Ananthanarayan and Paniker's Textbook of Microbiology

Part I General Microbiology

1. Introduction to Microbiology 1

Historical perspective and notable milestones in microbiology 1

Classification, nomenclature and taxonomy 3

2. Morphology and Physiology of Bacteria 7

Microscopy 7

Morphology of bacteria 10

Bacterial cell structure 10

–– Staining techniques 10

Shape of bacteria 13

Arrangement of bacteria 13

Bacterial anatomy 13

Cell envelope 14

Cell interior 16

Additional structures 17

Physiology of bacteria 20

Growth and multiplication of bacteria 20

Bacterial nutrition 22

Bacteriocins 23

3. Sterilisation and Disinfection 26

Sterilising agents 26

Physical agents 26

Chemical agents 31

Sterilisation and disinfection in a health care setting 35

–– Spaulding’s classification 35

–– New methods of sterilisation of

heat-sensitive articles 36

4. Culture and Identification of Bacteria 38

Culture media 38

Culture methods 41

Identification of bacteria 46

5. Genetics of Bacteria 53

Basic principles of molecular biology 53

–– Structure of DNA 53

–– Structure of RNA 54

Mutation 55

Gene transfer 56

Genetic mechanisms of drug resistance in bacteria 60

6. Molecular Techniques Applied to Microbiology 63

Molecular methods applied to disease detection and diagnosis 63

Application of genetic engineering in microbiology 66

Part II Immunology

7. Introduction to Infection and Immunity 68

Infection 68

Sources of infection 69

Methods of transmission of infection 70

Factors predisposing microbes to pathogenicity 70

Classification of infectious diseases 73

Immunity 73

Innate or native immunity 73

Acquired or adaptive immunity 77

Measurement of immune response 80

8. Structure and Functions of the Immune System 82

Central (primary) lymphoid organs 82

Peripheral (secondary) lymphoid organs 84

Cells of the lymphoreticular system 85

Major histocompatibility complex (MHC) 92

9. Antigens 97

Determinants of antigenicity 97

Antigenic specificity 98

Biological classes of antigens 99

Determinants recognised by the

innate immune system 100

10. Antibodies 103

Antibody structure 103

Immunoglobulin classes 106

Abnormal immunoglobulins 109

Immunoglobulin specificities 109

Antibody diversity 110

Class switching 111

Genetic regulation of immunoglobulins 111

Monoclonal antibodies 111

Humanised (chimeric) antibodies 113

Antibody engineering 113

11. Complement System 114

Properties of complement 114

Components of complement 114

Complement activation 115

Complement pathways 115

Regulation of complement activation 117

Biological effects of complement action 118

Quantitation of complement and its components 119

Biosynthesis of complement 120

Deficiencies of the complement system 120

12. Immune Response 122

Humoral immune response (antibody-mediated) 122

Cellular immune response / cell-mediated immunity (CMI) 127

Immunological tolerance 132

Factors affecting immunological tolerance 132

Theories of immune response 133

Idiotypes 134

13. Antigen–Antibody Reactions 136

Stages in antigen–antibody reactions 136

Uses of antigen–antibody

reactions 136

General features of antigen–antibody reactions 137

Reactions on which antigen–antibody

assays are based 137

Precipitation reaction 137

Agglutination reaction 140

Complement fixation test (CFT) 142

Neutralisation tests 143

Radioimmunoassay (RIA) 144

Enzyme immunoassay (EIA) 144

Chemiluminescence immunoassay (CLIA) 147

Immunoelectroblot / western blot techniques 147

Immunochromatographic assay / lateral flow assay 147

Immunoelectron microscopic assays 147

Immunofluorescence assay 147

14. Hypersensitivity 151

Classification of hypersensitivity reaction 151

Type I reactions

(immediate anaphylactic hypersensitivity) 152

Type II reactions: cytolytic and

cytotoxic reactions 155

Type III reactions: immune complex-mediated

hypersensitivity 156

Type IV reactions:

T cell-mediated hypersensitivity (delayed type) 156

15. Immunodeficiency Diseases 160

Primary immunodeficiencies 160

Disorders of specific immunity 160

Disorders of complement 164

Disorders of phagocytosis 164

Secondary immunodeficiencies 165

Laboratory methods to detect

immunodeficiency disorders 165

16. Autoimmunity and Immunohematology 168

Immunological tolerance 168

Mechanisms of autoimmunity 168

Classification of autoimmune diseases 169

Pathogenesis of autoimmune diseases 171

Laboratory tests to detect autoimmune disorders 171

Management of autoimmune disorders 172

Immunohematology 172

17. Immunology of Transplantation and Tumour

Immunity 176

Immunology of transplantation 176

Immunology of malignancy 182

Part III Bacteriology

18. Normal Microbial Flora of the Human Body 186

Role of normal microbial flora 186

Probiotics 188

Normal flora and the immune system 188

Therapeutic use of gut flora 188

19. Antimicrobial Agents 190

Mechanisms of action of antibiotics on

bacterial cells 190

Antimicrobial resistance 191

Antibiotic sensitivity tests 191

Antibiotic policy 194

–– Antibiotic stewardship 194

20. Staphylococci 196

Staphylococcus aureus 196

Other coagulase-positive staphylococci (CoPS) 202

Coagulase-negative staphylococci (CoNS) 202

Micrococci 202

21. Streptococci, Enterococci and Pneumococci 204

Streptococci 204

Streptococcus pyogenes group A streptococci (GAS)] 205

Other hemolytic streptococci 210

Other streptococci 211

Enterococci 212

Pneumococci 212

Streptococcus pneumoniae 212

22. Neisseria and Moraxella 218

Neisseria meningitidis 218

Neisseria gonorrhoeae 221

Non-gonococcal (non-specific) urethritis 223

Commensal neisseriae 223

Moraxella 224

23. Corynebacterium 225

Corynebacterium diphtheriae 225

Other pathogenic corynebacteria 230

Diphtheroids 230

Other coryneform bacteria 231

24. Bacillus 232

Bacillus anthracis 232

Anthracoid bacilli 236

Bacillus cereus 236

Bacillus thuringiensis 237

Bacillus species as sterilisation

indicators (controls) 237

25. Actinomycetes 238

Actinomyces 238

Nocardia 239

Mycetoma (bacterial) 240

–– Actinomycotic mycetoma 240

26. Clostridia 242

Clostridium perfringens 244

Clostridium septicum 246

Clostridium novyi (C. oedematiens) 246

Clostridium histolyticum 246

–– Gas gangrene 246

Clostridium tetani 249

–– Tetanus 250

Clostridium botulinum 252

–– Botulism 253

27. Non-sporing Anaerobic Bacteria 256

Anaerobic cocci 256

Non-sporing anaerobic gram-positive bacilli 256

Anaerobic gram-negative bacilli 257

Anaerobic infections 257

28. Mycobacteria I 260

Mycobacterium tuberculosis 260

Tuberculosis 262

Revised National Tuberculosis

Control Programme (RNTCP) 271

29. Mycobacteria II 273

–– Runyon classification 273

Mycobacterial skin infections 274

Mycobacterium leprae 275

Leprosy 276

30. Enteric Bacilli (Gram-Negative Rods) 281

Escherichia coli 281

Shigella 286

Salmonella 288

–– Enteric fever 290

–– Salmonella gastroenteritis 295

–– Salmonella septicemia 295

Yersinia enterocolitica 296

Edwardsiella tarda 296

Citrobacter diversus and Citrobacter freundii 296

Klebsiella pneumoniae 297

Enterobacter cloacae 298

Hafnia alvei 298

Serratia marcescens 298

Proteus 299

Morganella 299

Providencia 299

Erwinia herbicola 299

31. Vibrionaceae 301

Vibrio cholerae 301

Vibrio mimicus 308

Halophilic vibrios 308

Aeromonas and Plesiomonas 309

32. Gram-Negative Non-fermenters 310

Pseudomonas aeruginosa 310

Stenotrophomonas maltophila 312

Elizabethkingia meningosepticum 312

Alcaligenes and Achromobacter 312

Burkholderia 312

Acinetobacter 314

33. Haemophilus 316

Haemophilus influenzae 316

Haemophilus aegyptius 318

Haemophilus ducreyi 318

Haemophilus parainfluenzae 319

HACEK group of organisms 319

Aggregatibacter 319

Cardiobacterium 319

Kingella 319

Eikenella corrodens 320

34. Brucella and Bordetella 321

Brucella 321

Bordetella 324

Bordetella pertussis 324

Bordetella parapertussis 327

Bordetella bronchiseptica 327

35. Spirochetes 329

Treponema 330

Treponema pallidum 330

–– Syphilis 331

–– Non-venereal treponematoses 337

Non-pathogenic treponemes 338

Borrelia 339

Borrelia recurrentis (replapsing fever) 339

Borrelia vincentii (Vincent’s angina) 340

Borrelia burgdorferi (Lyme disease) 340

Leptospira 341

36. Chlamydia 345

Chlamydia trachomatis 348

–– Trachoma 348

–– Inclusion conjunctivitis 349

–– Infant pneumonia 349

–– Genital infections 349

Chlamydophila pneumoniae 350

Chlamydophila psittaci 350

–– Psittacosis 350

37. Mycoplasma and Ureaplasma 352

Mycoplasma 352

Ureaplasma urealyticum 354

–– Genital infections 354

––Mycoplasma as cell culture contaminants 355

38. Rickettsiae and Related Bacteria

(Arthropod-Borne Bacterial Infections) 356

Rickettsiae 356

Genus Rickettsia 356

–– Typhus fever group 357

–– Spotted fever group 359

Genus Orientia 359

Genus Ehrlichia 360

Genus Coxiella 361

Arthropod-borne bacterial infections 362

Bartonella bacilliformis 362

Bartonella (Rochalimaea) quintana 362

Bartonella henselae 362

39. Miscellaneous Bacteria Causing

Human Infections 364

Yersinia pestis 364

–– Plague 365

–– Yersiniosis 368

Pasteurella multocida 369

Francisella tularensis 369

Alcaligenes faecalis 369

Chromobacterium violaceum 369

Flavobacterium meningosepticum 369

Klebsiella granulomatis 369

Streptobacillus moniliformis and Spirillum minus 370

Campylobacter 371

Helicobacter pylori 372

Legionella pneumophila 373

Capnocytophaga 374

Gardnerella vaginalis 374

Moraxella (Branhamella) catarrhalis 374

Moraxella lacunata 374

Listeria monocytogenes 375

Erysipelothrix rhusiopathiae 375

Part IV Virology

40. Introduction to Virology 377

Morphology 377

Resistance of viruses to physical and

chemical agents 379

Viral replication 380

Viral genetics 382

Classification and nomenclature of

medically important viruses 384

Viroids 386

Prion 386

41. Basic Concepts of Viral Infections 388

Pathogenesis of viral infections 388

Host response to viral infections 390

Laboratory diagnosis of viral diseases 392

Cultivation of viruses 393

Viral assay 396

Assay of infectivity 396

Viral hemagglutination 396

Serological diagnosis 397

Molecular diagnosis 397

42. Bacteriophages 399

Morphology 399

Life cycle 399

Transmission of genetic information 401

Significance of phages in medical microbiology 401

Phage therapy 402

43. Herpesviruses 404

Herpes simplex virus 404

Varicella-zoster virus (VZV) 407

–– Varicella (Chickenpox) 407

Herpes zoster (shingles, zona) 409

Cytomegaloviruses 409

Epstein–Barr virus 411

–– Infectious mononucleosis (glandular fever) 412

Human herpesvirus types 6, 7, 8 413

Herpesvirus simiae: B virus 414

44. Pox and Other Viruses 416

Poxvirus 416

–– Variola and vaccinia 416

–– Smallpox 417

–– Other poxvirus diseases 418

Papillomavirus 418

Polyomavirus 419

Parvovirus 419

45. Adenovirus 421

Adenoviruses 421

Adeno-associated viruses (AAV) 423

46. Picornavirus 424

Enteroviruses 424

Poliovirus 425

Coxsackieviruses 430

Echoviruses 432

New enterovirus types 432

Rhinoviruses 433

47. Reoviridae 435

Reovirus 435

Orbivirus 435

Rotavirus 435

Other diarrheagenic viruses 436

–– Calicivirus 436

–– Adenovirus 436

–– Astrovirus 437

–– Coronavirus 437

48. Orthomyxovirus 438

Influenza virus 438

49. Paramyxovirus, Pneumovirus and Rubella 446

Antigenic structure of paramyxoviruses 446

Classification of paramyxoviruses 447

Parainfluenza virus 447

Mumps virus 447

Newcastle disease virus (NDV) 449

Pneumovirus 449

Respiratory syncytial virus (RSV) 449

Morbillivirus 450

Measles (Rubeola) virus 450

Nipah and Hendra viruses 453

Human metapneumovirus 454

Rubella virus 454

50. Arthropod- and Rodent-Borne Viral Infections 457

Arthropod-borne viruses 457

Togaviridae 460

–– Alphavirus 460

Flaviviridae 461

Filoviridae 465

Bunyaviridae 467

Reoviridae 467

Ungrouped arboviruses 468

Rodent-borne viruses 468

51. Rhabdovirus and Other Viral and

Prion Diseases 470

Rabies 470

Slow virus diseases 477

52. Hepatitis Viruses 480

Types of viral hepatitis 480

Hepatitis A virus (HAV) 480

Hepatitis B virus (HBV) 482

Hepatitis C virus (HCV) 489

Hepatitis D (delta) virus (HDV) 490

Hepatitis E virus (HEV) 490

Hepatitis G virus (HGV) 491

53. Retrovirus 493

Human immunodeficiency virus (HIV) 493

Acquired immune deficiency syndrome (AIDS) 498

54. Oncogenic Viruses and

Other Miscellaneous Viruses 510

Oncogenic viruses 510

Oncogenic DNA viruses 511

Oncogenic RNA viruses 512

Oncogenes 514

Miscellaneous viruses 515

–– Human papillomaviruses 515

–– Human polyomaviruses 515

–– Parvoviruses 515

Viral hemorrhagic fevers 516

–– Arenaviruses 516

–– Filoviruses 516

Coronaviruses 517

–– Severe acute respiratory syndrome (CoV-SARS) 518

––MERS-CoV 518

–– COVID-19 519

55. Antiviral Chemotherapy and

Immunoprophylaxis 521

Inhibitors of nucleic acid synthesis 522

Protease inhibitors 522

Other types of antiviral agents 522

Interferons 523

Resistance to antiviral agents 523

Immunoprophylaxis of viral diseases 523

Part V Medical Mycology

56. Basic Mycology and Superficial Mycoses 526

Characteristics of fungi 526

Classification of fungi 526

Superficial mycoses 529

–– Cutaneous mycoses 529

–– Subcutaneous mycoses 534

57. Systemic Fungal Infections 541

Systemic mycoses (dimorphic fungi) 541

Histoplasmosis 541

Blastomycosis 542

Paracoccidioidomycosis 543

Coccidioidomycosis 543

Treatment of systemic mycoses 544

Opportunistic mycoses 545

Aspergillosis 545

Penicillosis 547

Zygomycosis (mucormycosis, phycomycosis) 547

Candidosis (candidiasis/moniliasis) 548

Cryptococcosis (torulosis) 550

Pneumocystis jirovecii 551

Specific fungal infections 552

Otomycosis 552

Oculomycosis (keratomycosis,

fungal keratitis, mycotic keratitis) 552

Mycotic poisoning 553

58. Laboratory Diagnosis of Fungal Infections 556

Specimen 556

Laboratory methods of isolation and identification 556

Treatment 559

Part VI Clinical Microbiology as Applied to Infectious

Diseases

59. Diagnostic Microbiology 560

Specimen collection and transport (pre-test) 561

Processing of samples in the laboratory

(test procedure) 561

Reporting of results (post-test) 562

Quality control in a clinical microbiology laboratory 563

60. Systemic Infections and

Their Laboratory Diagnosis 565

CVS and bloodstream infections 565

Fever of unknown origin 569

Gastrointestinal and hepatobiliary tract infections 572

Skin, soft tissue and musculoskeletal infections 575

Central nervous system infections 578

Respiratory tract infections 582

Genitourinary and sexually transmitted infections 585

Vector-borne and zoonotic diseases 591

Miscellaneous infections 592

Congenital infections 594

61. Emerging and Re-emerging Infections 596

Disease transmission from animals to humans 596

Public health emergency infections 596

–– Zika virus disease 597

Indian scenario of various infections 597

Drug resistance 598

Bioterrorism 598

Communicable disease programmes

under the national health mission 598

62. Health Care-Associated Infections 601

Common types of health care-associated infections 602

Sources and reservoirs of health

care-associated infections 604

Measures to control Infection in the

health care setting 605

Investigation and follow-up of outbreaks of disease 608

Monitoring and regulation of HCAI:

Hospital Infection Control Committee (HICC) 609

63. Immunoprophylaxis 610

Active immunisation 610

Passive immunisation 612

Combined active and passive immunisation 612

Individual immunisation 612

Vaccination during outbreaks 613

Newer vaccines in the experimental or

clinical trial stages 613

Immunomodulation 613

64. Bacteriology of Water, Air, Milk and Food 615

65. Biomedical Waste Management 623

Types of biomedical waste 623

General principles of waste management 624

Steps in waste management 624

Methods of waste management 624

Spill management 624

BMW rules 2016, amended in 2018 625

66. Quality Control and Recent Advances

in Diagnostic Microbiology 627

Automated and semi-automated systems

for culture 627

Molecular methods 627

Quality control and accreditation of laboratories 629

Further Reading 631

Index 634

First published in 1978, Ananthanarayan and Paniker’s Textbook of Microbiology has been a trusted textbook on microbiology for more than four decades and has evolved with the rapidly changing field of medical microbiology. To stay abreast of recent developments across the global and local infectious disease spectra, the new Competency-Based Medical Education (CBME) curriculum is aimed at integrating microbiology into the system-based approach to human disease. The eleventh edition of Ananthanarayan and Paniker's Textbook of Microbiology has been revised to address this restructuring of the curriculum and to make it better suited for the shorter course duration and system-based integration. Chapters have been pruned without compromising on essential elements which have been presented in a lucid style and flow for an easy and enjoyable reading experience. Several clinical and laboratory images have been updated and line diagrams included for better visual impact and comprehension. Recent advances in disease detection, molecular diagnosis, quality control, infection prevention and control, public­ health and epidemiology and preventive strategies including national programmes have been brought up to date. An entire chapter (chapter 60) has been devoted to the essence of the competency-based integrated approach to system-wise infectious diseases. This chapter delves into the entire gamut of organisms involved in infectious diseases commonly affecting various systems of the human body and will pave the way for the study of pathogenic microorganisms as individuals and as groups. The traditional approach to the learning and understanding of the microbe–host–environment interaction, pathogenesis, clinical presentations, diagnosis, treatment and prevention of infections has been retained.