER 39: Viruses of Diarrhea CHAPTER 40: Arthropod-Borne and Other Zoonotic Viruses CHAPTER 41: Rabies CHAPTER 42: Retroviruses,Human Immunodeficiency Virus, and Acquired Immunodeficiency Syndrome CHAPTER 43: Papovaviruses CHAPTER 44: Persistent Viral Infections of the Central Nervous System CHAPTER 45: Characteristics of Fungi CHAPTER 46: Pathogenesis, Immunity, and Chemotherapy of Fungal Infections CHAPTER 47: Dermatophytes, Sporothrix, and Other Superficial and Subcutaneous Fungi CHAPTER 48: Candida, Aspergillus, and Other Opportunistic Fungi CHAPTER 49: Cryptococcus, Histoplasma, Coccidioides, and Other Systemic Fungal Pathogens CHAPTER 50: Pneumocystis carinii

Part V Pathogenic Bacteria

Part VI Pathogenic Virus

Part VII Pathogenic Fungi

Part VIII Parasites

Part IX Local and Systemic Infections

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

Text Book of Microbiology, 2010


INTRODUCTION HISTORY OF MICROBIOLOGY
Major Fields of Pure Sciences; Major Fields of Applied Microbiology. Discovery Era-Antony Van Leeuvenhoek; Transition Period-F. Redi, Needham, Spallanzani; Historical development in the field of Microbiology; Golden Age of Microbiology-Louis Pasteur, Tyndall, L.J. Lister, Robert Koch, Hesse, Jenner, Metchnikoff, Roux, Paul Ehrlich, Domagk, Flemming; Era of Molecular Biology - Beadle & Tatum, Delbruck & Luria; Nobel Laureates in Microbiology. Origin of Universe-Nebular Hypothesis; Planetesimal Hypothesis; Tidal Hypothesis; Recent Hypothesis; The Primitive Atmosphere of Earth; Chemical Origin of Life (Chemogeny); Biological Evolution of Biogeny; Cognogeny. Hierarchial Arrangement in Taxonomy; Whittaker Five Kingdom Concept; Major Differential Features among Bacteria, Archaea and Eukarya; Modern Trends in Classification; Characters used for the Classification of Bacteria; Genome Comparison; RNA Finger Printing and Sequencing; DNA Sequencing; Microbial Phylogeny; Molecular Chronometers; Phylogenetic Trees; Taxonomic Criteria used for Classification & Indentification of Bacteria. Organization of Bergey's Manual; Classification of Prokaryotes General Character; Plant Like Characteristic in Bacteria; Structure of Bacterial Cell-Shapes of Bacteria, Ultrastructure, Flagella, Pili, Capsule, Cell Wall-Gram +ve and Gram -ve bacteria; Cytoplasmic Membrane; Ribosomes; Chromatophores, Cytoplasmic Inclusions, Gas Vacuoles, Nuclear Material, Plasmid; Nutrition in Bacteria-Photosynthetic, Chemosynthetic, Heterotrophic Bacteria; Reproduction in BacteriaVegetative (Binary fission, Budding, Cyst, Gonidia); Asexual (Conidia, Oidiospores, Sporangiospores, Motile spores, Endospores); Genetic Recombination (Transformation, Conjugation, Transduction); Gram Staining, Pathogenic Bacteria. History, General Characters of Viruses, Difference of Virus from Bacteria and Mycoplasma, Nature of Viruses; Viroids; Virusoides; Prions; Size & Structure of Viruses; Chemical Composition; Viral Genome; Classification of Virus - LHT System, Gasjens & King Classification, Baltimore Scheme of Classification; Replication of Viruses - Lytic Cycle, Lysogenic Cycle; Interferon. DNA Bacterial Viruses (Phage M13; Bacterial Virus T4; Temperate Bacteriophages; A. Phage, Virus T7, MU Virus). Morphology, Satellite Virus & RNA; Virus Infection-Symptoms (External & Internal); Classification & Nomenclature; Physiology & Cytology of Plants Infected with Viruses; Change in Low Molecular Weight Metabolites; Viral Diseases of Tomato (Leaf Curl of Tomato, Mosaic of Tomato); Rice Tungro Viruses; Sugarcane Mosaic; Algal Viruses - The Cyanophage - Properties, Life Cycle; Other Algal Viruses; Fungal Viruses-The Mycophages-Characteristics, Examples of Mycophages; Taxonomic Position of Mycophages; Tobacco Mosaic Virus; Cauliflower Mosaic Virus; Potato Virus; Transmission of Plant Viruses. Replication of Animal Viruses (DNA Viruses, RNA Viruses); Classification of Animal Viruses; Classification of Human Viruses; Picomaviridae, Enteroviruses; Polioviruses; Coxsackieviruses, Echoviruses; Enteroviruses; Rhinoviruses; Rhabdoviruses; Rotaviruses; AIDS HIV Viruses; Poxviridae; Herpesvirus; Herpes Simplex Virus; Vericella-Zoster Virus; EpsteinBarr Virus; Cytomegalovirus; Adenovirus; Polymavirus; Hepatitis Viruses (Hepatitis A, B, C, D, E, G).

EVOLUTION OF MICROORGANISM CLASSIFICATION OF MICROORGANISM

NOMENCLATURE AND BERGEY'S MANUAL BACTERIA

VIRUS

BACTERIAL VIRUSES PLANT VIRUSES

THE ANIMAL VIRUSES

ARCHAEA MYCOPLASMA PHYTOPLASMA GENERAL ACCOUNT OF CYANOBACTERIA

GRAM -ve BACTERIA

GRAM +ve BACTERIA

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

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