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.
Editor: Reba Kanungo is Dean of Research, and Professor and Head of the Department of Microbiology, Pondicherry Institute of Medical Sciences (PIMS), prior to which she taught at JIPMER for over 15 years. She is a member of several national and international organisations, as well as of the committees of NACO, ICMR and CTD. Dr Kanungo is the Editor-in-Chief of JCRSM, former Editor, IJMM, and past President, IAMM. She is on the editorial boards of several national and international journals, and has published over 100 research papers and editorials.
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
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