Mims" Medical Microbiology (ebook)

Acknowledgements vi

Contributors vi

Student Consultants vii

A contemporary approach to microbiology xi

Microbes and parasites xi

The context for contemporary medical

microbiology xi

Microbiology past, present and future xii

The approach adopted in this book xiv

SECTION 1 THE ADVERSARIES ? MICROBES

1. Microbes as parasites 3

The varieties of microbes 3

Living inside or outside cells 4

Systems of classification 5

2. The bacteria 7

Structure 7

Nutrition 9

Growth and division 10

Gene expression 11

Survival under adverse conditions 16

Mobile genetic elements 16

Mutation and gene transfer 20

The genomics of medically important bacteria 23

3. The viruses 27

Infection of host cells 27

Replication 29

Outcome of viral infection 31

Major groups of viruses 33

4. The fungi 37

Major groups of disease-causing fungi 37

5. The protozoa 41

6. The helminths and arthropods 43

The helminths 43

The arthropods 46

7. Prions 49

?Rogue protein? pathogenesis 49

Development, transmission and diagnosis

of prion diseases 50

Prevention and treatment of prion diseases 51

8. The host?parasite relationship 53

The normal flora 53

Symbiotic associations 56

The characteristics of parasitism 58

The evolution of parasitism 59

SECTION 2 THE ADVERSARIES?HOST DEFENCES

9. The innate defences of the body 67

Defence against entry into the body 67

Defences once the microorganism

penetrates the body 68

10. Adaptive responses provide a ?quantum leap?

in effective defence 83

The role of antibodies 83

The role of T lymphocytes 86

Extracellular attack on large infectious agents 89

Local defences at mucosal surfaces 90

11. The cellular basis of adaptive immune

responses 95

B- and T-cell receptors 98

Clonal expansion of lymphocytes 98

The role of memory cells 99

Stimulation of lymphocytes 101

Cytokines 102

Regulatory mechanisms 105

Tolerance mechanisms 106

SECTION 3 THE CONFLICTS

12. Background to the infectious diseases 111

Host?parasite relationships 111

Causes of infectious diseases 115

The biologic response gradient 117

13. Entry, exit and transmission 119

Sites of entry 119

Exit and transmission 125

Types of transmission between humans 127

Transmission from animals 132

14. Immune defences in action 137

Complement 137

Acute phase proteins and pattern

recognition receptors 137

Fever 139

Natural killer cells 139

Phagocytosis 139

Cytokines 142

Antibody-mediated immunity 144

Cell-mediated immunity 146

Recovery from infection 149

15. Spread and replication 153

Features of surface and systemic infections 154

Mechanisms of spread through the body 155

Genetic determinants of spread and replication 158

Other factors affecting spread and replication 159

16. Parasite survival strategies and persistent

infections 163

Parasite survival strategies 164

Antigenic variation 169

Immunosuppression 170

Persistent infections 173

17. Pathologic consequences of infection 179

Pathology caused directly by microorganism 179

Diarrhea 183

Pathologic activation of natural

immune mechanisms 183

Pathologic consequences of the

immune response 187

Skin rashes 191

Viruses and cancer 192

SECTION 4 CLINICAL MANIFESTATION AND

DIAGNOSIS OF INFECTIONS BY BODY SYSTEM

Introduction to Section 4: The clinical

manifestations of infection 197

18. Upper respiratory tract infections 199

Rhinitis 199

Pharyngitis and tonsillitis 200

Parotitis 208

Otitis and sinusitis 209

Acute epiglottitis 210

Oral cavity infections 210

19. Lower respiratory tract infections 213

Laryngitis and tracheitis 213

Diphtheria 213

Whooping cough 214

Acute bronchitis 215

Acute exacerbations of chronic bronchitis 216

Bronchiolitis 216

Respiratory syncytial virus infection 216

Hantavirus pulmonary syndrome (HPS) 217

Pneumonia 217

Bacterial pneumonia 218

Viral pneumonia 221

Parainfluenza virus infection 221

Adenovirus infection 223

Human metapneumovirus 223

Human bocavirus 223

Influenza virus infection 223

Severe acute respiratory syndrome-associated

coronavirus infection 228

Measles 229

Cytomegalovirus infection 230

Tuberculosis 230

Cystic fibrosis 233

Lung abscess 233

Fungal infections 234

Parasitic infections 235

20. Urinary tract infections 237

Acquisition and aetiology 237

Pathogenesis 238

Clinical features and complications 240

Laboratory diagnosis 241

Treatment 242

Prevention 243

21. Sexually transmitted infections 245

STIs and sexual behaviour 245

Syphilis 245

Gonorrhoea 249

Chlamydial infection 251

Other causes of inguinal lymphadenopathy 253

Mycoplasmas and non-gonococcal urethritis 255

Other causes of vaginitis and urethritis 255

Genital herpes 256

Human papillomavirus infection 257

Human immunodeficiency virus 257

Opportunist STIs 267

Arthropod infestations 267

22. Gastrointestinal tract infections 269

Diarrheal diseases caused by bacterial or viral

infection 270

Food poisoning 283

Helicobacter pylori and gastric ulcer disease 284

Parasites and the gastrointestinal tract 284

Systemic infection initiated in the

gastrointestinal tract 291

23. Obstetric and perinatal infections 303

Infections occurring in pregnancy 303

Congenital infections 303

Infections occurring around the time of birth 308

24. Central nervous system infections 311

Invasion of the central nervous system 311

The body?s response to invasion 311

Meningitis 313

Encephalitis 319

Neurologic diseases of possible viral aetiology 324

Spongiform encephalopathies caused

by scrapie-type agents 324

CNS disease caused by parasites 324

Brain abscesses 325

Tetanus and botulism 326

25. Infections of the eye 329

Conjunctivitis 329

Infection of the deeper layers of the eye 332

26. Infections of the skin, soft tissue, muscle and

associated systems 335

Bacterial infections of skin, soft tissue and

muscle 337

Mycobacterial diseases of the skin 343

Fungal infections of the skin 345

Parasitic infections of the skin 350

Mucocutaneous lesions caused by viruses 351

Smallpox 358

Measles 358

Rubella 360

Other infections producing skin lesions 361

Kawasaki syndrome 361

Viral infections of muscle 361

Parasitic infections of muscle 362

Joint and bone infections 363

Infections of the haemopoietic system 365

27. Vector-borne infections 367

Arbovirus infections 367

Infections caused by rickettsiae 369

Borrelia infections 373

Protozoal infections 375

Helminth infections 380

28. Multisystem zoonoses 383

Arenavirus infections 383

Haemorrhagic fever with renal syndrome

(HFRS) 385

Marburg and Ebola haemorrhagic fevers 385

Crimean?Congo haemorrhagic fever,

a tick-borne virus 385

Q fever 386

Anthrax 386

Plague 387

Yersinia enterocolitica infection 389

Tularemia 389

Pasteurella multocida infection 389

Leptospirosis 389

Rat-bite fever 390

Brucellosis 390

Helminth infections 391

29. Fever of unknown origin 395

Definitions of fever of unknown origin 395

Causes of FUO 395

Investigation of classic FUO 396

Treatment of FUO 399

FUO in specific patient groups 399

Infective endocarditis 400

30. Infections in the compromised host 403

The compromised host 403

Infections of the host with deficient innate

immunity due to physical factors 405

Infections associated with secondary adaptive

immunodeficiency 408

Other important opportunist pathogens 409

SECTION 5 DIAGNOSIS AND CONTROL

31. Diagnosis of infection and assessment of host

defense mechanisms 419

Aims of the clinical microbiology laboratory 419

Specimen processing 419

Non-cultural techniques for the laboratory

diagnosis of infection 420

Cultivation (culture) of microorganisms 428

Identification of microorganisms

grown in culture 429

Antibody detection methods for the

diagnosis of infection 432

Assessment of host defence systems 432

Putting it all together: detection, diagnosis,

and epidemiology 436

32. Epidemiology and control of infectious

diseases 439

Outcome measurements 439

Types of epidemiological studies 439

Transmission of infectious disease 444

Vaccine efficacy 446

33. Attacking the enemy: antimicrobial agents

and chemotherapy 447

Selective toxicity 447

Discovery and design of antimicrobial agents 447

Classification of antibacterial agents 448

Resistance to antibacterial agents 449

Classes of antibacterial agents 452

Inhibitors of cell wall synthesis 452

Inhibitors of protein synthesis 458

Inhibitors of nucleic acid synthesis 465

Antimetabolites affecting nucleic acid synthesis 467

Other agents that affect DNA 469

Inhibitors of cytoplasmic membrane function 469

Urinary tract antiseptics 470

Antituberculosis agents 470

Antibacterial agents in practice 471

Antibiotic assays 473

Antiviral therapy 473

Antifungal agents 481

Antiparasitic agents 483

Control by chemotherapy versus vaccination 483

Control versus eradication 487

Use and misuse of antimicrobial agents 487

34. Protecting the host: vaccination 491

vaccination - A four hundred year history 491

Aims of vaccination 491

Vaccines can be of different types 493

35. Passive and non-specific immunotherapy 505

Passive immunization with antibody 505

Non-specific cellular immunostimulation 508

Correction of host immunodeficiency 509

Probiotics 510

36. Hospital infection, sterilization and

disinfection 511

Common hospital infections 511

Important causes of hospital infection 511

Sources and routes of spread of

hospital infection 513

Host factors and hospital infection 514

Consequences of hospital infection 515

Prevention of hospital infection 517

Investigating healthcare-associated infection 521

Sterilization and disinfection 526

Online only ? Pathogen parade

Bibliography 531

Index 539