The 13th edition of Ananthanarayan and Paniker’s Textbook of Microbiology, has been meticulously developed to align with the principles of the competency-based medical education (CBME) curriculum prescribed by the National Medical Council (NMC).
The content in this edition has been curated not only to cover the essential aspects of microbiology but also to foster the development of core competencies that are vital for medical practice. The approach integrates foundational knowledge with clinical applications, encouraging learners to bridge the gap between theoretical understanding and practical patient care.
The introduction to bacteriology has been split into two chapters—Basic Concepts of Bacteriology, which deals with concepts such as staining, growth characteristics, and identification methods, and Systematic Bacteriology, which has been expanded to include the virulence factors and diseases caused by various organism groups.
Content has been revised to include updated information on plasma sterilisation, CSSD, and the care bundle approach. New techniques such as VITEK, BioFilm Array, and AST have been added. In the section on applied microbiology, various infective syndromes have been discussed, along with their causative organisms, epidemiology, relevant investigations, treatment, and prevention, in keeping with the syndromic approach prescribed by the NMC. Parasitology has been integrated into all the syndromes. Topics such as HIV, direct-acting antivirals, National Hepatitis Control Programme guidelines, and zoonotic diseases have also been updated. A new chapter has been added on the AETCOM elements applicable to microbiology.
Dr Sonal Saxena is Director Professor and Head of the Department of Microbiology at Maulana Azad Medical College, New Delhi. She obtained her MBBS and MD degrees from the aforementioned institution and possesses over 28 years of extensive teaching experience. Dr Saxena successfully completed the esteemed FAIMER fellowship in 2023 and was awarded the WHO fellowship in Antimicrobial Resistance at the Karolinska Institutet, Stockholm. Additionally, she serves as the Secretary of the Indian Association of Medical Microbiologists.
Part I General Microbiology 1. History and scope of microbiology (Competency MI1.1) • Historical perspective • Scope of microbiology 2. Microscopy (Competency MI1.1) • Optical or light microscopy • Phase contrast microscopy • Dark-field microscopy • Fluorescence microscopy • Differential interference contrast microscopy • Confocal scanning laser microscopy • Electron microscopy • Atomic force microscopy
3. Basic concepts of bacteriology (Competency MI1.2 and 1.3) • Staining • Morphology and physiology of bacteria • Growth and nutrition, isolation, and identification for the laboratory diagnosis of bacterial infections 4. Systematic bacteriology (Competency MI1.1–1.3, 8.9–8.13) • Classification, nomenclature, and taxonomy of bacteria • General concepts of pathogenesis and disease spectrum • Gram-positive cocci and bacilli • Gram-negative cocci and bacilli • Mycobacteria • Miscellaneous bacteria • Normal flora of the human body • Principles of laboratory diagnosis
5. Basic concepts of virology (Competency MI 1.1–1.3, 8.3, 8.9–8.13) • General virology • DNA viruses • RNA viruses • General concepts in the pathogenesis of viral infections • Classification of viruses • Replication of viruses • Viral genetics • Pathogenesis of viral infections • Laboratory diagnosis of viral diseases • Prions • Bacteriophages
6. Basic concepts of mycology (Competency MI 1.1–1.3, 8.3, 8.9–8.13) • General characteristics of fungi • Classification of fungi • Pathogenesis of fungal infections • Laboratory diagnosis of fungal infections 7. Basic concepts of medical parasitology (Competency MI 1.1–1.3, 8.9–8.13) • General parasitology: nomenclatures and definitions • Classification of parasites • Protozoa • Helminths • Characteristics, life cycles, and modes of transmission of parasites • Concepts of the pathogenesis of parasitic infections • Laboratory diagnosis of parasitic diseases
8. Microbial genetics (Competency MI 1.1) Principles of molecular biology • Structure of DNA and RNA • Mutations • Clinical applications • Gene transfer in bacteria • Gene sequencing • Application of genetic engineering in microbiology
9. Epidemiology of infectious diseases (Competency MI 1.3) Communicable disease • Sources of infection • Routes of transmission of infection • Host–parasite interaction • Microbial factors predisposing to infection • Epidemiology of infections
10. Sterilisation and disinfection (Competency MI 1.4, 1.5) • Sterilising agents – Spaulding’s classification – Physical agents – Chemical sterilants – Plasma sterilisation – Gas sterilisation – Biological indicators • Disinfection – Chemical agents – Testing of disinfectants • Applications in healthcare settings • CSSD • Bacteriology of water, air, milk, and food
11. Antimicrobial agents (Competency MI 1.6) • Antibacterial agents – Mechanisms of action of antibiotics on bacterial cells – Antimicrobial resistance – Antibiotic sensitivity tests – Antibiotic policy and antibiotic stewardship • Antiviral agents • Antifungal agents • Antiprotozoal agents • Anthelmintic agents
12. Healthcare-associated infections and their control (Competency MI 8.5–8.7) • Types of healthcare-associated infections • Standard precautions for hospital infection control • Biomedical waste management • Infection control practices in the hospital
Part II Immunology 13. Immunological mechanisms in health (Competency MI 1.7) • Innate immunity • Acquired or adaptive immunity • Cells involved in immune response – T cells – B cells – Null cells – Phagocytic cells • Abnormalities of immune cells
14. Antigens, antibodies, and the complement system (Competency MI 1.7 and 1.8) • Antigens – Determinants of antigenicity – Biological classes of antigens • Antibodies – Antibody structure – Immunoglobulin classes – Immunoglobulin specificities – Antibody diversity – Genetic regulation of immunoglobulins – Monoclonal antibodies • Complement – Components of complement – Complement pathways – Biological effects of complement action – Quantitation of complement and its components
15. Mechanisms of immune response (Competency MI 1.8) • Humoral immune response (antibody-mediated) – Primary and secondary responses – Antigen processing – Elimination of antigens – Factors influencing antigen–antibody reactions – Outcomes of antigen–antibody reactions – Adjuvants – Immunosuppressive agents • Cellular immune response/cell-mediated immunity – Delayed-type hypersensitivity – Cytotoxic T lymphocyte-mediated response – Induction of CMI • Paths of humoral and cellular immune responses • Immunological tolerance • Theories of immune response
16. Laboratory methods used in the detection of immunological response (antigen–antibody reactions) (Competency MI 1.10) • Precipitation test • Agglutination test • Complement fixation test • Neutralisation test • Enzyme immunoassay (EIA) • Chemiluminescence immunoassay (CLIA) • Immunoelectroblot/Western blot techniques • Immunoelectron microscopic assays • Immunochromatographic (ICT) assay/Lateral flow assay • Immunofluorescence assay • Immunohistochemical techniques • Flow cytometry • Detection of cell-mediated immmnity 17. Hypersensitivity (Competency MI 1.10) • Type I (Immediate anaphylactic hypersensitivity) • Type II (Cytolytic/cytotoxic hypersensitivity) • Type III (Immune complex-mediated hypersensitivity) • Type IV (Delayed-type T cell-mediated hypersensitivity) 18. Autoimmune disorders and immunodeficiency states (Competency MI 1.10) • Autoimmune disorders – Immunological tolerance – Autoimmunity • Immunodeficiency – Primary immunodeficiency – Disorders of specific immunity – Secondary immunodeficiencies – Laboratory methods to detect immunodeficiency disorders 19. Immunological mechanisms of transplantation, immunohematology, and tumour Immunity (Competency MI 1.11) • Immunology of transplantation – Major histocompatibility complex – Transplantation reaction – Graft-versus-host reaction – Laboratory tests required prior to transplantation – Immunosuppression – Privileged sites – Other sources of transplants – Post-transplant infections • Immunohematology – ABO system – Rh blood group system – Medical implications of blood groups • Immunology of malignancy – Tumour antigens – Immunological surveillance – Immunotherapy of cancer 20. Immunoprophylaxis (Competency MI 1.9) • Active immunisation • Passive immunisation • Combined active and passive immunisation • Individual immunisation • Vaccination during outbreaks and pandemics • Newer vaccines
Part III Microbiology as Applied to Infectious Diseases 21. Cardiovascular and bloodstream infections (Competency MI 2.1–2.6) • Cardiovascular infections – Acute rheumatic fever—Group A Streptococcus – Rheumatic heart disease – Other CVS infections – Infective endocarditis – Myocarditis and pericarditis • Infections of the bloodstream • Fever of unknown origin • Fever due to infections transmitted by blood transfusion • Bacterial bloodstream infections – Staphylococcus aureus – Coagulase-negative staphylococci (CoNS) • Bacterial bloodstream infections causing fever – Enteric fever—Salmonella – Non-typhoid salmonellosis – Plague—Yersinia pestis – Leptospirosis—Leptospira – Brucellosis—Brucella species – Scrub typhus—Orientia tsutsugamushi – Ehrlichiosis—Ehrlichia – Q fever—Coxiella burnetii – Epidemic typhus—Rickettsia prowazeki – Recrudescent typhus (Brill-Zinsser disease) – Endemic typhus (flea-borne typhus)—Rickettsia typhi – Trench fever—Bartonella quintana – Oroya fever—Bartonella bacilliformis • Viral bloodstream infections • Viral hemorrhagic fever (VHF) – Arthopod-borne hemorrhagic fever
– Crimean Congo hemorrhagic fever—CCHF virus – Rodent-borne hemorrhagic fevers
– Filoviral hemorrhagic fevers
• Fungal bloodstream infections – Candidiasis—Candida • Parasitic infections of the bloodstream – Malaria—Plasmodium – Kala-azar/Visceral leishmaniasis—Leishmania – Trypanosomiasis—Trypanosoma
– Babesiosis—Babesia – Lymphatic filariasis
– Schistosomiasis
• Infections causing anemia
22. Acquired immunodeficiency syndrome (AIDS) (Competency MI 2.7, 8.15, and 8.16) • Morphology of HIV • Viral genes and antigens • Antigenic variation and diversity of HIV • Subtypes of HIV • Pathogenesis • Clinical features • Opportunistic infections • Laboratory diagnosis of HIV and AIDS • NACO strategies for HIV testing • Prognosis of HIV • Prophylaxis • Antiretroviral treatment • Post-exposure prophylaxis
23. Infections of the respiratory system (Competency MI 6.1–6.3 • Upper respiratory tract infections (URI) – Streptococcal throat infection—Streptococcus pyogenes – Diphtheria—Corynebacterium diphtheriae • Miscellaneous bacterial URIs – Vincent’s angina – Borrelia vincentii – Fusobacterium fusiforme – Moraxella catarrhalis • Viral URIs – Common cold—Adenovirus – Influenza—Influenza virus – Parainfluenza—Parainfluenza virus – Mumps—Mumps virus – Measles—Measles virus – Respiratory syncytial viral infections (RSV) – Rhinoviral disease—Rhinovirus – Newcastle viral disease—Newcastle virus – Rubella (German measles)—Rubella virus – Herpes viral infections of respiratory tract
• Infections in the oral cavity – Oral candidiasis—Candida – Periodontal infection – Dental caries • Lower respiratory tract infections – Lung abscess, empyema, pneumonia – Bacterial pneumonia
– Viral pneumonia
– Fungal pneumonia
– Parasitic lung infections
• Secondary parasitic infections of the lung – Amoebic lung abscess – Schistosomiasis – Echinococcosis – Loeffler’s syndrome – Tropical pulmonary eosinophilia (occult filariasis) – Alveolar echinococcosis (AE) • Tuberculosis—Mycobacterium tuberculosis • Prevention of respiratory infections
24. Central nervous system infections (Competency MI 5.1–5.3) • Meningitis • Encephalitis • Brain abscess – Acute bacterial (pyogenic) meningitis – Meningococcal meningitis—Neisseria meningitidis – Neonatal meningitis—Streptococcus agalactiae – Listeriosis—Listeria monocytogenes • Chronic bacterial meningitis – Tetanus—Clostridium tetani – Botulism—Clostridium botulinum • Aseptic viral meningitis – Enteroviral infections
– Rabies—Rabies virus • Slow viral diseases – Subacute sclerosing panencephalitis (SSPE) – Progressive multifocal leukoencephalopathy (PML) – Prion diseases • Arboviral diseases – Encephalitis
• Fever with arthritis—Chikungunya virus • Parasitic CNS infections – Taeniasis—Taenia solium – Neurocysticercosis (NCC) – Primary amoebic meningoencephalitis (PAM)—Naegleria fowleri – Granulomatous amoebic encephalitis (GAE)—Acanthamoeba species – Toxoplasmosis—Toxoplasma gondii – Trypanosomiasis—Trypanosoma • Fungal CNS infections – Candidiasis—Candida – Cryptococcal meningitis—Cryptococcus – Histoplasmosis—Histoplasma – Microsporidiosis—Encephalitozoonii
25. Gastrointestinal infections (Competency MI 3.1–3.8) • Bacterial gastrointestinal infections • Salmonellosis—Non-typhoidal salmonellae • Diarrheal diseases—Escherichia coli • Cholera—Vibrio cholerae • Shigellosis—Shigella • Campylobacteriosis—Campylobacter • Peptic ulcer disease—Helicobacter pylori • Pseudomembranous colitis (PMC)—Clostridioides difficile • Food poisoning – Staphylococcus aureus – Botulism—C. botulinum – Clostridium perfringens – Bacillus cereus • Fungal causes of food poisoning – Mycotoxicoses – Mycetism • Viral gastroenteritis – Rotavirus – Calicivirus – Norwalk virus – Adenovirus – Astrovirus – Coronavirus • Parasitic infections of the gastrointestinal tract – Giardiasis—Giardia duodenalis – Opportunistic GI infections
– Parasitic dysentery
– Helminthiasis
– Visceral larva migrans
– Intestinal cestode infections
– Intestinal trematode infestation
26. Hepatobiliary infections (Competency MI 3.7 and 3.8) • Viral hepatitis • Enteric viral hepatitis – HAV – HEV • Bloodborne or serum hepatitis – HBV – HCV – HDV – HGV – Yellow fever • Parasitic infections of the liver – Hydatid cyst—Echinococcus granulosus – Alveolar echinococcosis—Echinococcus multilocularis – Fascioliasis—Fasciola hepatica – Clonorchiasis—Clonorchis sinensis – Opisthorchiasis—Opisthorchis • Liver abscess • Biliary tract infections
27. Genitourinary and sexually transmitted infections (Competency MI 7.1 and 7.3) • Bacterial STIs – Gonorrhea—Neisseria gonorrhoeae – Non-gonococcal (non-specific) urethritis
– Lymphogranuloma venereum—Chlamydia trachomatis serovar L1-L3 – Syphilis—Treponema pallidum – Non-venereal treponematoses—Yaws, bejel, and pinta – Chancroid—Haemophilus ducreyi – Donovanosis—Klebsiella granulomatis • Viral STIs – Genital warts—Human papillomavirus – Genital herpes—Herpes simplex virus • Parasitic STIs – Vaginitis—Trichomonas vaginalis – Urogenital schistosomiasis—Schistosoma haematobium
28. Urinary tract infections (Competency MI 7.3) • Types of UTIs • Predisposing factors • Pathogenesis • Etiology • Clinical features • Laboratory diagnosis • Treatment
29. Skin, soft tissue, and musculoskeletal infections (Competency 41.–4.3) • Bacterial infections of the skin and soft tissues
– Streptococcal skin infections – Staphylococcal scalded skin syndrome (SSSS) – Other staphylococcal skin diseases – Erythrasma—Corynebacterium minutissimum – Anthrax—Bacillus anthracis – Gas gangrene
– Bacterial mycetoma
– Melioidosis—Burkholderia pseudomallei – Glanders—Burkholderia mallei – Lyme disease—Borrelia burgdorferi – Skin diseases by non-tuberculous mycobacteria
• Viral infections of the skin and soft tissues – Varicella (chickenpox)—Varicella-zoster virus (VZV) – Herpes-zoster (shingles, zona)—VZV – Hand, foot, and mouth disease—Coxsackievirus A16 and enterovirus A71 – Erythema infectiosum—Parvovirus B19 – Exanthema subitem or roseola infantum—HHV6 – Poxviral diseases—Monkeypox, orf, cowpox – Molluscum contagiosum—Molluscum contagiosum virus – Skin warts—Human papilloma virus • Parasitic infections of the skin and subcutaneous tissues – Protozoan infections of the skin
– Nematodes affecting the skin
– Cestodes affecting the skin
– Trematodes affecting the skin
– Ectoparasites • Fungal infections of the skin – Superficial mycoses
– Subcutaneous mycoses
30. Infections of the eyes and ears and congenital infections (Competency MI 8.15) • Infections of the eyes • Infections of the ear • Congenital infectious syndromes – Congenital cytomegalovirus infection – Congenital herpes simplex – Fetal varicella syndrome – Congenital Zika syndrome – Congenital parvovirus infection – Congenital syphilis – Congenital listeriosis – Congenital malaria – Congenital trypanosomiasis/leishmaniasis
31. Zoonotic and vector-borne infections (Competency MI 8.1) • Zoonotic infections • Vector-borne infections • Control of zoonotic and vector-borne infections • Cat scratch disease—Bartonella henselae • Rat bite fever—Bartonella henselae, Streptobacillus moniliformis, Spirillum minus • One health
32. Opportunistic infections (Competency MI 8.2) • Cytomegaloviruses • Epstein–Barr virus • Polyoma virus • Fungal infections • Laboratory diagnosis of opportunistic infections
33. Emerging infections (Competency MI 8.4) • Emerging infections in the Indian scenario • Re-emerging infections • Infections leading to public health emergencies • Antibiotic resistance • Bioterrorism
34. Oncogenic viruses (Competency MI 8.3) • Mechanisms of viral oncogenesis • Oncogenic DNA viruses – Human polyomaviruses – Simian virus 40 – Poxvirus – Adenovirus – Herpes virus – Cytomegalovirus – Hepatitis B virus • Oncogenic RNA viruses – Retrovirus – Oncogenes – Current trends
35. National health programmes, disease detection, and reporting (Competency 8.16) • Communicable disease programmes under the National Health Mission • Bioterrorism
36. AETCOM (Competency AETCOM 2.2, 2.3, 2.5)
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