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Book Details
Abstract
Medical microbiology concerns the nature, distribution and activities of microbes and their impact on health and wellbeing. In spite of the introduction of many antimicrobial agents and immunisations, we continue to face major challenges in combatting infection, not least the gathering crisis in antimicrobial resistance.
Now in a fully revised and updated 19th edition, Medical Microbiology provides comprehensive coverage of infection from the microbial perspective, combining a clear introduction to key principles with a focus explicitly geared to modern clinical practice. It provides ideal coverage for medical and biomedical students – with ‘Key Points’ boxes throughout to highlight the essentials – and sufficient detail to also inform specialists in training.
Building on the success of previous editions, updates in Medical Microbiology 19e include:
- New and expanded coverage of hot topics and emerging areas important to clinical practice, including:
- Genomics
- The Human Microbiome
- Direct acting antiviral agents for the treatment of HCV infection
- Molecular methods in diagnostic microbiology
- Antibiotic Stewardship
- A new and improved downloadable eBook (from studentconsult) – for anytime access to the complete contents plus BONUS interactive learning materials:
- Clinical cases - to introduce how patients with infections present and help relate key principles to practice
- MCQs for each chapter - to check understanding and aid exam preparation
Table of Contents
| Section Title | Page | Action | Price |
|---|---|---|---|
| Front Cover | cover | ||
| Inside Front Cover | ifc1 | ||
| Medical Microbiology | i | ||
| Copyright Page | iv | ||
| Preface | v | ||
| Acknowledgements | vi | ||
| Contributors | vii | ||
| Table Of Contents | xiii | ||
| 1 Microbial biology | 1 | ||
| 1 Microbiology and medicine | 2 | ||
| Key points | 2 | ||
| An outline history of microbiology and infection | 3 | ||
| Microorganisms and infection | 3 | ||
| Hygiene, treatment and prevention of infection | 5 | ||
| Sources and spread of infection | 6 | ||
| Recommended reading | 7 | ||
| Websites | 7 | ||
| MCQs | 7.e1 | ||
| Microbiology and medicine | 7.e1 | ||
| 2 Morphology and nature of microorganisms | 8 | ||
| Key points | 8 | ||
| Prokaryotic and eukaryotic cells | 9 | ||
| Anatomy of the bacterial cell | 10 | ||
| Bacterial nucleoid | 11 | ||
| Ribosomes | 12 | ||
| Cytoplasmic membrane | 12 | ||
| Cell wall | 12 | ||
| Extracellular polysaccharides: capsules, microcapsules and loose slime | 16 | ||
| S-layers | 16 | ||
| Flagella and motility | 16 | ||
| Fimbriae and pili | 17 | ||
| Importance of microbial surface structures in infection | 18 | ||
| The bacterial ‘life cycle’ | 18 | ||
| Bacterial spores | 18 | ||
| Conidia (exospores) | 19 | ||
| Pleomorphism and involution | 19 | ||
| Spheroplasts, protoplasts and L-forms | 19 | ||
| The nature and composition of viruses | 20 | ||
| Structure | 20 | ||
| Viral nucleic acid | 21 | ||
| Virion enzymes | 21 | ||
| Viral proteins | 21 | ||
| Viroids, defective viruses and prions | 21 | ||
| Recommended reading | 21 | ||
| Websites | 21 | ||
| MCQs | 21.e1 | ||
| 3 Classification, identification, typing and diversity of bacteria | 22 | ||
| Key points | 22 | ||
| Taxonomy | 23 | ||
| Methods of classification | 23 | ||
| Polyphasic approaches | 24 | ||
| DNA composition | 24 | ||
| DNA homology (DNA:DNA hybridisation) | 24 | ||
| Sequencing of genes encoding 16S ribosomal RNA and other housekeeping genes | 25 | ||
| Whole genome sequencing (WGS) | 25 | ||
| Classification in clinical practice | 25 | ||
| Actinobacteria | 26 | ||
| Firmicutes | 27 | ||
| Proteobacteria | 27 | ||
| Bacteroidetes | 27 | ||
| Spirochaetes | 27 | ||
| Chlamydiae | 27 | ||
| Identification of bacteria | 27 | ||
| Microscopy | 28 | ||
| Cultural characteristics | 28 | ||
| Biochemical reactions | 28 | ||
| Matrix-assisted laser desorption ionisation-time of flight mass spectrometry (MALDI-TOF MS) | 28 | ||
| Nucleotide sequence-based identification | 29 | ||
| Antigenic characterisation | 29 | ||
| Typing of bacteria | 29 | ||
| Restriction endonuclease typing | 30 | ||
| Gene probe typing | 31 | ||
| Polymerase chain reaction-based methods | 31 | ||
| Multilocus sequence typing | 31 | ||
| Variable number tandem repeat analysis | 31 | ||
| Whole genome–based typing | 32 | ||
| Recommended reading | 32 | ||
| Websites | 32 | ||
| MCQs | 32.e1 | ||
| 4 Bacterial growth, physiology and death | 33 | ||
| Key points | 33 | ||
| Bacterial growth | 34 | ||
| Types of growth | 34 | ||
| Growth phases in broth culture | 34 | ||
| Media for bacterial growth | 36 | ||
| Media used for isolation and identification of pathogens | 36 | ||
| Selective and indicator media | 36 | ||
| Media for laboratory studies | 36 | ||
| Bacterial physiology | 37 | ||
| Nutritional types | 37 | ||
| Physical conditions required for growth | 37 | ||
| Growth atmosphere | 38 | ||
| Growth temperature | 38 | ||
| Extremophiles | 39 | ||
| Bacterial metabolism | 39 | ||
| Adaptive responses in bacteria | 39 | ||
| Bacterial defence against antibiotics and other noxious chemicals | 41 | ||
| Bacterial viability | 41 | ||
| Bacterial death | 42 | ||
| Sterilisation and disinfection | 42 | ||
| Key definitions | 42 | ||
| Sterilisation | 42 | ||
| Disinfection | 42 | ||
| Antisepsis | 43 | ||
| Methods used in sterilisation and disinfection | 43 | ||
| Heat | 43 | ||
| Ionising radiation | 43 | ||
| Filtration | 43 | ||
| Gaseous chemical agents | 43 | ||
| Liquid chemical agents | 43 | ||
| Incorporation of agents into solids for surface antisepsis | 43 | ||
| Choice of method | 43 | ||
| Measurement of microbial inactivation | 44 | ||
| D value | 44 | ||
| Resistance to sterilisation and disinfection | 44 | ||
| Sterilisation by moist heat | 45 | ||
| Sterilisation by dry heat | 45 | ||
| Disinfection by chemicals | 45 | ||
| Recommended reading | 46 | ||
| Websites | 46 | ||
| MCQs | 46.e1 | ||
| 5 Antimicrobial agents | 47 | ||
| Key points | 47 | ||
| Antibacterial agents | 47 | ||
| Sites of action and mechanisms of resistance | 47 | ||
| Inhibitors of bacterial cell wall synthesis | 48 | ||
| β-lactam agents | 48 | ||
| Penicillins | 48 | ||
| Cephalosporins | 49 | ||
| Other β-lactam agents | 51 | ||
| Glycopeptides | 51 | ||
| Other inhibitors of bacterial cell wall synthesis | 51 | ||
| Inhibitors of bacterial protein synthesis | 51 | ||
| Tetracyclines | 51 | ||
| Chloramphenicol | 51 | ||
| Aminoglycosides | 51 | ||
| Macrolides | 52 | ||
| Lincosamides | 52 | ||
| Fusidic acid | 52 | ||
| Linezolid | 52 | ||
| Streptogramins | 53 | ||
| Mupirocin | 53 | ||
| Inhibitors of nucleic acid synthesis | 53 | ||
| Sulphonamides and diaminopyrimidines | 53 | ||
| Quinolones | 53 | ||
| Nitroimidazoles | 54 | ||
| Nitrofurans | 54 | ||
| Rifamycins | 54 | ||
| Disruption of cell membranes | 54 | ||
| Polymyxins | 54 | ||
| Daptomycin | 54 | ||
| Antimycobacterial agents | 54 | ||
| Antifungal agents | 54 | ||
| Antiviral agents | 55 | ||
| Treatment of herpesvirus infections | 56 | ||
| Nucleoside analogues | 56 | ||
| Nonnucleoside antiherpes agents | 57 | ||
| Treatment of influenza | 57 | ||
| Neuraminidase inhibitors | 57 | ||
| Agents that block viral uncoating | 58 | ||
| Treatment of chronic hepatitis B virus infection | 58 | ||
| Interferons | 58 | ||
| HBV DNA polymerase inhibitors | 58 | ||
| Treatment of chronic hepatitis C virus infection | 58 | ||
| Other antiviral drugs—ribavirin | 58 | ||
| Antiretroviral agents | 58 | ||
| Nucleoside and nucleotide reverse transcriptase inhibitors | 58 | ||
| Nonnucleoside reverse transcriptase inhibitors | 59 | ||
| HIV protease inhibitors | 59 | ||
| HIV fusion inhibitors | 59 | ||
| HIV entry inhibitors | 59 | ||
| HIV integrase inhibitors | 59 | ||
| Recommended reading | 59 | ||
| Websites | 59 | ||
| MCQs | 59.e1 | ||
| 6 Bacterial genetics | 60 | ||
| Key points | 60 | ||
| Genetic organisation and regulation of the bacterial cell | 60 | ||
| Processes leading to protein synthesis | 61 | ||
| Gene regulation | 61 | ||
| Mutation | 62 | ||
| Phenotypic variation | 63 | ||
| Types of mutations | 64 | ||
| Horizontal gene transfer | 64 | ||
| Transformation | 64 | ||
| Conjugation | 65 | ||
| Mobilisation of chromosomal genes by conjugation | 65 | ||
| Transduction and bacteriophages | 65 | ||
| Lysogenic conversion | 66 | ||
| Plasmids | 66 | ||
| Properties encoded by plasmids | 66 | ||
| Plasmid classification | 66 | ||
| Plasmid epidemiology and distribution | 66 | ||
| Transposons, integrons and genomic islands | 66 | ||
| Genetic basis of antibiotic resistance | 67 | ||
| Intrinsic resistance | 67 | ||
| Acquired resistance | 67 | ||
| Chromosomal mutations | 67 | ||
| Transferable antibiotic resistance | 68 | ||
| Control of antibiotic resistance | 68 | ||
| The bacterial species and molecular typing of microorganisms | 69 | ||
| Microbial genomes and genomics | 70 | ||
| Recommended Reading | 73 | ||
| MCQs | 73.e1 | ||
| 7 Virus–cell interactions | 74 | ||
| Key points | 74 | ||
| The cytolytic or cytocidal growth cycle | 74 | ||
| Attachment (adsorption) | 75 | ||
| Entry (penetration) | 75 | ||
| Uncoating | 76 | ||
| Synthesis of viral components | 76 | ||
| Class 1: Double-stranded DNA viruses | 76 | ||
| Class 2: Single-stranded DNA viruses | 77 | ||
| Class 3: Double-stranded RNA viruses | 77 | ||
| Class 4: + single-stranded RNA viruses | 77 | ||
| Class 5: − single-stranded RNA viruses | 77 | ||
| Class 6: Retroviruses | 78 | ||
| Class 7: Partial double-stranded DNA viruses | 78 | ||
| Assembly and release | 78 | ||
| Microscopy of infected cells | 79 | ||
| Chronic/persistent infections | 80 | ||
| Latency | 80 | ||
| Transformation | 81 | ||
| Recommended reading | 82 | ||
| MCQs | 82.e1 | ||
| 2 Infection and immunity | 83 | ||
| 8 Innate and adaptive immunity | 84 | ||
| Key points | 84 | ||
| Innate and adaptive immunity | 84 | ||
| The immune system | 84 | ||
| Lymphoid cells | 84 | ||
| Myeloid cells | 85 | ||
| Mononuclear phagocytes | 85 | ||
| Granulocytes | 85 | ||
| Innate immunity | 85 | ||
| Features of innate immunity | 86 | ||
| Mechanisms of innate immunity | 86 | ||
| Mechanical barriers and surface secretions | 86 | ||
| Humoral defence mechanisms | 87 | ||
| Lysozyme | 87 | ||
| Basic polypeptides | 87 | ||
| Acute-phase proteins | 87 | ||
| Interferon | 87 | ||
| Complement | 87 | ||
| Regulation | 88 | ||
| Membrane attack complex (MAC) | 89 | ||
| Functions | 89 | ||
| Innate immune cells | 89 | ||
| Phagocytes | 89 | ||
| Phagocytosis | 90 | ||
| Natural killer (NK) cells | 90 | ||
| Eosinophils | 90 | ||
| Inflammation | 91 | ||
| Adaptive immunity | 91 | ||
| Antibodies | 92 | ||
| IgG | 93 | ||
| IgA | 93 | ||
| IgM | 93 | ||
| IgD | 93 | ||
| IgE | 93 | ||
| Antibody diversity | 93 | ||
| Antibody function | 93 | ||
| T cell receptor | 93 | ||
| Tissues involved in adaptive immune reactions | 94 | ||
| Development of the immune system | 94 | ||
| Lymphocyte trafficking | 95 | ||
| Initiation of adaptive responses | 95 | ||
| Thymus-independent antigens | 95 | ||
| Thymus–dependent antigens | 95 | ||
| Antigen processing and presentation | 96 | ||
| T cell activation | 96 | ||
| Humoral immunity – synthesis of antibody | 96 | ||
| Cell-mediated immunity | 97 | ||
| Regulatory T cells | 98 | ||
| Recommended reading | 98 | ||
| Websites | 98 | ||
| MCQs | 98.e1 | ||
| 9 Immunity in infection | 99 | ||
| Key points | 99 | ||
| Immunity in infection | 99 | ||
| Immunopathology | 99 | ||
| The response to viral infections | 99 | ||
| Interferons | 99 | ||
| Acquired immunity | 101 | ||
| Humoral immunity | 102 | ||
| Cell-mediated immunity | 103 | ||
| Induction of an immune response | 103 | ||
| Immunopathology | 103 | ||
| Persistence of virus | 104 | ||
| Vaccines | 105 | ||
| Immunity in bacterial infection | 105 | ||
| Host defences | 105 | ||
| Inflammation | 105 | ||
| Humoral immunity | 106 | ||
| Cell-mediated immunity | 106 | ||
| Evasion | 107 | ||
| Intracellular bacteria | 107 | ||
| Immunopathology | 107 | ||
| Effects of endotoxin | 107 | ||
| Mycobacterial disease | 108 | ||
| Parasitic infections: pathogenesis and immunity | 108 | ||
| Pathogenic mechanisms | 108 | ||
| Mechanical tissue damage | 108 | ||
| Physiological effects | 108 | ||
| Tissue damage | 109 | ||
| Immune defence mechanisms | 109 | ||
| Innate defences | 109 | ||
| Macrophages | 109 | ||
| Granulocytes | 110 | ||
| Mast cells | 110 | ||
| Acquired immunity | 110 | ||
| Antibody | 110 | ||
| T cells | 110 | ||
| Evasion mechanisms | 111 | ||
| Seclusion | 111 | ||
| Evasion | 111 | ||
| Immunosuppression | 111 | ||
| Immunopathology | 112 | ||
| Vaccination | 112 | ||
| Recommended reading | 112 | ||
| Websites | 112 | ||
| MCQs | 112.e1 | ||
| 10 Bacterial pathogenicity | 113 | ||
| Key points | 113 | ||
| Types of bacterial pathogens | 113 | ||
| Opportunistic pathogens | 113 | ||
| Primary pathogens | 114 | ||
| Zoonoses and nonzoonotic pathogens | 114 | ||
| Virulence determinants | 114 | ||
| Expression and analysis of virulence determinants | 114 | ||
| Establishment of infection | 115 | ||
| Colonisation | 115 | ||
| Adhesion | 115 | ||
| Fimbrial adhesins | 116 | ||
| Nonfimbrial adhesins | 116 | ||
| Binding to connective tissue proteins | 117 | ||
| Consequences of adhesion | 117 | ||
| Invasion | 117 | ||
| Uptake into host cells | 117 | ||
| Role of cell receptors | 118 | ||
| Survival and multiplication | 118 | ||
| Avoidance of host defence mechanisms | 118 | ||
| Capsules | 118 | ||
| Streptococcal M protein | 119 | ||
| Meningococcal Factor H–binding protein | 119 | ||
| Resistance to killing by phagocytic cells | 119 | ||
| Antigenic variation | 119 | ||
| Immunoglobulin A proteases | 120 | ||
| Serum resistance | 120 | ||
| Iron acquisition | 120 | ||
| Damage or dysfunction | 121 | ||
| Toxins | 121 | ||
| Endotoxin | 121 | ||
| Exotoxins | 121 | ||
| Systemic effects of toxins | 123 | ||
| Other extracellular aggressin | 123 | ||
| Recommended reading | 124 | ||
| MCQs | 124.e1 | ||
| 11 The natural history of infection and the human microbiome | 125 | ||
| Key points | 125 | ||
| Meetings between human beings and microorganisms | 125 | ||
| Obligate pathogens | 126 | ||
| Accidental or incidental pathogens | 126 | ||
| Pathogens in the environment | 126 | ||
| Stages of infection | 126 | ||
| Pathological patterns associated with infection | 127 | ||
| Toxin-mediated bacterial infections | 127 | ||
| Acute pyogenic bacterial infections | 128 | ||
| Subacute bacterial infections | 129 | ||
| Chronic granulomatous bacterial infections | 129 | ||
| Timing of key events in infection | 129 | ||
| Virulence and infectivity | 129 | ||
| The human microbiome in health and disease | 130 | ||
| Microbiomic methods and analyses | 131 | ||
| Examples of disordered physiology and diseases associated with microbiomic imbalances (dysbioses) | 131 | ||
| Recommended reading | 132 | ||
| Website | 132 | ||
| MCQs | 132.e1 | ||
| 3 Bacterial pathogens and associated diseases | 133 | ||
| 12 Staphylococcus | 134 | ||
| Key points | 134 | ||
| Staphylococcus aureus | 134 | ||
| Description | 134 | ||
| Pathogenesis | 135 | ||
| Virulence factors | 135 | ||
| Staphylococcal toxins | 135 | ||
| Enterotoxins | 135 | ||
| Toxic shock syndrome toxin (TSST) | 136 | ||
| Epidermolytic toxins | 136 | ||
| Panton-Valentine leukocidin (PVL) | 136 | ||
| Epidemiology | 136 | ||
| Sources and acquisition of infection | 136 | ||
| Infected lesions | 136 | ||
| Healthy carriers | 136 | ||
| Animals | 136 | ||
| Environment | 137 | ||
| Meticillin-resistant Staph. aureus (MRSA) | 137 | ||
| Laboratory investigation | 137 | ||
| Typing | 137 | ||
| Treatment | 138 | ||
| Susceptibility to antibiotics | 138 | ||
| Choice of antibiotic for therapy | 138 | ||
| Coagulase-negative staphylococci | 138 | ||
| Description | 139 | ||
| Pathogenesis | 139 | ||
| Treatment | 139 | ||
| Recommended reading | 140 | ||
| Websites | 140 | ||
| MCQs | 140.e1 | ||
| Clinical scenario | 140.e2 | ||
| Staphylococcal infection | 140.e2 | ||
| 13 Streptococcus and Enterococcus | 141 | ||
| Key points | 141 | ||
| Classification | 141 | ||
| Haemolytic activity | 142 | ||
| Lancefield grouping | 142 | ||
| Streptococcus pyogenes | 142 | ||
| Pathogenesis | 143 | ||
| Virulence factors | 143 | ||
| Adhesion | 143 | ||
| M proteins | 143 | ||
| Capsule | 144 | ||
| C5a peptidase | 144 | ||
| Streptolysins | 144 | ||
| Pyrogenic exotoxins | 144 | ||
| Hyaluronidase | 145 | ||
| Streptokinase | 145 | ||
| Deoxyribonucleases (DNAases) | 145 | ||
| Clinical features | 145 | ||
| Noninvasive streptococcal disease | 145 | ||
| Pharyngitis | 145 | ||
| Scarlet fever | 145 | ||
| Skin infections | 146 | ||
| Invasive soft tissue infections | 146 | ||
| Necrotising fasciitis | 147 | ||
| Streptococcal toxic shock syndrome | 147 | ||
| Other suppurative infections | 147 | ||
| Bacteraemia | 147 | ||
| Nonsuppurative sequelae | 147 | ||
| Rheumatic fever | 148 | ||
| Acute poststreptococcal glomerulonephritis | 148 | ||
| Streptococcus agalactiae | 148 | ||
| Pathogenesis | 148 | ||
| Virulence factors | 148 | ||
| Clinical features | 149 | ||
| Infection in the neonate | 149 | ||
| Early-onset disease | 149 | ||
| Late-onset disease | 149 | ||
| Infections in the adult | 149 | ||
| Other pyogenic streptococci | 150 | ||
| Streptococcus pneumoniae | 150 | ||
| Pathogenesis | 150 | ||
| Virulence factors | 150 | ||
| Capsule | 150 | ||
| IgA1 protease | 150 | ||
| Pneumolysin | 150 | ||
| Autolysin | 150 | ||
| Clinical features | 150 | ||
| Predisposing factors | 150 | ||
| Pneumonia | 151 | ||
| Otitis media and sinusitis | 151 | ||
| Meningitis | 151 | ||
| Conjunctivitis | 151 | ||
| Commensal streptococci | 152 | ||
| Viridans streptococci | 152 | ||
| Mitis group | 152 | ||
| Mutans group | 152 | ||
| Anginosus group | 152 | ||
| Bovis group | 152 | ||
| Enterococcus species | 152 | ||
| Laboratory investigation | 153 | ||
| Collection of specimens | 153 | ||
| Cultivation and identification | 153 | ||
| Antigen detection | 153 | ||
| Antibody detection | 154 | ||
| Typing of streptococci | 154 | ||
| Treatment | 154 | ||
| Prevention and control | 155 | ||
| Hygienic measures | 155 | ||
| Chemoprophylaxis | 155 | ||
| Vaccines | 155 | ||
| Pyogenic streptococci | 155 | ||
| Pneumococci | 156 | ||
| Recommended reading | 156 | ||
| Websites | 156 | ||
| MCQs | 156.e1 | ||
| Clinical scenario | 156.e2 | ||
| A case of necrotising fasciitis | 156.e2 | ||
| 14 Coryneform bacteria, Listeria and Erysipelothrix | 157 | ||
| Key points | 157 | ||
| Coryneform bacteria | 157 | ||
| Corynebacterium diphtheriae and C. ulcerans | 157 | ||
| Description | 157 | ||
| Pathogenesis | 158 | ||
| Clinical features | 158 | ||
| Diagnosis | 159 | ||
| Treatment | 160 | ||
| Epidemiology | 160 | ||
| Control | 161 | ||
| Other medically important corynebacteria | 161 | ||
| Corynebacterium pseudotuberculosis | 161 | ||
| Corynebacterium jeikeium | 161 | ||
| Treatment | 162 | ||
| Corynebacterium urealyticum | 162 | ||
| Corynebacterium amycolatum | 162 | ||
| Corynebacterium glucuronolyticum | 163 | ||
| Corynebacterium minutissimum | 163 | ||
| Corynebacterium striatum | 163 | ||
| Corynebacterium pseudodiphtheriticum | 163 | ||
| Corynebacterium kroppenstedtii | 163 | ||
| Arcanobacterium haemolyticum | 163 | ||
| Rhodococcus equi | 163 | ||
| Other Corynebacterium species and coryneform bacteria | 164 | ||
| Listeria | 164 | ||
| Listeria monocytogenes | 164 | ||
| Description | 164 | ||
| Pathogenesis | 164 | ||
| Clinical aspects of infection | 165 | ||
| Infection in pregnancy and the neonate | 165 | ||
| Adult and juvenile infection | 165 | ||
| Meningitis | 166 | ||
| Bacteraemia | 166 | ||
| Gastroenteritis | 166 | ||
| Other infections | 166 | ||
| Epidemiology | 166 | ||
| Incidence | 166 | ||
| Transmission | 167 | ||
| Diagnosis and treatment | 167 | ||
| Prognosis | 168 | ||
| Erysipelothrix | 168 | ||
| Recommended reading | 168 | ||
| Websites | 168 | ||
| MCQs | 168.e1 | ||
| Listeria monocytogenes and Corynebacterium diphtheriae | 168.e1 | ||
| Clinical scenario | 168.e2 | ||
| 15 Bacillus | 169 | ||
| Key points | 169 | ||
| Bacillus anthracis | 169 | ||
| Description | 169 | ||
| Pathogenesis | 170 | ||
| Virulence factors | 170 | ||
| Clinical features | 170 | ||
| Cutaneous anthrax | 171 | ||
| Inhalational anthrax | 171 | ||
| Gastrointestinal anthrax | 172 | ||
| Injectional anthrax | 172 | ||
| Meningitis | 172 | ||
| Naturally occurring infections of animals | 172 | ||
| Human infections in the United Kingdom (since the 1980s) | 173 | ||
| Animal models of disease | 173 | ||
| Laboratory investigation | 173 | ||
| Clinical specimens | 173 | ||
| Environmental samples | 174 | ||
| Treatment | 174 | ||
| Epidemiology and control | 174 | ||
| Immunisation | 175 | ||
| Bacillus cereus | 175 | ||
| Description | 175 | ||
| Pathogenesis | 175 | ||
| Food poisoning | 176 | ||
| Laboratory investigation | 176 | ||
| Treatment | 176 | ||
| Control | 176 | ||
| Other bacillus species | 176 | ||
| Sterilisation test bacilli | 176 | ||
| Recommended reading | 177 | ||
| Websites | 177 | ||
| MCQs | 177.e1 | ||
| Clinical scenario | 177.e2 | ||
| 16 Escherichia coli and Shigella | 178 | ||
| Key points | 178 | ||
| Classification | 178 | ||
| Laboratory investigation | 179 | ||
| Typing | 179 | ||
| Clinical syndromes associated with extraintestinal E. coli | 181 | ||
| Pathogenesis | 181 | ||
| Gastrointestinal disease | 182 | ||
| Enteropathogenic E. coli (EPEC) | 182 | ||
| Enterotoxigenic E. coli (ETEC) | 182 | ||
| Enteroaggregative E. coli (EAEC) | 183 | ||
| Shiga toxin–producing E. coli (STEC) | 183 | ||
| Enteroinvasive E. coli (EIEC) | 184 | ||
| Shigella | 184 | ||
| Treatment | 185 | ||
| Control | 186 | ||
| Vaccination | 186 | ||
| Recommended reading | 186 | ||
| Websites | 187 | ||
| MCQs | 187.e1 | ||
| Clinical scenario | 187.e2 | ||
| E. coli 0157 haemolytic uraemic syndrome (HUS) | 187.e2 | ||
| 17 Salmonella | 188 | ||
| Key points | 188 | ||
| Description | 188 | ||
| Host range | 188 | ||
| Pathogenesis | 188 | ||
| Clinical syndromes | 189 | ||
| Enteric fever | 189 | ||
| Onset | 190 | ||
| Progression | 190 | ||
| Relapse | 190 | ||
| Morbidity and mortality | 190 | ||
| Gastroenteritis and food poisoning | 190 | ||
| Bacteraemia and metastatic disease | 190 | ||
| The prolonged carrier state | 191 | ||
| Infective dose | 191 | ||
| Laboratory investigation | 191 | ||
| Enteric fever | 191 | ||
| Blood culture | 191 | ||
| Stool and urine culture | 191 | ||
| Serological tests | 192 | ||
| Serotyping and phage typing | 192 | ||
| Molecular typing | 192 | ||
| Treatment | 193 | ||
| Enteric fever | 193 | ||
| Gastroenteritis | 193 | ||
| Salmonella bacteraemia | 194 | ||
| Chronic asymptomatic carriers | 194 | ||
| Epidemiology | 194 | ||
| Incidence of enteric fever | 194 | ||
| Gastroenteritis and Salmonella food poisoning | 194 | ||
| Source attribution | 195 | ||
| Outbreaks | 195 | ||
| Surveillance | 196 | ||
| Prevention and control | 196 | ||
| Enteric fever | 196 | ||
| Nontyphoidal Salmonella | 196 | ||
| Vaccination | 196 | ||
| Recommended reading | 197 | ||
| Websites | 197 | ||
| MCQs | 197.e1 | ||
| Clinical scenario | 197.e2 | ||
| Typhoid | 197.e2 | ||
| 18 Klebsiella, Enterobacter, Proteus and other enterobacteria | 198 | ||
| Key points | 198 | ||
| Klebsiella | 198 | ||
| Classification | 198 | ||
| Description | 198 | ||
| Pathogenesis | 199 | ||
| Pathogenic mechanisms | 200 | ||
| Treatment | 200 | ||
| Enterobacter | 200 | ||
| Description | 200 | ||
| Pathogenesis | 200 | ||
| 4 Viral pathogens and associated diseases | 361 | ||
| 37 Adenoviruses | 362 | ||
| Key points | 362 | ||
| Description | 362 | ||
| Classification | 363 | ||
| Replication | 364 | ||
| Clinical features | 364 | ||
| Respiratory diseases | 364 | ||
| Eye infections | 365 | ||
| Gut infections | 365 | ||
| Other diseases of immunocompetent patients | 366 | ||
| Disease in immunosuppressed transplant recipients | 366 | ||
| Pathogenesis | 366 | ||
| Laboratory Investigation | 366 | ||
| Direct demonstration of virus | 366 | ||
| Detection of viral DNA | 366 | ||
| Virus antigen | 367 | ||
| Electron microscopy | 367 | ||
| Culture | 367 | ||
| Serology | 367 | ||
| Treatment | 367 | ||
| Epidemiology | 367 | ||
| Control | 367 | ||
| Adenovirus-associated viruses | 368 | ||
| Recommended reading | 368 | ||
| MCQs | 368.e1 | ||
| Clinical scenario | 368.e2 | ||
| Disseminated adenovirus disease | 368.e2 | ||
| 38 Herpesviruses | 369 | ||
| Key points | 369 | ||
| Latent infection | 369 | ||
| Reactivation | 369 | ||
| Recurrence or recrudescence | 369 | ||
| Description | 370 | ||
| Biological classification | 370 | ||
| Replication | 370 | ||
| Herpes simplex virus | 371 | ||
| Description | 371 | ||
| HSV glycoproteins | 371 | ||
| Pathogenesis | 371 | ||
| Primary infection | 371 | ||
| Latent infection | 372 | ||
| Reactivation | 372 | ||
| Clinical features | 372 | ||
| Primary infection | 372 | ||
| Recurrent infection | 372 | ||
| Oral infection | 373 | ||
| Skin infection | 373 | ||
| Herpetic whitlow | 373 | ||
| Eczema herpeticum | 373 | ||
| Eye infection | 373 | ||
| Central nervous system (CNS) infection | 373 | ||
| HSV encephalitis | 374 | ||
| HSV meningitis | 374 | ||
| Genital tract infection | 375 | ||
| Recurrent genital herpes | 375 | ||
| Neonatal herpes | 375 | ||
| Laboratory investigation | 376 | ||
| Diagnosis of HSV | 376 | ||
| Antibody tests for HSV | 377 | ||
| Treatment | 377 | ||
| Epidemiology | 377 | ||
| Control | 378 | ||
| Varicella–zoster virus (VZV) | 378 | ||
| Description | 378 | ||
| Pathogenesis | 378 | ||
| Varicella | 378 | ||
| Zoster | 379 | ||
| Clinical features | 379 | ||
| Varicella | 379 | ||
| Pneumonitis | 380 | ||
| Central nervous system | 380 | ||
| Varicella in pregnancy | 380 | ||
| Zoster | 380 | ||
| Postherpetic neuralgia | 381 | ||
| Ophthalmic zoster | 381 | ||
| Recurrent and chronic VZV | 381 | ||
| Laboratory Investigation | 381 | ||
| Virus detection | 381 | ||
| Serological diagnosis | 381 | ||
| Treatment | 381 | ||
| Epidemiology | 382 | ||
| Control | 382 | ||
| Passive immunization | 382 | ||
| Varicella vaccine | 383 | ||
| Epstein–Barr virus | 383 | ||
| Description | 383 | ||
| Replication | 383 | ||
| Pathogenesis | 384 | ||
| Clinical features | 385 | ||
| Infectious mononucleosis/glandular fever | 385 | ||
| Complications of infectious mononucleosis/glandular fever | 385 | ||
| Other EBV-associated disease, tumours and immunosuppression | 385 | ||
| Laboratory Investigation | 385 | ||
| Treatment | 386 | ||
| Epidemiology | 386 | ||
| Control | 386 | ||
| Cytomegalovirus | 387 | ||
| Description | 387 | ||
| Replication | 388 | ||
| Pathogenesis | 388 | ||
| Intrauterine infection | 388 | ||
| Perinatal infection | 388 | ||
| Postnatal infection | 388 | ||
| Host responses | 389 | ||
| Clinical features | 389 | ||
| Congenital CMV infection | 389 | ||
| Infection in children and adults | 389 | ||
| Infection in immunocompromised patients | 389 | ||
| Laboratory Investigation | 389 | ||
| Virus detection | 390 | ||
| Serology for CMV | 390 | ||
| Treatment | 390 | ||
| Epidemiology | 390 | ||
| Control | 391 | ||
| Human herpesviruses 6 and 7 | 391 | ||
| Description | 391 | ||
| Pathogenesis and clinical features | 391 | ||
| Exanthem subitum (roseola infantum) | 391 | ||
| Neurological disease | 392 | ||
| Other associations | 392 | ||
| Laboratory Investigation | 392 | ||
| Treatment | 392 | ||
| Epidemiology | 392 | ||
| Human herpesvirus 8 (Kaposi’s sarcoma–associated herpesvirus) | 392 | ||
| Kaposi’s sarcoma | 393 | ||
| Body cavity–associated B lymphoma/primary effusion lymphoma/multicentric Castleman’s disease | 393 | ||
| Laboratory Investigation | 393 | ||
| Epidemiology | 393 | ||
| Treatment and control | 394 | ||
| Cercopithecine herpesvirus 1 (herpesvirus B; B virus; herpesvirus simiae) | 394 | ||
| Description | 394 | ||
| Diagnosis and treatment | 394 | ||
| Prevention of B virus infection | 394 | ||
| Recommended reading | 395 | ||
| Websites | 395 | ||
| MCQs | 395.e1 | ||
| Clinical scenario | 395.e2 | ||
| Key points | 395.e2 | ||
| 39 Poxviruses | 396 | ||
| Key points | 396 | ||
| Description | 396 | ||
| Classification | 396 | ||
| The virion | 397 | ||
| The genome | 398 | ||
| Replication | 398 | ||
| Clinical features | 398 | ||
| Control of smallpox | 398 | ||
| Before vaccination | 398 | ||
| Vaccination | 398 | ||
| The eradication campaign | 398 | ||
| Smallpox and bioterrorism | 399 | ||
| Other human poxvirus infections | 399 | ||
| Molluscum contagiosum | 399 | ||
| Monkeypox | 400 | ||
| Parapoxvirus infections | 400 | ||
| Vaccinia | 400 | ||
| Vaccinia virus as a vaccine vector | 400 | ||
| Myxomatosis: an evolving disease | 400 | ||
| Recommended reading | 401 | ||
| MCQs | 401.e1 | ||
| Clinical scenario | 401.e2 | ||
| Smallpox, London, 1973. A case report | 401.e2 | ||
| 40 Papillomaviruses | 402 | ||
| Key points | 402 | ||
| Description | 402 | ||
| Introduction including classification and major features | 402 | ||
| Classification | 402 | ||
| Genome organisation | 402 | ||
| Epidemiology | 403 | ||
| Major patterns including reservoir and transmission | 403 | ||
| Replication | 404 | ||
| Life cycle | 404 | ||
| Transformation | 405 | ||
| Clinical features and pathogenesis | 406 | ||
| HPV infections | 406 | ||
| Cutaneous warts | 406 | ||
| Anogenital warts | 406 | ||
| Orolaryngeal warts | 407 | ||
| Recurrent respiratory papillomatosis (RRP) | 407 | ||
| Oral papillomatosis | 408 | ||
| HPV and cancer | 408 | ||
| Cervical cancer (CC) | 408 | ||
| Anal and penile cancer (AC) | 408 | ||
| Vulvar and vaginal cancer | 409 | ||
| Squamous cancers of the head and neck | 409 | ||
| Diagnosis | 409 | ||
| Clinical and morphological identification | 409 | ||
| Serology | 409 | ||
| Molecular detection | 409 | ||
| Treatment and control | 409 | ||
| Vaccines | 410 | ||
| Acknowledgment | 410 | ||
| Recommended reading | 410 | ||
| MCQs | 410.e1 | ||
| Clinical scenario | 410.e2 | ||
| HPV | 410.e2 | ||
| Comments | 410.e2 | ||
| 41 Polyomaviruses | 411 | ||
| Key points | 411 | ||
| Introduction | 411 | ||
| Replication and transformation | 411 | ||
| Clinical features and pathogenesis | 411 | ||
| Haemorrhagic cystitis (HC) | 412 | ||
| Polyomavirus-associated nephropathy (PVAN) | 412 | ||
| Progressive multifocal leuco-encephalopathy (PML) | 412 | ||
| Laboratory Investigation | 413 | ||
| Transmission and epidemiology | 413 | ||
| Treatment | 413 | ||
| Recommended reading | 414 | ||
| MCQs | 414.e1 | ||
| Clinical scenario | 414.e2 | ||
| 42 Hepadnaviruses | 415 | ||
| Key points | 415 | ||
| Hepatitis B virus | 415 | ||
| Structure | 415 | ||
| Genetic variation | 416 | ||
| Stability | 416 | ||
| Replication | 417 | ||
| Acute infection | 417 | ||
| Pathology of acute infection | 417 | ||
| Chronic infection | 417 | ||
| Pathology and pathogenesis of chronic infection | 419 | ||
| Hepatocellular carcinoma (HCC) | 419 | ||
| HBV variants | 419 | ||
| HBsAg variants | 420 | ||
| HBcAg variants | 420 | ||
| Polymerase variants | 420 | ||
| Laboratory Investigation | 420 | ||
| Acute infection | 420 | ||
| Chronic infection | 421 | ||
| Treatment | 421 | ||
| Epidemiology | 422 | ||
| Control | 423 | ||
| Passive immunization | 423 | ||
| Active immunisation | 423 | ||
| Who should be immunised? | 423 | ||
| The delta agent (hepatitis D virus, HDV) | 424 | ||
| Clinical features and pathogenesis | 424 | ||
| Diagnosis | 424 | ||
| Epidemiology | 424 | ||
| Treatment and control | 425 | ||
| Recommended reading | 425 | ||
| Websites | 425 | ||
| MCQs | 425.e1 | ||
| Clinical Scenario | 425.e2 | ||
| 43 Parvoviruses | 426 | ||
| Key points | 426 | ||
| Description | 426 | ||
| Epidemiology | 426 | ||
| Replication | 427 | ||
| Pathogenesis | 427 | ||
| Clinical features | 429 | ||
| Minor illness or subclinical infection | 429 | ||
| Rash illness | 429 | ||
| Joint disease | 429 | ||
| Transient aplastic crisis (TAC) | 430 | ||
| Persistent infection in the immunocompromised | 431 | ||
| B19V in pregnancy | 431 | ||
| Other | 431 | ||
| Diagnosis (Table 43.2) | 431 | ||
| Clinical | 431 | ||
| Cultivation | 431 | ||
| Molecular | 431 | ||
| Immunological | 432 | ||
| Investigations during pregnancy and infection in the foetus | 432 | ||
| Treatment (Table 43.2) | 433 | ||
| Control | 433 | ||
| Acknowledgment | 433 | ||
| Recommended reading | 434 | ||
| Website | 434 | ||
| MCQs | 434.e1 | ||
| Clinical Scenario | 434.e2 | ||
| 44 Picornaviruses | 435 | ||
| Key points | 435 | ||
| Enteroviruses | 435 | ||
| Description and classification | 435 | ||
| Composition | 436 | ||
| Properties of enteroviruses | 436 | ||
| Replication | 437 | ||
| Clinical features | 437 | ||
| Paralytic poliomyelitis | 437 | ||
| Viral meningitis | 438 | ||
| Encephalitis | 438 | ||
| Neonatal infections | 438 | ||
| Epidemic pleurodynia | 438 | ||
| Myocarditis, pericarditis and dilated cardiomyopathy | 438 | ||
| Herpangina | 439 | ||
| Maculopapular rash | 439 | ||
| Hand, foot and mouth disease | 439 | ||
| Respiratory infections | 439 | ||
| Conjunctivitis | 440 | ||
| Pathogenesis | 440 | ||
| Epidemiology and transmission | 440 | ||
| Prevention and control | 440 | ||
| Immunisation | 440 | ||
| Inactivated polio vaccine (Salk vaccine) | 441 | ||
| Live-attenuated oral polio vaccine (Sabin vaccine) | 442 | ||
| Global eradication | 442 | ||
| Prospects for the future | 443 | ||
| Rhinoviruses | 443 | ||
| Properties | 443 | ||
| Classification | 444 | ||
| Stability | 444 | ||
| Replication | 444 | ||
| Clinical features and pathogenesis | 444 | ||
| Immunity | 445 | ||
| Epidemiology and transmission | 445 | ||
| Parechoviruses | 445 | ||
| Properties | 445 | ||
| Clinical features | 445 | ||
| Epidemiology | 446 | ||
| Laboratory Investigation of enterovirus, rhinovirus and parechovirus infections | 446 | ||
| Culture | 446 | ||
| Molecular methods | 446 | ||
| Serological tests | 447 | ||
| Treatment and control of enterovirus, rhinovirus and parechovirus infections | 447 | ||
| Hepatoviruses | 447 | ||
| Hepatitis a virus | 447 | ||
| Clinical features | 448 | ||
| Pathogenesis | 448 | ||
| Laboratory investigation | 448 | ||
| Epidemiology | 448 | ||
| Prevention and control | 448 | ||
| Recommended Reading | 449 | ||
| Websites | 449 | ||
| MCQs | 449.e1 | ||
| Clinical scenario | 449.e3 | ||
| 45 Orthomyxoviruses | 450 | ||
| Key points | 450 | ||
| Influenza A, B and C host range | 450 | ||
| Nomenclature | 451 | ||
| Physical characteristics | 451 | ||
| The viruses | 451 | ||
| Virus variability | 453 | ||
| Epidemic and pandemic influenza | 453 | ||
| Cross-species influenza a infection | 454 | ||
| Zoonotic transmission to humans | 455 | ||
| Human seasonal influenza A, B and C infections | 456 | ||
| Clinical features in human seasonal influenza A infection | 457 | ||
| Complications of human seasonal influenza | 457 | ||
| Clinical features in zoonotic influenza A infections | 457 | ||
| Clinical features in human seasonal influenza B infection | 458 | ||
| Influenza C | 458 | ||
| Seasonal influenza a epidemics | 458 | ||
| Pathogenesis | 458 | ||
| Immunity | 459 | ||
| Laboratory investigation | 459 | ||
| Serology | 459 | ||
| Treatment | 459 | ||
| Control measures | 461 | ||
| Infection control | 461 | ||
| Immunisation | 461 | ||
| Global surveillance | 462 | ||
| Recommended reading | 463 | ||
| Websites | 463 | ||
| Clinical scenario | 463.e1 | ||
| Influenza | 463.e1 | ||
| Learning points | 463.e1 | ||
| MCQs | 463.e2 | ||
| 46 Paramyxoviruses and Pneumoviruses | 464 | ||
| Key points | 464 | ||
| Structure and replication | 464 | ||
| Structure | 464 | ||
| Replication | 466 | ||
| The paramyxoviridae | 466 | ||
| Parainfluenza viruses | 466 | ||
| Classification | 466 | ||
| Clinical features and pathogenesis | 467 | ||
| Laboratory investigation | 467 | ||
| Epidemiology and transmission | 467 | ||
| Mumps virus | 467 | ||
| Description | 467 | ||
| Clinical features and pathogenesis | 468 | ||
| Laboratory investigation | 468 | ||
| Detection and isolation | 468 | ||
| Serology | 468 | ||
| Epidemiology | 468 | ||
| Control | 469 | ||
| Measles virus | 469 | ||
| Description | 469 | ||
| Clinical features and pathogenesis | 469 | ||
| Laboratory investigation | 470 | ||
| Epidemiology | 470 | ||
| Control | 470 | ||
| Nipah and hendra viruses | 471 | ||
| The pneumoviridae | 471 | ||
| Human respiratory syncytial virus | 471 | ||
| Description | 471 | ||
| Clinical features | 471 | ||
| Laboratory investigation | 472 | ||
| Detection and isolation | 472 | ||
| Serology | 472 | ||
| Treatment | 472 | ||
| Epidemiology | 472 | ||
| Control | 473 | ||
| Human metapneumovirus | 473 | ||
| Description | 473 | ||
| Clinical features | 473 | ||
| Laboratory investigation | 473 | ||
| Epidemiology | 473 | ||
| Treatment and control | 474 | ||
| Acknowledgment | 474 | ||
| Recommended reading | 474 | ||
| MCQs | 474.e1 | ||
| Clinical scenario | 474.e2 | ||
| 47 Arboviruses: alphaviruses, flaviviruses and bunyaviruses | 475 | ||
| Key points | 475 | ||
| Description | 475 | ||
| Classification | 475 | ||
| Properties | 476 | ||
| Replication | 477 | ||
| Alphaviruses | 477 | ||
| Flaviviruses | 478 | ||
| Bunyaviruses | 478 | ||
| Pathogenesis | 478 | ||
| Clinical features | 479 | ||
| Encephalitis | 479 | ||
| Yellow fever | 479 | ||
| Dengue | 479 | ||
| Dengue haemorrhagic fever | 480 | ||
| Miscellaneous tropical fevers | 481 | ||
| Undifferentiated fever | 481 | ||
| Hantavirus pulmonary syndrome | 481 | ||
| Congenital Zika Syndrome | 481 | ||
| Laboratory Investigation | 481 | ||
| Virus isolation | 481 | ||
| Arbovirus-specific RNA detection | 481 | ||
| Serology | 482 | ||
| Treatment | 482 | ||
| Epidemiology | 482 | ||
| Natural cycles | 482 | ||
| Alphaviruses | 482 | ||
| Western equine encephalitis virus | 482 | ||
| Eastern equine encephalitis virus | 483 | ||
| Venezuelan equine encephalitis virus | 483 | ||
| Ross River virus | 484 | ||
| Chikungunya virus | 485 | ||
| O’nyong-nyong virus | 485 | ||
| Flaviviruses: mosquito-borne | 485 | ||
| St. Louis encephalitis virus | 485 | ||
| Japanese encephalitis virus | 485 | ||
| West Nile virus | 485 | ||
| Usutu virus | 486 | ||
| Murray Valley encephalitis virus | 486 | ||
| Yellow fever virus | 486 | ||
| Dengue viruses | 486 | ||
| Zika virus | 487 | ||
| Flaviviruses: tick-borne | 487 | ||
| Powassan virus | 487 | ||
| Tick-borne encephalitis viruses | 487 | ||
| Bunyaviruses: Bunyavirus genus | 488 | ||
| California (CAL) serogroup | 488 | ||
| Oropouche (ORO) | 488 | ||
| Garissa virus | 488 | ||
| Bunyaviruses: Phlebovirus genus | 488 | ||
| Rift Valley fever virus | 488 | ||
| Severe fever with thrombocytopenia syndrome virus | 489 | ||
| Sandfly fever group | 489 | ||
| Toscana virus | 489 | ||
| Bunyaviruses: Nairovirus genus | 489 | ||
| Crimean–Congo haemorrhagic fever virus | 489 | ||
| Bunyaviruses: Hantavirus genus | 489 | ||
| Hantaan and Puumala viruses | 489 | ||
| Sin Nombre virus | 489 | ||
| Control | 490 | ||
| Vector control | 490 | ||
| Vaccines | 490 | ||
| Alphaviruses | 490 | ||
| Flaviviruses | 490 | ||
| Bunyaviruses | 491 | ||
| Recommended reading | 491 | ||
| MCQs | 491.e1 | ||
| Clinical scenario | 491.e2 | ||
| Yellow fever case history | 491.e2 | ||
| Examination | 491.e2 | ||
| Laboratory tests | 491.e2 | ||
| Management | 491.e2 | ||
| Comments | 491.e2 | ||
| 48 Hepatitis C virus | 492 | ||
| Key points | 492 | ||
| Properties | 492 | ||
| Structure | 492 | ||
| Replication | 492 | ||
| Classification | 494 | ||
| Virus stability | 494 | ||
| Diagnosis | 494 | ||
| Serological diagnosis | 494 | ||
| Direct detection methods | 495 | ||
| Genetic variation | 496 | ||
| Epidemiology | 496 | ||
| Clinical features | 496 | ||
| Acute hepatitis | 497 | ||
| Chronic hepatitis | 497 | ||
| Extrahepatic manifestations | 497 | ||
| Treatment and control | 497 | ||
| Treatment | 497 | ||
| Prevention | 499 | ||
| Immunisation | 500 | ||
| Recommended reading | 500 | ||
| MCQs | 500.e1 | ||
| Clinical Scenario | 500.e2 | ||
| Learning points | 500.e2 | ||
| 49 Hepeviruses | 501 | ||
| Key points | 501 | ||
| Description | 501 | ||
| Epidemiology | 501 | ||
| Developing world | 501 | ||
| Developed world | 503 | ||
| Replication | 503 | ||
| Clinical features | 504 | ||
| Acute HEV infection | 504 | ||
| Chronic HEV infection | 504 | ||
| Extrahepatic manifestations | 504 | ||
| Diagnosis | 504 | ||
| Treatment | 505 | ||
| Control | 506 | ||
| Immunisation | 506 | ||
| Reducing exposure | 506 | ||
| Transfusion-transmitted HEV | 506 | ||
| Recommended reading | 506 | ||
| MCQs | 506.e1 | ||
| Clinical scenario | 506.e2 | ||
| 50 Arenaviruses and filoviruses | 507 | ||
| Key points | 507 | ||
| Arenaviruses | 507 | ||
| Introduction | 507 | ||
| Properties | 508 | ||
| Replication | 508 | ||
| Clinical features and pathogenesis | 510 | ||
| Lymphocytic choriomeningitis virus | 510 | ||
| Lassa fever | 510 | ||
| South American haemorrhagic fever | 511 | ||
| Diagnosis | 512 | ||
| Genome detection | 512 | ||
| Antigen detection | 512 | ||
| Serology | 512 | ||
| Virus isolation | 512 | ||
| Treatment | 512 | ||
| Epidemiology and transmission | 513 | ||
| Control | 513 | ||
| Filoviruses | 513 | ||
| Introduction | 513 | ||
| Properties | 513 | ||
| Replication | 514 | ||
| Clinical features and pathogenesis | 515 | ||
| Diagnosis | 516 | ||
| Genome detection | 516 | ||
| Antigen detection | 516 | ||
| Serology | 516 | ||
| Virus isolation | 516 | ||
| Treatment | 516 | ||
| Epidemiology and transmission | 517 | ||
| Control | 517 | ||
| Recommended reading | 519 | ||
| MCQs | 519.e1 | ||
| Clinical scenario | 519.e2 | ||
| Ebola Virus Disease | 519.e2 | ||
| 51 Reoviruses | 520 | ||
| Key points | 520 | ||
| Rotaviruses | 520 | ||
| Epidemiology | 520 | ||
| Morphology | 521 | ||
| Genome and gene-coding assignments | 522 | ||
| Antigenic and genetic diversity | 523 | ||
| Replication | 524 | ||
| Pathogenesis and immunity | 525 | ||
| Clinical features | 525 | ||
| Laboratory investigation | 526 | ||
| Treatment | 526 | ||
| Control | 526 | ||
| Recommended reading | 526 | ||
| MCQs | 526.e1 | ||
| Clinical scenario | 526.e2 | ||
| History | 526.e2 | ||
| Examination | 526.e2 | ||
| Investigations | 526.e2 | ||
| Management | 526.e2 | ||
| Progress | 526.e2 | ||
| Comment | 526.e2 | ||
| 52 Retroviruses | 527 | ||
| Key points | 527 | ||
| Description | 527 | ||
| Classification | 527 | ||
| Genome and gene coding assignment | 529 | ||
| Replication | 530 | ||
| HIV infection | 530 | ||
| Epidemiology of HIV | 530 | ||
| Transmission | 531 | ||
| Sexual intercourse | 531 | ||
| Mother to child | 531 | ||
| Blood and blood products | 531 | ||
| Clinical features | 531 | ||
| Pathogenesis of HIV infection and AIDS | 533 | ||
| Disease progression | 534 | ||
| Paediatric infection | 534 | ||
| Laboratory investigation | 534 | ||
| Tests for anti-HIV | 534 | ||
| Combination assays | 535 | ||
| PCR | 535 | ||
| Treatment | 535 | ||
| Monitoring progress | 536 | ||
| Prevention and control | 536 | ||
| Sexual transmission | 536 | ||
| Mother to child transmission | 536 | ||
| Exposure to blood | 537 | ||
| Vaccines | 537 | ||
| HTLV-I and -II infection | 538 | ||
| Epidemiology and transmission | 538 | ||
| Pathogenesis | 538 | ||
| Clinical features | 538 | ||
| Laboratory investigation | 539 | ||
| Treatment | 539 | ||
| Control | 539 | ||
| Recommended reading | 539 | ||
| Websites | 539 | ||
| MCQs | 539.e1 | ||
| Clinical scenario | 539.e3 | ||
| 53 Caliciviruses and astroviruses | 540 | ||
| Key points | 540 | ||
| Description | 540 | ||
| Morphology and classification | 540 | ||
| Caliciviridae | 540 | ||
| Norovirus | 540 | ||
| Sapovirus | 541 | ||
| Astroviridae | 541 | ||
| Major features | 541 | ||
| Norovirus genome organisation | 541 | ||
| Sapovirus genome organisation | 542 | ||
| Astrovirus genome organisation | 542 | ||
| Norovirus structure | 542 | ||
| Sapovirus structure | 543 | ||
| Astrovirus structure | 543 | ||
| Epidemiology | 543 | ||
| Replication | 544 | ||
| Clinical features | 544 | ||
| Diagnosis | 545 | ||
| Clinical | 545 | ||
| Cultivation | 545 | ||
| Antigen detection assays | 545 | ||
| Genome detection assays | 545 | ||
| Treatment | 546 | ||
| Control | 546 | ||
| Recommended reading | 546 | ||
| Websites | 547 | ||
| MCQs | 547.e1 | ||
| Clinical scenario | 547.e2 | ||
| 54 Coronaviruses | 548 | ||
| Key points | 548 | ||
| TAXONOMY | 548 | ||
| Properties | 549 | ||
| Morphology and structure | 549 | ||
| Replication | 550 | ||
| Pathogenesis | 550 | ||
| Transmission | 551 | ||
| Epidemiology | 551 | ||
| SARS and MERS coronavirus | 551 | ||
| Clinical features | 552 | ||
| SARS and MERS coronaviruses | 552 | ||
| Gastrointestinal disease caused by coronaviruses and toroviruses | 552 | ||
| Laboratory investigation | 552 | ||
| Case study of the discovery of a new human pathogen, SARS coronavirus | 553 | ||
| Control | 554 | ||
| Treatment | 554 | ||
| Prevention | 554 | ||
| Recommended reading | 554 | ||
| Clinical scenario | 554.e1 | ||
| 55 Rhabdoviruses | 555 | ||
| Key points | 555 | ||
| Virus structure and life cycle | 555 | ||
| Virion morphology | 555 | ||
| Virus genome structure | 555 | ||
| Viral life cycle | 556 | ||
| Virus transmission, pathogenesis and treatment | 557 | ||
| Clinical features | 558 | ||
| Epidemiology | 558 | ||
| Laboratory Investigation | 559 | ||
| Diagnostic methods | 560 | ||
| Rabies virus antigen detection techniques | 560 | ||
| Rabies virus isolation | 560 | ||
| Histopathological examination | 560 | ||
| Serological assays | 560 | ||
| Molecular methods for the detection of rabies viral RNA | 560 | ||
| Prevention | 561 | ||
| Vaccination | 561 | ||
| Preexposure prophylaxis | 561 | ||
| Postexposure prophylaxis (PEP) | 561 | ||
| Control | 562 | ||
| Recommended reading | 562 | ||
| Websites | 562 | ||
| MCQs | 562.e1 | ||
| Clinical scenario | 562.e3 | ||
| Human case of rabies-encephalitis | 562.e3 | ||
| Learning points | 562.e4 | ||
| 56 Togaviruses | 563 | ||
| Key points | 563 | ||
| Description | 563 | ||
| Epidemiology | 563 | ||
| Replication (virology) | 563 | ||
| Clinical features | 564 | ||
| Postnatal primary rubella | 564 | ||
| Rubella reinfection | 564 | ||
| Congenital rubella | 564 | ||
| Pathogenesis | 565 | ||
| 5 Fungal pathogens, parasitic infections and medical entomology | 577 | ||
| 58 Fungi | 578 | ||
| Key points | 578 | ||
| Fungal diseases of humans | 579 | ||
| Fungal pathogens | 579 | ||
| Epidemiology | 579 | ||
| Types of infection | 579 | ||
| Superficial mycoses | 579 | ||
| Subcutaneous mycoses | 579 | ||
| Systemic mycoses | 579 | ||
| Incidence | 580 | ||
| Diagnosis | 580 | ||
| Clinical features | 580 | ||
| Laboratory investigation | 580 | ||
| Types of specimen | 580 | ||
| Direct microscopy | 580 | ||
| Histology | 581 | ||
| Culture | 581 | ||
| Serology | 581 | ||
| Polymerase chain reaction | 581 | ||
| Treatment | 581 | ||
| Superficial infections | 582 | ||
| Dermatophytosis | 582 | ||
| Epidemiology | 582 | ||
| Clinical features | 583 | ||
| Laboratory investigation | 584 | ||
| Collection of samples | 584 | ||
| Wood’s lamp | 584 | ||
| Hairbrush sampling | 584 | ||
| Processing of specimens | 584 | ||
| Direct microscopy | 585 | ||
| Culture | 585 | ||
| Treatment and prevention | 585 | ||
| Superficial candidosis | 585 | ||
| Epidemiology | 585 | ||
| Clinical features | 586 | ||
| Mucosal infection | 586 | ||
| Skin and nail infection | 586 | ||
| Chronic mucocutaneous candidosis | 586 | ||
| Laboratory investigation | 586 | ||
| Treatment and prevention | 587 | ||
| Pityriasis versicolor | 587 | ||
| Epidemiology | 587 | ||
| Clinical features | 587 | ||
| Laboratory investigation | 587 | ||
| Treatment | 587 | ||
| Other superficial infections | 588 | ||
| Skin and nail | 588 | ||
| Otomycosis | 588 | ||
| Mycotic keratitis | 588 | ||
| Subcutaneous infections | 588 | ||
| Mycetoma | 588 | ||
| Epidemiology | 588 | ||
| Clinical features | 589 | ||
| 6 Diagnosis, treatment and control of infection | 639 | ||
| 62 Infective syndromes | 640 | ||
| Key points | 640 | ||
| Specific syndromes | 640 | ||
| Upper respiratory tract | 640 | ||
| Pharyngitis | 640 | ||
| Sinusitis and otitis media | 642 | ||
| Lower respiratory tract | 642 | ||
| Epiglottitis | 642 | ||
| Pneumonia | 643 | ||
| Gastrointestinal infection | 644 | ||
| Acute diarrhoea | 644 | ||
| Intraabdominal sepsis, peritonitis, biliary sepsis and pancreatitis | 644 | ||
| Urinary tract infections | 644 | ||
| Infections of the central nervous system | 645 | ||
| Meningitis | 645 | ||
| Cerebral infections | 646 | ||
| Cardiovascular infections | 646 | ||
| Infective endocarditis | 646 | ||
| Infections associated with intravascular lines | 647 | ||
| Skin and soft tissue infections | 647 | ||
| Genital tract infections | 648 | ||
| Eye infections | 648 | ||
| Infection of bone and joints | 649 | ||
| Infective arthritis | 649 | ||
| Acute osteomyelitis | 649 | ||
| General syndromes | 649 | ||
| Fever of unknown origin | 649 | ||
| Sepsis | 650 | ||
| Travel-associated infections | 650 | ||
| Recommended reading | 651 | ||
| MCQs | 651.e1 | ||
| 63 Laboratory investigations | 652 | ||
| Key points | 652 | ||
| Collection of specimens | 653 | ||
| Transport | 655 | ||
| Reception | 655 | ||
| Specimen processing in the laboratory | 656 | ||
| Microscopy | 656 | ||
| Nonculture methods | 656 | ||
| Antigen detection | 656 | ||
| Nucleic acid–based tests | 657 | ||
| Detection of host immunological response to microorganisms | 657 | ||
| Laboratory culture of microorganisms | 657 | ||
| Identification | 658 | ||
| Point-of-care testing | 659 | ||
| Antimicrobial susceptibility testing | 659 | ||
| Communication of results of laboratory investigations | 659 | ||
| Notification of infectious diseases | 660 | ||
| Recommended reading | 660 | ||
| MCQs | 660.e1 | ||
| 64 Molecular methods in diagnostic microbiology | 661 | ||
| Key points | 661 | ||
| Introduction | 661 | ||
| Molecular diagnostics—the historical perspective | 661 | ||
| Molecular techniques—the gold standards | 662 | ||
| Global trends in molecular techniques | 662 | ||
| Molecular techniques: polymerase chain reaction (PCR) | 662 | ||
| Molecular characterisation | 664 | ||
| Selective fragment amplification typing methods | 664 | ||
| Developments in selective fragment amplification typing methods | 664 | ||
| Gel-based characterisation methods | 664 | ||
| Pulsed-field gel electrophoresis | 665 | ||
| Restriction fragment length polymorphism | 665 | ||
| Multiple-locus enzyme electrophoresis | 665 | ||
| Amplified fragment length polymorphism | 665 | ||
| Single-stranded conformational polymorphism analysis | 666 | ||
| Sequence-based detection and typing methods | 666 | ||
| Multilocus sequence typing | 666 | ||
| Matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) analysis | 668 | ||
| Pyrosequencing | 668 | ||
| Microarrays | 669 | ||
| Whole genome sequencing | 669 | ||
| Key challenges for the future | 669 | ||
| Recommended reading | 670 | ||
| MCQs | 670.e1 | ||
| 65 Management of antimicrobial chemotherapy | 671 | ||
| Key points | 671 | ||
| Principles of antimicrobial therapy | 671 | ||
| Principles of in vitro susceptibility testing and the different methods | 672 | ||
| Empiric and directed therapy | 675 | ||
| Selecting the right agent | 676 | ||
| Pharmacodynamics | 677 | ||
| Principles of using antimicrobials agents in prophylaxis | 678 | ||
| Antimicrobial stewardship | 678 | ||
| Recommended Reading | 680 | ||
| Websites | 680 | ||
| MCQs | 680.e1 | ||
| 66 Epidemiology and control of community infections | 681 | ||
| Key points | 681 | ||
| Introduction | 681 | ||
| Epidemiological principles | 682 | ||
| Definitions | 682 | ||
| The microorganism | 682 | ||
| The host | 683 | ||
| Herd immunity | 683 | ||
| The environment | 683 | ||
| Socioeconomic development and infection | 683 | ||
| Climate change | 683 | ||
| The spread of infection | 683 | ||
| Efficacy of transmission | 683 | ||
| Spread of infections | 684 | ||
| Infection spread directly from one person to another | 684 | ||
| Infection in which healthy carriers are involved | 684 | ||
| Infection in which persons harbour the organism before the onset of clinical illness | 684 | ||
| Infection derived from animal sources | 684 | ||
| Infections derived from environmental sources | 684 | ||
| Outbreaks of infection | 685 | ||
| Nomenclature of outbreaks | 685 | ||
| Types of outbreaks | 685 | ||
| Point source outbreak | 685 | ||
| Continuous common-source outbreak | 685 | ||
| Intermittent common-source outbreak | 686 | ||
| Propagated outbreak | 686 | ||
| Mixed outbreak | 686 | ||
| Analysis of outbreaks | 686 | ||
| Investigation of outbreaks | 687 | ||
| The application of new technologies to outbreak investigations | 688 | ||
| Control of outbreaks | 688 | ||
| Sources of infection | 688 | ||
| Route of transmission | 689 | ||
| Persons at risk | 690 | ||
| Mathematical models | 690 | ||
| Association and causation of infection | 690 | ||
| Conclusion | 691 | ||
| Acknowledgments | 691 | ||
| Recommended reading | 691 | ||
| Websites | 692 | ||
| MCQs | 692.e1 | ||
| 67 Healthcare–associated infections | 693 | ||
| Key points | 693 | ||
| Definition and classification | 693 | ||
| Epidemiology | 694 | ||
| Sources | 694 | ||
| Patients and staff as a source of infection | 695 | ||
| Inanimate reservoirs of infection | 695 | ||
| Role of antibiotic treatment | 695 | ||
| Common infections | 695 | ||
| Common organisms | 695 | ||
| Routes of transmission | 696 | ||
| Airborne transmission | 696 | ||
| Contact spread | 696 | ||
| Foodborne spread | 697 | ||
| Bloodborne spread | 697 | ||
| Prevention and control | 697 | ||
| Exclusion of sources of microorganisms from health-care settings | 697 | ||
| Interrupting spread of microorganisms from source to susceptible hosts | 698 | ||
| Enhancing the host’s ability to resist infection | 699 | ||
| Infection control policy | 699 | ||
| Surveillance and the role of the laboratory | 699 | ||
| Efficacy of infection control | 699 | ||
| Recommended reading | 700 | ||
| Websites | 700 | ||
| MCQs | 700.e1 | ||
| 68 Immunisation | 701 | ||
| Key points | 701 | ||
| Rationale of immunisation | 701 | ||
| Passive immunization | 701 | ||
| Pooled immunoglobulins | 702 | ||
| Specific immunoglobulins | 702 | ||
| Active immunisation | 702 | ||
| Types of vaccines | 702 | ||
| Toxoids | 702 | ||
| Inactivated killed vaccines | 702 | ||
| Attenuated live vaccines | 702 | ||
| Special procedures | 702 | ||
| Immune response | 702 | ||
| Duration of immunity | 703 | ||
| Age of commencement of active immunisation | 703 | ||
| Controlled studies of vaccines | 703 | ||
| Contraindications to the use of vaccines | 703 | ||
| Hazards of immunisation | 704 | ||
| Site of injection | 704 | ||
| Herd immunity | 705 | ||
| Immunisation programmes | 705 | ||
| Immunisation schedules | 705 | ||
| Notes on common vaccines in use | 705 | ||
| Adsorbed tetanus and diphtheria toxoid | 705 | ||
| Pertussis vaccine | 705 | ||
| Poliomyelitis vaccines | 707 | ||
| Haemophilus influenzae type B (Hib) vaccine | 707 | ||
| Meningococcal vaccines (MenC, Men B, MenACWY) | 707 | ||
| Pneumococcal vaccines | 707 | ||
| Measles, mumps and rubella (MMR) vaccine | 708 | ||
| Rotavirus | 708 | ||
| Human papillomavirus vaccine types 6, 11, 16 and 18 (HPV) | 708 | ||
| Hepatitis B vaccine | 708 | ||
| BCG | 709 | ||
| Other vaccines | 709 | ||
| Protecting the traveller | 709 | ||
| Unresolved problems | 709 | ||
| Recommended reading | 710 | ||
| Websites | 710 | ||
| MCQs | 710.e1 | ||
| Index | 711 | ||
| A | 711 | ||
| B | 713 | ||
| C | 715 | ||
| D | 719 | ||
| E | 720 | ||
| F | 721 | ||
| G | 722 | ||
| H | 723 | ||
| I | 725 | ||
| J | 727 | ||
| K | 727 | ||
| L | 727 | ||
| M | 728 | ||
| N | 731 | ||
| O | 732 | ||
| P | 732 | ||
| Q | 735 | ||
| R | 735 | ||
| S | 736 | ||
| T | 739 | ||
| U | 741 | ||
| V | 741 | ||
| W | 742 | ||
| X | 743 | ||
| Y | 743 | ||
| Z | 743 | ||
| Inside Back Cover | ibc1 |