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 APPLIED MICROBIOLOGY: AGRO/FOOD

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 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

APPLIED MICROBIOLOGY: INDUSTRIAL

ARCHAEA BACTERIA

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

CELL STRUCTURE CHEMICAL COMPOSITION

ENVIRONMENTAL MICROBIOLOGY AND ECOLOGY

EVOLUTION AND SYSTEMATICS FUNGI GENETICS, GENOMICS

Adhesion- Microbial, Aeromicrobiology/Air Quality, Algal Blooms Bacteriophage Ecology, Biofilms-Microbial, Deep Sub-Surface Deep-Sea Hydrothermal Vents, Ecology-Microbial Extremophiles : Acidic Environments, Hot Environments, Cold Environments, Dry Environments (including Cryptoendoliths) Food Webs-Microbial, Freshwater Habitats, Heavy Metals Cycle (Arsenic, Mercury, Selenium, others), Heavy Metals, Bacterial Resistance, HighPressure Habitats, Low-Nutrient Environments, Marine Habitats, MatsMicrobial, Methanotrophy/methane oxidation, Nitrogen Cycle,Phosphorus Cycle, Rhizosphere, Sediment Habitats, including Watery, Sulfur Cycle 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-NonHost Innate or Inducible, Plant Pathogens and Disease: GeneralIntroduction, 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, BacteriocinsBiology- Ecology-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

1106-31 1146-68 1184-95 1211-59 1243 1278-09 1324-32 1344-82 1397-26 1439-65 1474-94 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

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

PHYSIOLOGY

Glycogen Biosynthesis, Glyoxylate Cycle, Growth Kinetics- Bacterial Heme Biosynthesis, Iron Metabolism, Lipid Biosynthesis, Magnetotaxis Metabolism-Central (Intermediary), Methanogenesis, Methylation and other Modifications of Nucleic Acids and Proteins, Nucleotide Metabolism Nutrition- Microbial, Photosynthesis: Microbial, Posttranscriptional Regulation, Quorum-Sensing in Bacteria, Regulation of CarbonAssimilation 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

PROTISTS

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 PUBLIC ISSUES 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 PredictionTECHNIQUES Microbial, 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, PhylogeneticMethods, 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 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 Fungal Infection Diagnosis and Management 3rd 2003 The nature of fungi, Classification and nomenclature of fungi and fungal 1 Introduction 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, 2 Laboratory diagnosis Eye, Blood, Cerebrospinal fluid, Urine, Other fluids, Pus, Bone marrow, of fungal Tissue, Specimens for serological tests, Specimens for antifungal drug infection, 14 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

2734-53 2766-01 2816-41 2863-08 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 1

14

3 Antifungal drugs

4 Dermatophytosis

3.1 Introduction, 29 3.2 Amphotericin 29 3.3 Other polyene compounds for topical administration, 40 3.3.1 Natamycin, 40 3.3.2 Nystatin, 41 3.4 Fluconazole, 41 3.5 Itraconazole, 46 3.6 Ketoconazole, 51 3.7 Voriconazole, 54 3.8 Other imidazole compounds for topical administration, 59 3.8.1 Bifonazole, 59 3.8.2 Butoconazole, 59 3.8.3 Clotrimazole, 59 3.8.4 Econazole nitrate, 60 3.8.5 Fenticonazole nitrate, 60 3.8.6 Isoconazole nitrate, 60 3.8.7 Miconazole nitrate, 60 3.8.8 Oxiconazole, 60 3.8.9 Sulconazole nitrate, 61 3.8.10 Terconazole, 61 3.8.11 Tioconazole, 61 3.9 Terbinafine, 61 4.1 Introduction, 80 4.2 The causal organisms and their habitat, 80 4.3 Laboratory diagnosis of dermatophytosis, 82 4.4 Tinea capitis, 83 4.5 Tinea corporis, 90 4.6 Tinea cruris, 93

5 Supelficial candidosis

6 Other cutaneous fungal infections

7 Mould infections of nails

3.10 Other allylamine compounds for topical administration, 64 3.10.1 Naftifine, 64 3.11 Caspofungin, 64 3.12 Flucytosine, 66 13.13 Griseofulvin, 70 3.14 Other miscellaneous compounds for topical administration, 72 3.14.1 Amorolfine hydrochloride 3.14.2 Butenafine hydrochloride 3.14.3 Ciclopirox, 72 3.14.4 Haloprogin, 73 3.14.5 Tolnaftate, 73 3.15 Empirical treatment of suspected fungal infection in the neutropenic patient, 73 3.16 Prophylactic treatment for prevention of fungal infection, 74 3.17 Laboratory monitoring, 76 3.17.1 Antifungal drug susceptibility testing, 76 3.17.2 Monitoring of blood concentrations of antifungal drugs 4.7 Tinea pedis, 95 4.8 Tinea manuum, 99 4.9 Tinea unguium, 102 =(Definition, Geographical distribution, Epidemiology, Clinical manifestations, Differential diagnosis, Essential investigations and their interpretation, Management, 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 and their interpretation, Management: Oropharyngeal, Vaginal, Penile, Cutaneous,Cundidu nail infection, Chronic mucocutaneous, Prevention 6.1 Pityriasis versicolor, 129 6.3 Piedra, 134 6.2 Other Mulusseziu infections, 6.4 White piedra, 134 133 6.6.4 Epidemiology, 138 CONTENTS /xi 6.6.5 Clinical manifestations, 138 6.2.1 Mulusseziu folliculitis, 133 6.7 Scytultdtum infection, 139 6.2.2 Seborrhoeic dermatitis, 133 6.8 Alternariu infection, 140 7.1 Definition, 142 7.6 Differential diagnosis, 143 7.2 Geographical distribution, 142 7.7 Essential investigations and 7.3 The causal organisms and their their interpretation, 143 habitat, 142 7.8 Management, 144 7.4 Epidemiology, 142 7.9 Prevention, 145 7.5 Clinical manifestations, 143

29-77

80-107

109-126

129-140

142-145

8 Keratomycosis

9 Otomycosis

10 Aspergillosis

11 lnvasive candidosis

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 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

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 10.6.2 Culture, 170 10.6.3 Skin tests, 171 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 strategies, 182

147-150

153-155

156-182

185-207 11.7 Essential investigations and 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

12 Cryptococcosis

13 Mucormycosis

14 Blastomycosis

15 Coccidioidomycosis

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, 230 Epidemiology, 231 Clinical manifestations, 232 13.5.1 Rhinocerebral mucormycosis, 232 13.5.2 Pulmonary mucormycosis, 13.5.3 Gastrointestinal mucormycosis, 234 13.5.4 Cutaneous mucormycosis, 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

Osteomyelitis and arthritis, 207 Peritonitis, 208 Endocarditis and vascular infection, 209 Meningitis, 210 Endophthalmitis, 210 Oesophagitis, 210 11.9 Prevention, 21 1

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 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

215-228

230-238

241-248 14.6 Differential diagnosis, 245 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

17 Paracoccidioidomycosis

18 Chromoblastomycosis

19 Entomophthoramycosis

20 Lobomycosis

21 Mycetoma

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 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

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 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 interpretation, 290 18.7.1 Microscopy, 290 18.7.2 Culture, 291 18.7.3 Serological tests, 291 Management, 291 281-286

288-291

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 20.6 Differential diagnosis, 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, 305 298-299

300-305

22 Rhinosporidiosis

23 Sporotrichosis

24 Hyalohyphomycosis

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

22.6 Differential diagnosis, 309 22.7 Essential investigations and their interpretation, 310 22.8 Management, 310 Essential investigations and their interpretation, 315 23.7.1 Microscopy, 315 23.7.2 Culture, 315 23.7.3 Serological tests, 316 Management, 3 16 Prevention, 317

308-310

311-317

25 Penici//ium marneffei infection

26 Phaeohyphomycosis

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, 328 330-334 25.1 Definition, 330 interpretation, 332 25.2 Geographical distribution, 330 25.7.1 Microscopy, 332 25.3 The causal organism and its 25.7.2 Culture, 332 habitat, 330 25.7.3 Serological tests, 333 25.4 Epidemiology, 330 25.8 Management, 333 25.5 Clinical manifestations, 331 25.9 Prevention, 334 25.6 Differential diagnosis, 332 25.7 Essential investigations and their 336-344 Definition, 336 Essential investigations and their Geographical distribution, 336 interpretation, 342 The causal organisms and their 26.7.1 Microscopy, 342 habitat, 336 26.7.2 Culture, 342 Epidemiology, 337 26.7.3 Serological tests, 342 Clinical manifestations, 339 Management, 342 26.5.1 Subcutaneous 26.8.1 Subcutaneous phaeohyphomycosis, 339 phaeohyphomycosis, 342 26.5.2 Sinusitis, 339 26.8.2 Sinusitis, 343 26.5.3 Cerebral 26.8.3 Cerebral phaeohyphomycosis, 340 phaeohyphomycosis, 343 26.5.4 Other forms of 26.8.4 Disseminated phaeohyphomycosis, 341 phaeohyphomycosis, 344 Differential diagnosis, 341

27 Other invasive yeast infections

Part 1: Infection, Pathogens and Antimicrobial Agents Part 2: Systematic Infectious Diseases

346-349 27.1 Introduction, 346 27.3.1 Geographical distribution, 27.2 Systemic Malassezta infection, 27.3.2 The causal organisms and 27.2.1 Geographical distribution, their habitat, 349 27.2.2 The causal organisms and 27.3.3 Epidemiology, 350 their habitat, 346 27.3.4 Clinical manifestations, 350 27.2.3 Epidemiology, 347 27.3.5 Essential investigations and 27.2.4 Clinical manifestations, 347 their interpretation, 351 27.2.5 Essential investigations and 27.3.6 Management, 352 their interpretation, 348 27.4 Other yeast infections, 352 27.2.6 Management, 349 27.3 Trichosporonosis, 349 Handbook of Microbiological Media, 4th ed. 2010 Infection; Microbiology and Management, 3rd ed. 2006 1-53 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 83-302

Part 3: Genital, Sexually Transmitted and Birth-Related Infections 18 Tuberculosis and Other Mycobacterial Diseases, 363 Part 4: Disorders 19 Bacteraemia and Sepsis, 389 Affecting More Than 20 Pyrexia of Unknown Origin, 406 One System

313-344

361-517

21 Post-infectious Disorders, 418 22 Infections in Immunocompromised Patients, 431 Part 5: Special Hosts, 23 Hospital Infections, 443 Environments and the 24 Travel-associated and Exotic Diseases, 460 Community 25 Control of Infection in the Community, 502 26 Emerging and Re-emerging Infections, 517 Kim - Bacterial Physiology and Metabolism (Cambridge, 2008)

429-517

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

1-7

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

7-30 2.3.3.2 Outer membrane 13 2.3.3.3 Cell wall and periplasm 17 2.3.4 Cytoplasmic membrane 21 2.3.4.1 Properties and functions 21 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

3 Membrane transport nutrient uptake and protein excretion

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

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

3.8.1.2 Twin-arginine translocation 35-51 (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 47 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 three steps 60-78 4.1.1 Phosphofructokinase (PFK): 4.3.2 Additional functions of the key enzyme of the EMP HMP pathway 70 pathway 61 4.3.2.1 Utilization of pentoses 71 4.1.2 ATP synthesis and production 4.3.2.2 Oxidative HMP cycle 71 of 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 some 4.1.4 Regulation of the EMP Gram-negative bacteria 72 pathway 66 4.4.2 Key enzymes of the ED 72 4.1.4.1 Regulation of 4.4.3 Modified ED pathways 72 phosphofructokinase 66 4.4.3.1 Extracellular oxidation of 4.1.4.2 Regulation of pyruvate glucose by Gram-negative kinase 67 bacteria 72 4.1.4.3 Global regulation 67 4.4.3.2 Modified ED pathways in 4.2 Glucose-6-phosphate synthesis: archaea 74 gluconeogenesis 67 4.5 Phosphoketolase pathways 74 4.2.1 PEP synthesis 67 4.5.1 Glucose fermentation by 4.2.2 Fructose diphosphatase 68 Leuconostoc mesenteroides 75 4.2.3 Gluconeogenesis in archaea 4.5.2 Bifidum pathway 77 4.2.4 Regulation ofgluconeogenesis 4.6 Use of radiorespirometry to 4.3 Hexose monophosphate (HMP) determine glycolytic pathways 78 pathway 69 5.1 Oxidative decarboxylation of 5.7.2 Acidophilicity and alkalophilicity pyruvate 8 5.7.3 Proton motive force in acidophiles 5.2 Tricarboxylic acid (TCA) cycle 86 5.7.4 Proton motive force and sodium 5.2.1 Citrate synthesis and the TCA cyl motive force in alkalophiles 104 5.2.2 Regulation of the TCA cycle 88 5.8 Electron transport (oxidative) 5.3 Replenishment of TCA cycle phosphorylation 105 intermediates 88 5.8.1 Chemiosmotic theory 105 5.3.1 Anaplerotic sequence 88 5.8.2 Electron carriers and the electron 5.3.2 Glyoxylate cycle 89 transport chain 105 5.3.2.1 Regulation of the glyoxylate cy 5.8.2.1 Mitochondrial electron transport 5.4 Incomplete TCA fork and reductive chain 105 TCA cycle 91 5.8.2.2 Electron carriers 107

6 Biosynthesis and microbial growth 126

5.4.1 Incomplete TCA fork 91 5.8.2.3 Diversity of electron transport 5.4.2 Reductive TCA cycle 92 chains in prokaryotes 108 5.5 Energy transduction in prokaryotes 5.8.2.4 Inhibitors of electron transport 5.5.1 Free energy 93 phosphorylation (ETP) 110 5.5.1.1 _G00 from the free energy of 5.8.2.5 Transhydrogenase 110 formation 94 5.8.3 Arrangement of electron carriers 5.5.1.2 _G00 from the equilibrium con in the H-translocating membrane 111 5.5.1.3 _G from _G00 95 5.8.3.1 Q-cycle and Q-loop 111 5.5.1.4 _G00 from _G0 95 5.8.3.2 Proton pump 112 5.5.2 Free energy of an 5.8.4 ATP synthesis 112 oxidation/reduction reaction 95 5.8.4.1 ATP synthase 112 5.5.2.1 Oxidation/reduction potential 95 5.8.4.2 H/O ratio 113 5.5.2.2 Free energy from _E00 96 5.8.4.3 H/ATP stoichiometry 114 5.5.3 Free energy of osmotic pressure 5.8.5 Uncouplers 114 5.5.4 Sum of free energy change in a 5.8.6 Primary H (Na) pumps in series of reactions 97 fermentative metabolism 115 5.6 Role of ATP in the biological energy 5.8.6.1 Fumarate reductase 115 transduction process 98 5.8.6.2 Na-dependent decarboxylase 5.6.1 High energy phosphate bonds 99 5.8.6.3 _p formation through 5.6.2 Adenylate energy charge 100 fermentation product/H 5.6.3 Phosphorylation potential (_Gp) symport 116 5.6.4 Interconversion of ATP and proton 5.9 Other biological energy transduction motive force (_p) 101 processes 116 5.6.5 Substrate-level phosphorylation 5.9.1 Bacterial bioluminescence 116 5.7 Proton motive force (_p) 102 5.9.2 Electricity as an energy source in 5.7.1 Proton gradient and membrane microbes 117 potential 102 6.1 Molecular composition of bacterial cells 126 6.2 Assimilation of inorganic nitrogen 127 6.2.1 Nitrogen fixation 128 6.2.1.1 N2-fixing organisms 128 6.2.1.2 Biochemistry of N2 fixation 129 6.2.1.3 Bioenergetics of N2 fixation 132 6.2.1.4 Molecular oxygen and N2 fixation 132 6.2.1.5 Regulation of N2 fixation 134 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 141 6.4.3 The 2-ketoglutarate family 141 6.4.4 Aromatic amino acids 141 6.4.5 Histidine biosynthesis 145 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 pathway 148 6.5.3 De novo synthesis of purine nucleotides 149 6.5.4 Synthesis of deoxynucleotides 149 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 156 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 161 6.8.2 Monomers of murein 163 6.8.3 Monomers of teichoic acid 164 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 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 bacteria 169 6.9.3 Outer membrane assembly 169 6.9.3.1 Protein translocation 169 6.9.3.2 Lipopolysaccharide (LPS) translocation 169 6.9.3.3 Phospholipid translocation 170 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 6.10.3 Post-replicational modification 173 6.10.4 Chromosome segregation 173 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 177 6.12.2.3 Termination 178 6.12.3 Post-translational modification and protein folding 178 6.13 Assembly of cellular structure 181 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

7 Heterotrophic metabolism on substrates other than glucose 202

8 Anaerobic fermentation 252

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 189 6.14.4 Growth yield using different electron acceptors and maintenance energy 189 6.14.5 Maintenance energy 192 7.1 Hydrolysis of polymers 202 7.1.1 Starch hydrolysis 202 7.1.2 Cellulose hydrolysis 203 7.1.3 Other polysaccharide hydrolases 204 7.1.4 Disaccharide phosphorylases 205 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 213 7.5 Amino acid utilization 214 7.5.1 Oxidative deamination 215 7.5.2 Transamination 215 7.5.3 Amino acid dehydratase 215 7.5.4 Deamination of cysteine and methionine 216 7.5.5 Deamination products of amino acids 217 7.5.6 Other amino acids 220 7.6 Degradation of nucleic acid bases 220 7.7 Oxidation of aliphatic hydrocarbons 223 7.8 Oxidation of aromatic compounds 225 7.8.1 Oxidation of aromatic amino acids 225 7.8.2 Ortho and meta cleavage, and the gentisate pathway 227 7.8.3 Oxygenase and aromatic compound oxidation 229 7.9 Utilization of methane and methanol 229 7.9.1 Methanotrophy and methylotrophy 229 7.9.2 Methanotrophy 230 7.9.2.1 Characteristics of methanotrophs 230 7.9.2.2 Dissimilation of methane by methanotrophs 233 7.9.3 Carbon assimilation by methylotrophs 235 7.9.3.1 Ribulose monophosphate (RMP) pathway 235 7.9.3.2 Serineisocitrate lyase (SIL) pathway 236 7.9.3.3 Xylulose monophosphate (XMP) pathway 240 7.9.4 Energy efficiency in C1 metabolism 241 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 8.1 Electron acceptors used in anaerobic metabolism 252 8.1.1 Fermentation and anaerobic respiration 252 8.1.2 Hydrogen in fermentation 252 8.2 Molecular oxygen and anaerobes 253 8.3 Ethanol fermentation 255 8.4 Lactate fermentation 257 8.4.1 Homolactate fermentation 257

9 Anaerobic respiration 298

8.4.2 Heterolactate fermentation 257 8.4.3 Biosynthesis in lactic acid bacteria (LAB) 259 8.4.4 Oxygen metabolism in LAB 260 8.4.5 Lactate/H symport 260 8.4.6 LAB in fermented food 260 8.5 Butyrate and acetonebutanolethanol fermentations 263 8.5.1 Butyrate fermentation 263 8.5.1.1 Phosphoroclastic reaction 263 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 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 272 8.6.2 Butanediol fermentation 273 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 8.8.1 Fermentation of individual amino acids 281 8.8.2 Stickland reaction 286 8.8.3 Fermentation of purine and pyrimidine bases 287 8.9 Fermentation of dicarboxylic acids 287 8.10 Hyperthermophilic archaeal fermentation 287 8.11 Degradation of xenobiotics under fermentative conditions 289 9.1 Denitrification 299 9.1.1 Biochemistry of denitrification 299 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 302 9.1.3 Regulation of denitrification 303 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 306 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 and sulfur 312 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

10 Chemolithotrophy 354

9.4.1.1 Hydrogenotrophic methanogens 320 9.4.1.2 Methylotrophic methanogens 322 9.4.1.3 Aceticlastic methanogens 322 9.4.2 Coenzymes in methanogens 322 9.4.3 Methanogenic pathways 324 9.4.3.1 Hydrogenotrophic methanogenesis 324 9.4.3.2 Methylotrophic methanogenesis 325 9.4.3.3 Aceticlastic methanogenesis 326 9.4.4 Energy conservation in methanogenesis 327 9.4.5 Biosynthesis in methanogens 328 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 335 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 340 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 10.1 Reverse electron transport 354 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 iron oxidation 362 10.5 Hydrogen oxidation 364 10.5.1 Hydrogen-oxidizing bacteria 364 10.5.2 Hydrogenase 364 10.5.3 Anaerobic H2-oxidizers 365 10.5.4 CO2 fixation in H2-oxidizers 366 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 370 10.8.1.2 Photorespiration 372 10.8.2 Reductive TCA cycle 373 10.8.3 Anaerobic CO2 fixation through the acetyl-CoA pathway 374 10.8.4 CO2 fixation through the 3-hydroxypropionate cycle 375 10.8.5 Energy expenditure in CO2 fixation 377

11 Photosynthesis 386

12 Metabolic regulation 408

10.9 Chemolithotrophs: what makes them unable to use organics? 377 11.1 Photosynthetic microorganisms 386 11.1.1 Cyanobacteria 387 11.1.2 Anaerobic photosynthetic bacteria 387 11.1.3 Aerobic anoxygenic phototrophic bacteria 388 11.2 Photosynthetic pigments 389 11.2.1 Chlorophylls 390 11.2.2 Carotenoids 390 11.2.3 Phycobiliproteins 392 11.2.4 Pheophytin 392 11.2.5 Absorption spectra of photosynthetic cells 393 11.3 Photosynthetic apparatus 394 11.3.1 Thylakoids of cyanobacteria 394 11.3.2 Green bacteria 395 11.3.3 Purple bacteria 395 11.3.4 Heliobacteria and aerobic anoxygenic phototrophic bacteria 395 11.4 Light reactions 396 11.4.1 Properties of light 397 11.4.2 Excitation of antenna molecules and resonance transfer 397 11.4.3 Electron transport 398 11.4.3.1 Photosystem I and II in cyanobacteria 398 11.4.3.2 Green sulfur bacteria 398 11.4.3.3 Purple bacteria 400 11.4.3.4 Aerobic anoxygenic photosynthetic bacteria 401 11.5 Carbon metabolism in phototrophs 401 11.5.1 CO2 fixation 401 11.5.2 Carbon metabolism in photoorganotrophs 402 11.5.2.1 Purple bacteria, heliobacteria and aerobic anoxygenic photosynthetic bacteria 402 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 synthesis 408 12.1.1 Regulation of transcription by promoter structure and sigma (_) factor activity 409 12.1.2 Induction of enzymes 411 12.1.2.1 Inducible and constitutive enzymes 411 12.1.2.2 Enzyme induction 412 12.1.2.3 Positive and negative control 413 12.1.3 Catabolite repression 413 12.1.3.1 Carbon catabolite repression by the cAMPCRP complex 414 12.1.3.2 Catabolite repressor/activator 415 12.1.3.3 Carbon catabolite repression in Gram-positive 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 424 12.1.6.1 Termination and antitermination aided by protein 424 12.1.6.2 Termination and antitermination aided by tRNA 426

13 Energy, environment and microbial survival 482

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 12.2 Global regulation: responses to environmental stress 435 12.2.1 Stringent response 437 12.2.2 Response to ammonia limitation 439 12.2.3 Response to phosphate limitation: the pho system 441 12.2.4 Regulation by molecular oxygen in facultative anaerobes 442 12.2.4.1 arc system 443 12.2.4.2 fnr system 444 12.2.4.3 RegB/RegA system in purple non-sulfur photosynthetic bacteria 445 12.2.5 Oxidative stress 445 12.2.6 Heat shock response 446 12.2.7 Cold shock response 448 12.2.8 Quorum sensing 452 12.2.9 Response to changes in osmotic pressure 453 12.2.10 Other two-component systems 454 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 463 12.3.2.5 Regulation through physical modification and dissociation/association 463 12.4 Metabolic regulation and growth 464 12.4.1 Regulation in central metabolism 464 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 13.1 Survival and energy 482 13.2 Reserve materials in bacteria 483 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

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

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) 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

The Viruses

PA RT VII The Diversity of the Microbial World

PA RT VIII Ecology and Symbiosis

PA RT IX Nonspecific Resistance and the Immune Response PA RT X Microbial Diseases and Their Control

The Viruses: Introduction and General Characteristics Chapter 17 The Viruses: Bacteriophages Chapter 18 The Viruses:Viruses of Eucaryotes Chapter 19 Microbial Taxonomy Chapter 20 The Archaea Chapter 21 Bacteria:The Deinococci and Nonproteobacteria Gram Negatives Chapter 22 Bacteria:The Proteobacteria Chapter 23 Bacteria:The Low G _ C Gram Positives Chapter 24 Bacteria:The High G _ C Gram Positives Chapter 25 The Fungi (Eumycota), Slime Molds, and Water Molds Chapter 26 The Algae Chapter 27 The Protozoa Chapter 28 Microorganism Interactions and Microbial Ecology Chapter 29 Microorganisms in Aquatic Environments Chapter 30 Microorganisms in Terrestrial Environments 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 37 The Epidemiology of Infectious Disease

PA RT XI Food and Industrial Microbiology PART ONE Fundamentals of Microbiology

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 PART I LIFE AND DEATH OF

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 Microbiology 10th edition by Tortora 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 Microbiology A Human Perspective 6th 2009 1 Humans and the Microbial World 1 2 The Molecules of Life 18

MICROORGANISMS

PART II THE MICROBIAL WORLD

PART III MICROORGANISMS AND HUMANS

PART IV INFECTIOUS DISEASES

PART V APPLIED MICROBIOLOGY

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 Moat - Microbial Physiology 4e (Wiley, 2002)

CONTENTS PREFACE xix 1 INTRODUCTION TO MICROBIAL PHYSIOLOGY 1 The Escherichia coli Paradigm / 1 Cell Structure / 1 The Cell Surface / 1 Synthesis of DNA, RNA, and Protein / 7 Metabolic and Genetic Regulation / 10 Microbial Genetics / 11 Chemical Synthesis / 12 Chemical Composition / 12 Energy / 13 OxidationReduction Versus Fermentation / 15 Nitrogen Assimilation / 18 Special Topics / 19 Endospores / 19 Growth / 19 Continuous Culture / 22

Factors Affecting Growth / 22 Nutrition / 22 Oxygen / 24 Carbon Dioxide / 24 v vi CONTENTS Extremophiles / 25 Microbial Stress Responses / 26 Summary / 26 2 MACROMOLECULAR SYNTHESIS AND PROCESSING: DNA, RNA, AND PROTEIN SYNTHESIS 27 Structure of DNA / 28 Bacterial Nucleoids / 31 REP Elements / 35 DNA Replication / 36 DNA Replication is Bidirectional and Semiconservative / 36 DNA Polymerase Functions as a Dimer / 36 Model of DNA Replication / 39 Initiation of DNA Replication / 42 Termination of DNA Replication and Chromosome Partitioning / 46 RNA Synthesis: Transcription / 47 RNA Synthesis / 47 RNA Turnover / 53 RNA Processing / 54 Protein Synthesis: Translation / 57 Transfer RNA / 59 Charging of tRNA / 62 Ribosome Structure and Synthesis / 62 Initiation of Polypeptide Synthesis / 68 Elongation / 69 Peptide Bond Formation / 71 Translocation / 71 Termination / 72 Posttranslational Processing / 73 When Nonsense Makes Sense / 74 Coupled Transcription and Translation / 74 Protein Folding and Chaperones / 74 Folding Stages / 75 Protein Folding and Chaperone Mechanisms Outside the Cytoplasm / 76 Quality Control / 77 Protein Trafficking / 77 Insertion of Integral Membrane Proteins and Export of Periplasmic Proteins / 77 Secretion of Proteins Across the Outer Membrane / 81 vii Protein Degradation / 83 Degradation of Abnormal Proteins / 83 Energy-Dependent Proteases / 86 Antibiotics that affect Nucleic Acid and Protein Synthesis / 88 Agents Affecting DNA Metabolism / 88 Agents Affecting Transcription / 91 Agents Affecting Translation / 92

Nucleoids / 98 DNA Replication / 98 Transcription and Translation / 98 Protein Folding, Trafficking, and Degradation / 99 Antibiotics / 100 3 BACTERIAL GENETICS: DNA EXCHANGE, RECOMBINATION, MUTAGENESIS, AND REPAIR 101 Transfer of Genetic Information in Prokaryotes / 101 Plasmids / 102 Partitioning / 102 Incompatibility / 103 Nonconjugative, Mobilizable Plasmids / 103 Resistance Plasmids / 104 Plasmids in Other Bacterial Genera / 104 Plasmid Replication / 104 Addiction Modules: Plasmid Maintenance by Host Killing: The ccd Genes / 108 Conjugation / 108 F Factor / 108 cis/trans complementation Test / 115 Conjugation and Pheromones in Enterococci / 116 Conjugation, CellCell Signaling, and Bacterial-Induced Tumors / 117 Transformation / 118 Gram-Positive Transformation / 119 Gram-Negative Transformation / 123 Transfection and Forced Competence / 124 Transduction / 124 Recombination / 127 General Recombination / 128 Genetics of Recombination / 131 Restriction and Modification / 133 viii CONTENTS 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 Repair / 160 SOS-Inducible Repair / 162 Replication Restart / 165

Adaptive Mutations / 166 Plasmids / 167 Transformation / 167 Conjugation / 168 Recombination / 168 Restriction Modification / 169 Transposition / 169 Mutagenesis / 169 Repair Mechanisms / 170 4 MICROBIAL PHYSIOLOGY IN THE GENOMIC ERA: A REVOLUTIONARY TALE 171 Genomic and Proteomic Tools / 172 Cloning a Genome / 172 DNA Sequencing / 172 Web Science: Internet Tools for DNA Sequence Analysis / 173 Gene Replacement / 176 Gene Arrays / 177 Proteomics / 177 ix Traditional Tools / 181 Mutant Hunts / 181 Transcriptional and Translational Gene Fusions (Reporter Genes) / 182 Polymerase Chain Reaction / 183 DNA Mobility Shifts (Gel Shifts and Supershifts) / 185 Finding Transcriptional Starts by Primer Extension / 186 Detecting DNA, RNA, Protein, and DNA-Binding Proteins by Southern, Northern, Western, and Southwestern Blots / 187 Two-Hybrid Analysis / 190 Summary / 192 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 Class I and Class II CRP-Dependent Genes / 204 The Catabolite Repressor/Activator Protein Cra / 204 Catabolite Control: The Gram-Positive 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 Gene 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 / 224

Regulation of Nitrogen Assimilation and Nitrogen Fixation: Examples of Integrated Biochemical and Genetic Controls / 227 Phosphate Uptake: Communication Between Transport and Two-Component Regulatory Systems / 232 x CONTENTS Quorum Sensing: How Bacteria Talk to Each Other / 234 Proteolytic Control / 235 Summary / 236 6 BACTERIOPHAGE GENETICS 239 General Characteristics of Bacteriophages / 239 T4 Phage / 245 Structure / 245 General Pattern of T4 Gene Expression / 247 T4 Genome / 250 Phage / 256 The Lysis-Lysogeny Decision / 259 Transcription / 259 Function of Cro Versus CI Repressor and the Structure of OL and OR / 260 Establishment of Repressor Synthesis / 260 Control of Integration and Excision / 262 Negative Retroregulation of int by sib / 263 -Phage Replication / 264 Phage: Transposition as a Lifestyle / 266 _X174 / 271 Summary / 274 General / 274 T4 Bacteriophage / 274 Phage / 275 X174 / 275 Phage / 275 7 CELL STRUCTURE AND FUNCTION 277 The Eukaryotic Nucleus / 277 Bacterial Nucleoids / 279 Nucleosomes / 283 Mitochondria / 287 Microbial Cell Surfaces / 288 Eukaryotic Cell Surfaces / 288 Prokaryotic Cell Surfaces / 289 Surface Layers of Bacteria / 290 Peptidoglycans of Bacterial Cell Walls / 290 Peptidoglycan (Murein) Hydrolases / 295 Peptidoglycan (Murein) Synthesis / 295 Teichoic Acids and Lipoteichoic Acids / 300 Outer Membranes of Gram-Negative Bacteria / 303 xi Lipopolysaccharide Biosynthesis / 308 Enterobacterial Common Antigen / 309 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 / 328 Swarming Motility / 334 Motility in Spirochetes / 337 Gliding Motility / 339 Pili or Fimbriae / 340 Nucleus, Nucleosomes, and Nucleoids / 343 Mitochondria / 344 Eukaryotic Cell Surface / 344 Surface (S) layers / 344 Bacterial Cell Wall Peptidoglycan (Murein) / 345 Teichoic and Lipoteichoic Acids / 346 Outer Membrane / 346 Cytoplasmic Membrane / 346 Periplasm / 346 Capsules / 346 Biofilms / 347 Cilia and Flagella of Eukaryotes / 347 Bacterial Flagella / 347 Chemotaxis / 348 Swarming Motility / 348 Gliding Motility / 348 Motility in Spirochetes / 348 Pili or Fimbriae / 349 8 CENTRAL PATHWAYS OF CARBOHYDRATE METABOLISM 350 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 / 358 xii CONTENTS Gluconeogenesis / 360 Regulation / 360 Glycogen Synthesis / 361 Tricarboxylic Acid Cycle / 361 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 / 379 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 / 389 Iron / 389 Phosphotransferase System / 390 Summary / 392 Energy Production / 392 Metabolite Transport / 392 10 METABOLISM OF SUBSTRATES OTHER THAN GLUCOSE 394 Utilization of Sugars other than Glucose / 394 Lactose / 394 Galactose / 396 Maltose / 396 xiii Mannitol / 396 Fucose and Rhamnose / 397 Mellibiose, Raffinose, Stachyose, and Guar Gum / 399 Pectin and Aldohexuronate Pathways / 400 Cellulose Degradation / 402 Starch, Glycogen, and Related Compounds / 403 Metabolism of Aromatic Compounds / 407 Pectin Utilization / 410 Cellulose Utilization / 410 Utilization of Starch, Glycogen, and Related Compounds / 411 Utilization of Aromatic Hydrocarbons / 411 11 FERMENTATION PATHWAYS 412 Fermentation Balances / 412 Yeast Fermentation / 415 Lactic AcidProducing Fermentations / 417 Butyric Acidand Solvent-Producing Fermentations / 423 Fermentations of the Mixed-Acid Type / 425 Propionic Acid Fermentation / 428 Acetic Acid Fermentation / 430 Fermentation Pathways / 431 Yeast Fermentation / 431 Lactic Acid Fermentation / 432 Butyric Acid and Solvent-Producing Fermentations / 432 Mixed-Acid Fermentations / 433 Propionic Acid Fermentation / 433 Acetic Acid Fermentation / 433 12 PHOTOSYNTHESIS AND INORGANIC METABOLISM 434 Characteristics and Metabolism of Autotrophs / 434 Photosynthetic Bacteria and Cyanobacteria / 434 Autotrophic CO2 Fixation and Mechanisms of Photosynthesis / 437 Hydrogen Bacteria / 440 Nitrifying Bacteria / 442 Sulfur Bacteria / 442 Iron Bacteria / 443

Methylotrophs / 444 Methanogens / 446 xiv CONTENTS 13 LIPIDS AND STEROLS 450 Lipid Composition of Microorganisms / 451 Straight-Chain Fatty Acids / 451 Branched-Chain Fatty Acids / 453 Ring-Containing Fatty Acids / 454 Alk-1-enyl Ethers (Plasmalogens) / 455 Alkyl Ethers / 456 Phospholipids (Phosphoglycerides) / 457 Glycolipids / 458 Biosynthesis of Fatty Acids / 459 Biosynthesis of Phospholipids / 464 Degradation of Fatty Acids / 466 Biosynthesis of Isoprenoids / 468 14 NITROGEN METABOLISM 475 Biological Nitrogen Fixation / 475 The Nitrogen Fixation Process / 479 Components of the Nitrogenase System / 480 Symbiotic Nitrogen Fixation / 483 Inorganic Nitrogen Metabolism / 487 Assimilation of Inorganic Nitrogen / 492 General Reactions of Amino Acids / 494 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 / 499 The Stickland Reaction / 500 Nitrogen Fixation / 501 Inorganic Nitrogen / 502 Urease / 502 Assimilation of Inorganic Nitrogen / 502 15 BIOSYNTHESIS AND METABOLISM OF AMINO ACIDS 503 The Glutamate or -Ketoglutarate Family / 503 Glutamine and Glutathione Synthesis / 503 The Proline Pathway / 504 Aminolevulinate Synthesis / 504 The Arginine Pathway / 504 xv Polyamine Biosynthesis / 509 The -Ketoadipate Pathway to Lysine / 510 The Aspartate and Pyruvate Families / 513 Asparagine Synthesis / 513 The Aspartate Pathway / 514 The Bacterial Pathway to Lysine / 515 Threonine, Isoleucine, and Methionine Formation / 516 Isoleucine, Valine, and Leucine Biosynthesis / 518 Regulation of the Aspartate Family / 518 The Serine-Glycine Family / 520 Aminolevulinate and the Pathway to Tetrapyrroles / 523 The Aromatic Amino Acid Pathway / 523

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 / 534 Biosynthesis of Nicotinamide Adenine Dinucleotide (NAD) / 534 Histidine Biosynthesis / 539 Amino Acids / 541 Glutamate (-Ketoglutarate) Family / 541 Aspartate and Pyruvate Families / 542 Serine-Glycine Family / 543 Aromatic Amino Acid Family / 543 Histidine / 544 16 PURINES AND PYRIMIDINES 545 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 561 Cell Division in Gram-Negative Rods / 561 Cell Division in Gram-Positive Cocci / 570 xvi CONTENTS Cell Division in Gram-Positive Bacilli / 575 General Reviews / 578 Cell Division in Gram-Negative Rods / 579 Cell Division in Gram-Positive Cocci / 580 Cell Division in Gram-Positive Bacilli / 581 18 MICROBIAL STRESS RESPONSES 582 Osmotic Stress and Osmoregulation / 582 High Osmolality / 583 Low Osmolality / 584 Osmotic Control of Gene Expression / 585 Aerobic to Anaerobic Transitions / 587 Formate Nitrate Regulation / 589 Nitrate Response / 589 ArcAB System / 591 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 StarvationStress Response / 601 StarvationStress Response / 601 Stringent Control / 602 Extremophiles / 605 Summary / 608 Osmotic Stress and Osmoregulation / 608 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 612 Bacillus Endospore Formation / 612 Life Cycle of Bacillus / 613 Stages of Sporulation / 614 Physiological and Genetic Aspects of Sporulation / 616 Sporulation Genes / 616 Initiation / 617 xvii Transition from Stage II to Stage III / 619 Forespore Development / 620 Final Stages of Sporulation / 621 Spore Cortex Synthesis / 622 Spore Coat Protein Synthesis / 622 Activation, Germination, and Outgrowth of Bacterial Endospores / 623 Activation / 624 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 / 637 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 / 646 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 / 653 Exotoxins / 658 Quorum Sensing / 664 Paradigms of Bacterial Pathogenesis / 669 Enteropathogenic Escherichia coli / 669 Salmonella Enterica Serovars / 669 Listeria Monocytogenes / 670 Chlamydia spp / 672 Overview / 672 Adherence/Colonization / 672 Virulence Factor Secretion Systems / 673 xviii CONTENTS

Exotoxins / 673 Quorum Sensing / 674 Paradigms of Bacterial Pathogenesis / 675 Molecular Methods for Virus Detection 1995 Contents Contributors xi Preface xv 1. Nucleic Acid Detection Methods Danny L. Wiedbrauk and Ann M. Drevon I. Introduction 1 II. Specimen Processing III. Target Amplification IV. Probe Amplification V. Detection Systems VI. Potential Applications VII. Difficulties and Disadvantages VIII. Conclusions 22 References 22 2 4 8 11 19 2. Quality Assurance in the Molecular Virology Laboratory 25 Danny [. Wiedbrauk and Jay Stoerker I. Introduction 25 II. Specimen Quality 26 III. Facilities and Equipment 27 20 vi Contents 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 X. Conclusions 35 References 35 3. Nucleic Acid Blotting Techniques for Virus Detection Daniel L. Stoler and Nelson I.. Michael I. Introduction 4t) II. Sample Preparation 40 III. Nucleic Acid Quantification 44 IV. Southern Blotting 45 V. Northern Blotting 51 VI. Dot/Slot Blotting DNA and RNA 53 VII. Hybridization Theory 55 VIII. Hybridization Probes 57 IX. Filter Hybridization 62 X. Methods of Detection and Quantification 64 XI. Examples of Blotting Technology 66 XII. Southern Blotting and the Polymerase Chain Reaction

References 71 39 71 4. In Situ Hybridization 75 Jeanne Cart I. Introduction 75 II. General Procedures 76 III. Instrumentation 85 IV. Detection of Human Papillomavirus by in Situ Hybridization 85 V. Selected Studies 94 VI. In Situ Hybridization in Conjunction with Other Techniques 94 Contents vii VII. Vendors 96 VIII. Conclusion 97 References 97' 5. Antiviral Susceptibility Testing Using DNA-DNA Hybridization 103 Richard L. Hodinka 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 References 126 6. Quantification of Viral Nucleic Acids Using Branched DNA Signal Amplification 131 Judith C. Wilbur and Mickey S. Ordea I. Introduction 131 II. Description of the Procedure 132 III. Components of the bDNA Assay 134 IV. Uses of bDNA Assays 140 V. Sample Collection and Stability 142 VI. Conclusion 143 References 143 7. Detection Methods Using Chemiluminescence Irena Bronstein and Corinne E. M. Olesen I. General Introduction 147 II. Chemiluminescence Methods 148 III. Instrumentation for Chemiluminescence Assays IV. Chemiluminescence Assays for Virus Detection V. Chemiluminescence Detection Protocols 159 VI. Conclusion 166 References 167 147 153 154 viii Contents 8. Detection of Viral Pathogens Using PCR Amplification Bruce J. McCreedy 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 References 189 175 9. Quantitation of RNA Targets Using the Polymerase Chain Reaction 193 Francois Ferre, Patrick Pezzoli, Eric Buxton, Chris Duffy, Annie Marchese, and Anne Daigle 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 References 215 10. Multiplex Polymerase Chain Reaction James B. Mahony and Max A. Chernesky I. Introduction 219 II. Methodology 220 III. Developing a Multiplex PCR Assay IV. Quality Assurance 231 References 234 219 224 1 1. PCR in Situ Hybridization Gerard J. Nuovo I. Introduction 237 II. Methods 240 III. Applications 249 References 258 237 Contents i x 12. Nucleic Acid Sequence-Based Amplification 261 Roy Sooknanan, Bob van Gemen, and Lawrence T. Malek I. Background 261 II. Application for the Detection of HIV-1 RNA in Plasma or Serum 271 III. Required Materials and Solutions 278 References 284 13. The Self-Sustained Sequence Replication Reaction and Its Application in Clinical Diagnostics and Molecular Biology 287 Soumitra S. Ghosh, Eoin Fahy, and Thomas R. Gingeras I. Introduction 287 II. Characteristics of the 3SR Reaction 289 III. Hybridization and Detection of 3SR Products IV. Sterilization of 3SR Reactions 297 V. Applications of the 3SR Reaction 298 VI. Experimental Procedures for Detection of HIV-1 VII. Conclusions 311 References 312 295 301 14. Ligase Chain Reaction for the Detection of

Infectious Agents 315 John D. Burczak, Shanfon Ching, Hsiang-Yun Hu, and Helen H. Lee I. Introduction 315 II. Principle of the Ligase Chain Reaction 316 III. Application for Detection of Infectious Agents IV. Methodology 321 V. Conclusions 327 References 327 318 15. A Chemiluminescent DNA Probe Test Based on Strand Displacement Amplification 329 G. T. Walker, C. A. Spargo, C. M. Nycz, J. A. Down, M. S. Dey, A. H. Waiters, D. R. Howard, W. E. Keating, M. C. Little, J. G. Nadeau, S. R. Jurgensen, V. R. Neece, and P. 7wadyk, Jr. I. Introduction 330 X Contents II. Description of Strand-Displacement Amplification III. Detection of SDA Reactions 334 IV. Performance of SDA with Clinical Mycobacterium tuberculosis Specimens 335 V. Processing Clinical Specimens prior to SDA VI. Protocol for Chemiluminescent Detection VII. Conclusion 347 References 348 339 341 330 16. Ligation-Activated Transcription Amplification: Amplification and Detection of Human Papillomaviruses 351 David M. Schuster, Mark S. Beminger, and Ayoub Rashtchian 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 Development of Microbiology. Characteristics of Microorganisms.

TO MICROBIOLOGY 1 Chapter 2 THE CHEMICAL BASIS OF MICROBIOLOGY 12 Chapter 3 MICROBIAL SIZE AND MICROSCOPY 24 Chapter 4 PROKARYOTES AND EUKARYOTES 36 Chapter 5 MICROBIAL GROWTH AND CULTIVATION 49 Chapter 6 METABOLISM OF MICROORGANISMS 62

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.

Chapter 7 DNA AND GENE EXPRESSION 80 Chapter 8 MICROBIAL GENETICS 94 Chapter 9 CONTROL OF MICROORGANISMS 106 Chapter 10 THE MAJOR GROUPS OF BACTERIA 120 Chapter 13 THE UNICELLULAR ALGAE 155 Chapter 14 THE VIRUSES 162 Chapter 15 THE HOSTPARASITE RELATIONSHIP 176 Chapter 16 HOST RESISTANCE AND THE IMMUNE SYSTEM 187 Chapter 17 IMMUNE TESTS AND DISORDERS 201 Chapter 18 MICROBIAL DISEASES OF THE SKIN AND EYES 215 Chapter 19 MICROBIAL DISEASES OF THE NERVOUS SYSTEM 230 Chapter 20 MICROBIAL DISEASES OF THE RESPIRATORY SYSTEM Chapter 21 MICROBIAL DISEASES OF THE DIGESTIVE SYSTEM 255 Chapter 22 MICROBIAL DISEASES OF THE BLOOD AND VISCERA 269 Chapter 24 FOOD AND INDUSTRIAL MICROBIOLOGY 295 Chapter 25 ENVIRONMENTAL MICROBIOLOGY 308 Part I The Bacterial Cell

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. Bacterial Diseases. Viral Diseases. Other Skin Diseases. Eye and Wound Diseases. Bacterial Diseases. Viral Diseases. Fungal and Protozoal Diseases.

Bacterial Diseases. Viral Diseases. Fungal and Protozoal Diseases.

Bacterial Diseases. Viral Diseases. Other Microbial Diseases.

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

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

CHAPTER2 Bacterial Structures CHAPTER3 Bacterial Processes CHAPTER4

Part ii The Biology of Virus

Part iii Host Parasite Interactions

Part IV Spread Control Of Infections

Part V Pathogenic Bacteria

Bacterial Genetics CHAPTER5 Viral Structure CHAPTER6 Viral Multiplication CHAPTER7 Viral Genetics CHAPTER8 Immune Response to Infection CHAPTER9 Normal Microbial Flora CHAPTER10 Host-Parasite Relationships CHAPTER11 Sterilization and Disinfection CHAPTER12 Epidemiology of Infectious Diseases CHAPTER13 Antibacterial and Antiviral Agents CHAPTER14 Antimicrobial Resistance CHAPTER15 Principles of Laboratory Diagnosis of Infectious Diseases CHAPTER16 Staphylococci CHAPTER17 Streptococci and Enterococci CHAPTER18 Corynebacteria, Listeria, and Bacillus CHAPTER19 Clostridium, Peptostreptococcus, Bacteroides, and Other Anaerobes CHAPTER20

Neisseria

CHAPTER21 Enterobacteriaceae CHAPTER22

Vibrio, Campylobacter, and Helicobacter

259 Copyright 2004 by The McGraw-Hill Companies, Inc. Click here for terms of use. CHAPTER23 Pseudomonas and Other Opportunistic Gram-negative Bacilli CHAPTER24 Haemophilus and Bordetella CHAPTER25 Mycoplasma and Ureaplasma CHAPTER26

Legionella

CHAPTER27 Spirochetes CHAPTER28 Mycobacteria CHAPTER29

Actinomyces and Nocardia

CHAPTER30

Chlamydia

CHAPTER31

Rickettsia, Coxiella, Ehrlichia, and Bartonella

Part VI Pathogenic Virus

Part VII Pathogenic Fungi

CHAPTER32 Plague and Other Bacterial Zoonotic Diseases CHAPTER33 Influenza, Respiratory Syncytial Virus, Adenovirus, and Other Respiratory Viruses CHAPTER34 Mumps Virus,Measles, Rubella, and Other Childhood Exanthems CHAPTER35 Poxviruses CHAPTER36 Enteroviruses 493 Copyright 2004 by The McGraw-Hill Companies, Inc. Click here for terms of use. CHAPTER37 Hepatitis Viruses CHAPTER38 Herpesviruses CHAPTER39 Viruses of Diarrhea CHAPTER40 Arthropod-Borne and Other Zoonotic Viruses CHAPTER41 Rabies CHAPTER42 Retroviruses,Human Immunodeficiency Virus, and Acquired Immunodeficiency Syndrome CHAPTER43 Papovaviruses CHAPTER44 Persistent Viral Infections of the Central Nervous System CHAPTER45 Characteristics of Fungi CHAPTER46 Pathogenesis, Immunity, and Chemotherapy of Fungal Infections CHAPTER47 Dermatophytes, Sporothrix, and Other Superficial and Subcutaneous Fungi CHAPTER48 Candida, Aspergillus, and Other Opportunistic Fungi CHAPTER49 Cryptococcus, Histoplasma, Coccidioides, and Other Systemic Fungal Pathogens CHAPTER50

Pneumocystis carinii

Part VIII Parasites

CHAPTER51 Introduction to Pathogenic Parasites: Pathogenesis

Part IX Local and Systemic Infections

INTRODUCfION HISTORY OF MICROBIOLOGY

and Chemotherapy of Parasitic Diseases CHAPTER52 Sporozoa CHAPTER53 Rhizopods CHAPTER54 Flagellates CHAPTER55 Intestinal Nematodes 691 Copyright 2004 by The McGraw-Hill Companies, Inc. Click here for terms of use. CHAPTER56 Tissue Nematodes CHAPTER57 Cestodes CHAPTER58 Trematodes CHAPTER59 Skin and Wound Infections CHAPTER60 Bone and Joint Infections CHAPTER61 Eye, Ear, and Sinus Infections CHAPTER62 Dental and Periodontal Infections CHAPTER63 Upper Respiratory Tract Infections and Stomatitis 815 Copyright 2004 by The McGraw-Hill Companies, Inc. Click here for terms of use. CHAPTER64 Middle and Lower Respiratory Tract Infections CHAPTER65 Enteric Infections and Food Poisoning CHAPTER66 Urinary Tract Infections CHAPTER67 Central Nervous System Infections CHAPTER68 Intravascular Infections, Bacteremia, and Endotoxemia CHAPTER69 Infections of the Fetus and Newborn CHAPTER70 Sexually Transmitted Diseases CHAPTER71 Infections in the Immunocompromised Patient CHAPTER72 Nosocomial Infections and Infection Control Text Book of Microbiology, 2010 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

EVOLUTION OF MICROORGANISM CLASSIFICATION OF MICROORGANISM

NOMENCLATURE AND BERGEY'S MANUAL BACTERIA

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

Viruses

BACTERIAL VIRUSES PLANT VIRUSES

THE ANIMAL VIRUSES

ARCHAEA MYCOPLASMA PHYfOPLASMA

GENERAL ACCOUNT OF CYANOBACTERIA

GRAM -ve BACTERIA

GRAM +ve BACTERIA

EUKARYOTA

Virus; Cytomegalovirus; Adenovirus; Polymavirus; Hepatitis Viruses (Hepatitis A, B, C, D, E, G). 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