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. She is also Ex-Secretary of the Indian Association of Medical Microbiologists (IAMM).

PART I GENERAL MICROBIOLOGY
1. Introduction to Microbiology: Foundations, History, Classification, and Scope

• Historical perspective and notable milestones in microbiology
• Nobel laureates in microbiology
• The antibiotic era
• Scope of medical microbiology
• Classification, nomenclature, and taxonomy of microbes
• Molecular epidemiology

2. Epidemiology of Infectious Diseases

• Sources of infection
• Routes of transmission of infection
• Host–parasite interaction
• Microbial factors predisposing to infection
• Epidemiology of infections

3. General Bacteriology

• Morphology of bacteria
• Growth and physiology of bacteria
• Factors affecting the growth of bacteria
• Sources of metabolic energy in bacteria
• Bacterial metabolites
• Bacteriocins

4. Systematic Bacteriology

• General concepts of pathogenesis and disease spectrum
• Overview of important bacteria associated with human health and disease
• Aerobic, gram-positive cocci
• Anaerobic gram-positive cocci
• Aerobic, non-branching, non-spore-forming, gram-positive bacilli
• Aerobic, non-branching, spore-forming, gram-positive bacilli
• Branching, gram-positive bacilli
• Anaerobic, spore-forming, non-branching, gram-positive bacilli
• Gram-negative cocci
• Anaerobic, gram-negative cocci
• Aerobic, gram-negative bacilli
• Fermenting, gram-negative bacilli
• Non-fermenting, gram-negative bacilli
• Fastidious gram-negative bacteria
• Anaerobic, gram-negative bacilli
• Acid-fast bacilli
• Miscellaneous bacteria
• Normal bacterial flora of the human body

5. Basic Concepts of Virology

• Morphology of viruses
• Classification of viruses
• Susceptibility of viruses to physical and chemical agents
• Replication of viruses
• Viral genetics
• Pathogenesis of viral infections
• Viroids
• Prions
• Bacteriophages
• Viral infections

6. Basic Concepts of Mycology

• Characteristics of fungi
• Classification of fungi
• Pathogenesis of fungal infections
• Host response to fungal infections
• Fungal infections in humans

7. Basic Concept Medical Parasitology

• General concepts of parasitology
• Protozoology
• Helminthology
• General characteristics, life cycles, and modes of transmission of parasites
• Pathogenesis of parasitic diseases
• Immunity in parasitic diseases
• Management of parasitic diseases

8. Microbial Genetics

• Basic principles of molecular biology
• Terms related to genetics
• Extrachromosomal genetic elements
• Genetic variations
• Gene transfer in bacteria
• Transposition in bacteria
• Molecular techniques applied to disease detection and diagnosis in clinical microbiology and epidemiology
• Applications of genetic engineering in microbiology

9. Diagnostic Microbiology

• Clinical diagnosis
• Laboratory testing

Pre-analytical phase

• Sample collection for microbiology investigations
• Methods of collection and storage of various samples
• Sample transportation

Analytical phase: Test procedures and processing

• Microscopy

Laboratory investigations for bacterial infections

• Microscopy of unstained preparations
• Staining methods: Gram stain, Ziehl–Neelsen stain (acid-fast stain)
• Culture of bacteria
• Culture methods
• Preservation of microorganisms
• Identification of bacteria from culture
• Antibiotic susceptibility test (AST)
• Other methods of detection of pathogens: Antigen detection, antibody detection, molecular methods

Laboratory diagnosis of viral diseases

• Sample collection and transport
• Microscopy
• Cultivation of viruses
• Demonstration of virus antigens
• Detection of antibodies to viruses
• Molecular diagnosis

Laboratory diagnosis of fungal infections

• Specimen
• Microscopy
• Culture
• Other tests for the identification of fungi
• Immunological tests: Antigen detection, antibody detection
• Skin test
• Molecular tests

Laboratory diagnosis of parasitic diseases

• Examination of fecal samples for parasites
• Examination of blood samples: Peripheral blood smear (PBS)
• Culture of parasites
• Antigen detection
• Antibody detection
• Skin hypersensitivity tests
• Molecular diagnostic methods

Post-analytical phase

• Ethical issues involved in processing and reporting test results
• Quality control in a clinical microbiology laboratory
• Laboratory accreditation

10. Sterilisation and Disinfection

• Definitions
• Spaulding’s classification
• Resistance of microorganisms to disinfection and sterilisation

Sterilising agents

• Factors that influence sterilisation
  I. Physical agents
  II. Chemical sterilants
  III. Plasma sterilisation
  IV. Gases
• Biological indicators for quality control of sterilisation
• Commonly used methods of sterilisation in hospitals and laboratories

Disinfectants

• Chemical agents
• Routinely used concentrations of disinfectants
• Methods of antisepsis/disinfection by chemical agents
• Agents for surgical hand antisepsis
• Testing of disinfectants

Applications in healthcare settings

• Agents used in the hospital for achieving sterilisation, disinfection, and cleaning
• Central sterile supply department (CSSD)

11. Antimicrobial Agents

• Classification of antibiotics based on mode of action
• Mechanisms of action of antibiotics
• Antimicrobial resistance
• Control of antimicrobial resistance
• Antiviral agents
• Antifungal agents
• Antiparasitic drugs

PART II IMMUNOLOGY

12. Immunity: Introduction and Components

• Immunity
• Immune system
• Physical barriers: The first line of defence
• Innate immunity: The second line of defence
• Adaptive or acquired immunity
• Interaction between innate and adaptive immunity
• Types of immune responses
• Hematopoiesis
• Anatomy of the immune system
• Development of the immune system
• Cells of the lymphoreticular system
• Abnormalities of immune cells

13. Antigens and Antibodies

Antigens

• Terms related to antigens
• Adjuvants
• Types of antigens
• Determinants of antigenicity
• Types of specificity of antigens
• Biological classes of antigens

Antibodies

• Antibody structure
• Protective function of antibodies
• Immunoglobulin classes
• Factors influencing antibody production
• Immunoglobulin specificities
• Antibody diversity
• Genetic characteristics of immunoglobulins
• Abnormal immunoglobulins
• Monoclonal antibodies

14. Complement

• Properties of complement
• Components of complement
• Complement activation
• Complement pathways
• Biological effects of complement action
• Biosynthesis of complement
• Quantitation of complement and its components

15. Antigen–Antibody Reactions

• Stages in antigen–antibody reactions
• General features of antigen–antibody reactions
• Diagnostic uses of antigen–antibody reactions
• Types of antigen–antibody reactions used for diagnosis
• Detection of cell-mediated immunity (CMI)

16. Mechanisms of Immune Response

• Theories of immune response
• Antibody-mediated (humoral) immune response
• Phases of antibody production
• Primary and secondary responses
• Antigen processing and fate of antigens following an immune response
• Elimination of antigens
• Factors influencing antigen–antibody responses
• Outcomes of antigen–antibody reactions in humoral immunity
• Antibody-dependent enhancement (ADE)
• Cellular immune response/cell-mediated immunity (CMI)
• Functions of cell-mediated immunity
• Outcomes of activated T cells
• Induction of cell-mediated immunity
• Pathways of humoral and cellular immune responses to an antigen
• Immune responses in different types of infections
• Immunosuppressive agents

17. Hypersensitivity

• Classification of hypersensitivity
• Type I reactions: immediate hypersensitivity
• Type II reactions
• Type III reactions: immune complex-mediated hypersensitivity
• Type IV reactions: t cell-mediated hypersensitivity (delayed-type)

18. Autoimmune Disorders and Immunodeficiency States

• Immunological tolerance
• Autoimmunity
• Immunodeficiency

19. Transplant and Tumour Immunity

• Classification of transplants
• Immunology of transplantation
• Immunological basis of allograft rejection
• Types of allograft rejection
• Graft-versus-host reaction
• Laboratory tests required before transplantation
• Immunosuppression for successful transplantation
• Privileged sites for transplantation
• Other sources of transplants
• Post-transplant infections
• Immunohematology
• Immunology of malignancy (tumour immunity)
• Immunological surveillance
• Immunotherapy of cancer
• Immunomodulation

20. Immunoprophylaxis

• Types of immunisation
• Concept of herd immunity
• Vaccination programme
• Adult vaccination

PART III HOSPITAL-ACQUIRED INFECTIONS AND INFECTION CONTROL 288

21. Healthcare-Associated Infections

• Sources and reservoirs of HAIs
• Microbes causing HAIs
• Types of HAIs
• Prevention of HAIs

22. Surveillance of Healthcare-Associated Infections

• Monitoring and control of HAIs hospital infection control committee (HICC)

23. Infection Control Practices in the Hospital, Including Biosafety

• Infection control practices in the hospital
• Standard precautions
• Environmental cleaning

24. Antimicrobial Stewardship

• Factors responsible for the development of AMR
• Control of AMR
• Antibiogram
• Antimicrobial stewardship (AMS)

National action plan on AMR – India

25. Biomedical Waste Management

• Hazards of biomedical waste
• Types of biomedical waste
• Steps in waste management
• Methods of waste treatment and disposal
• Mandatory practices for all healthcare settings
• Legal framework for biomedical waste management in India

26. Bacteriology of Water, Air, Milk, and Food

• Bacteriology of water
• Bacteriology of air
• Bacteriology of milk
• Bacteriology of food

PART IV APPLIED MICROBIOLOGY: SYSTEMIC APPROACH

27. Cardiovascular and Bloodstream Infections
27.1 Introduction: Myocarditis, pericarditis
27.2 Bacterial infections of the cardiovascular system and bloodstream

• Infective endocarditis
• PUO
• Enteric fever
• Leptospirosis
• Brucellosis
  • Rickettsial infections
  • Ehrlichiosis
  • Q fever
  • Epidemic typhus
  • Recrudescent typhus (Brill-Zinsser disease)
  • Endemic typhus (Murine or flea-borne typhus)
  • Indian tick typhus
  • Rocky Mountain spotted fever
  • Trench fever
  • Oroya fever (carrion disease)

27.3 Viral bloodstream infections

• Viral hemorrhagic fever (VHF)
• Arthropod-borne hemorrhagic fevers
• Kyasanur forest disease (KFD)
• Crimean Congo hemorrhagic fever (CCHF)
• Rodent-borne hemorrhagic fevers
• South American hemorrhagic fevers
• Hemorrhagic fever with renal syndrome (HFRS)
• Filoviral hemorrhagic fevers
• Yellow fever

27.4 Fungal bloodstream infections—Candidiasis

27.5 Vector-borne parasitic infections of the bloodstream

• Malaria
• Babesiosis
• Leishmaniasis and trypanosomiasis
• Filariasis
• Schistosomiasis

Anemia due to infectious diseases

28. HIV/AIDS

• Morphology of HIV
• Viral genes and antigens
• Antigenic variation and diversity of HIV
• Susceptibility of HIV
• Mode of transmission
• Pathogenesis
• Clinical features
• Laboratory diagnosis of HIV and AIDS
• Prognosis of HIV infection
• Prophylaxis 398
• Antiretroviral treatment (ART)

Gastrointestinal Infections

29.1 Infections of the gastrointestinal tract (GIT): Clinical presentation, laboratory diagnosis, treatment

29.2 Bacterial infections of the GIT

• Salmonellosis (non-typhoidal salmonellae)
• Diarrheal diseases caused by E. coli
• Cholera
• Aeromonas and Plesiomonas infections
• Bacillary dysentery
• Acid peptic disease (APD)
• Pseudomembranous colitis (PMC)
• Food poisoning
• Yersinosis
• Botulism

29.3 Fungal infections of the GIT: Food poisoning

29.4 Viral infections of the GIT: Viral gastroenteritis

29.5 Parasitic infections

• Giardiasis
• Intestinal parasitic coccidian diarrhea (opportunistic infections)
• Parasitic dysentery
• Helminthiasis or intestinal nematode infestations

Visceral larva migrans (VLM)

Intestinal cestode infestations

30. Hepatobiliary Infections

30.1 Introduction

30.2 Viral hepatobiliary infections—hepatitis

• Acute viral hepatitis
• Enteric viral hepatitis
• Bloodborne or serum hepatitis

30.3 Parasitic infestations of the liver

• Hydatid cyst
• Alveolar echinococcosis
• Liver fluke infestations—trematodes affecting the hepatobiliary system
• Liver abscess

30.4 Bacterial infections of the hepatobiliary system

• Biliary tract infections

31. Skin, Soft Tissue, and Musculoskeletal Infections

31.1 Infections of the skin and soft tissues

• Infections of the skin
• Infection of a burn wound
• Approach to the diagnosis of skin and soft tissue infections
• Treatment of skin and soft tissue infections

31.2 Musculoskeletal infections

• Acute osteomyelitis
• Chronic osteomyelitis
• Septic arthritis
• Myositis

31.3 Bacterial infections of the skin and soft tissues

A. Anaerobic bacterial infections of the skin and soft tissues

• Gas gangrene

B. Aerobic bacterial infections of the skin and soft tissues

• Streptococcal skin infections
• Staphylococcal scalded skin syndrome (SSSS)
• Erythrasma
• Anthrax
• Melioidosis (Whitmore disease/Vietnam time bomb disease)
• Glanders
• Lyme disease
• Skin diseases caused by non-tuberculous mycobacteria (NTM)
• Mycetoma

31.4 Viral infections of the skin and soft tissues

• Varicella (chickenpox)
• Herpes-zoster (shingles, zona)
• Hand, foot, and mouth disease (HFMD)
• Herpetic whitlow/cold sores
• Erythema infectiosum (fifth disease or slapped cheek syndrome)
• Exanthema subitum or roseola infantum or sixth disease
• Poxviral skin diseases
• Skin warts

31.5 Parasitic infections of the skin and subcutaneous tissues

• Protozoan infections of the skin: Amoebiasis cutis, post-kala-azar dermal leishmaniasis, cutaneous leishmaniasis or oriental sores, Delhi boils, Aleppo boils, and Baghdad buttons
• Nematodes affecting the skin: Cutaneous larva migrans (creeping eruption), larva currens, guinea worm disease or dracunculiasis, trichinellosis, subcutaneous filariasis, dirofilariasis
• Cestodes affecting the skin: Cercarial dermatitis
• Trematodes affecting the skin: Cysticerci, subcutaneous hydatid cysts

31.6 Fungal infections of the skin and its appendages

• Superficial mycoses
• Subcutaneous mycoses

32. Infections of the Respiratory System

• Protective mechanisms of the respiratory tract
• Pathogens causing respiratory tract infections
• Upper respiratory tract infections (URIs)
• Lower respiratory tract infections (LRIs)

32.1 Bacterial infections of the respiratory system

• Streptococcal throat infection or streptococcal pharyngitis
• Diphtheria
• Miscellaneous bacterial URIs
• Whooping cough/pertussis
• Atypical bacterial pneumonia
• Tuberculosis

32.2 Viral infections of the respiratory system

• Common cold
• Myxoviral URIs
• Influenza
• Avian influenza
• Swine influenza
• Paramyxoviral infections
• Parainfluenza (HPIV) viral infections
• Newcastle viral disease
• Mumps
• Measles
• Rubella (German measles)
• Herpes viral infections of the respiratory tract
• Viral infections of the lower respiratory tract—viral pneumonia

32.3 Fungal infections of the respiratory system

• Aspergillosis
• Talaromycosis (formerly, penicilliosis)
• Mucormycosis
• Pneumocystis pneumonia (PCP)
• Histoplasmosis (Darling’s disease)
• Blastomycosis
• Coccidioidomycosis
• Paracoccidioidomycosis

32.4 Parasitic infestations of the respiratory system

• Paragonimiasis
• Secondary parasitic infections of the lung
• Loeffler’s syndrome
• Tropical pulmonary eosinophilia (occult filariasis)

Prevention of respiratory infections

33. Infections of the Central Nervous System

33.1 Introduction

• Meningitis
• Encephalitis
• Brain abscess

33.2 Bacterial infections of the CNS

• Acute bacterial (pyogenic) meningitis: Meningococcal meningitis, neonatal meningitis, listeriosis, chronic meningitis
• Anaerobic bacterial infections of the CNS: Tetanus, botulism

33.3 Viral infections of the CNS

• Aseptic viral meningitis: Enteroviral infections, rabies, slow viral diseases, arboviral diseases, Nipah virus infection, tick-borne viral encephalitis

33.4 Parasitic infestations of the CNS

• Human cysticercosis (taeniasis)
• Primary amoebic meningoencephalitis (PAM) and granulomatous amoebic encephalitis (GAE)
• Toxoplasmosis
• Trypanosomiasis (sleeping sickness)

33.5 Fungal infections of the CNS

• Candidiasis
• Cryptococcal meningitis
• Histoplasmosis
• Microsporidiosis

34. Genitourinary and Sexually Transmitted Infections

34.1 Sexually transmitted infections (STIs)

34.2 Bacterial STIs

• Gonococcal urethritis (gonorrhea)
• Non-gonococcal (non-specific) urethritis
• Syphilis

34.3 Viral STIs

• Genital warts
• Genital herpes infections (herpes genitalis/progenitalis)
• Human immunodeficiency virus infection

34.4 Parasitic STIs

• Trichomoniasis
• Urogenital schistosomiasis

34.5 Urinary tract infections

35. Infections of the Eyes and Ears

• Infections of the eyes
• Infections of the ear

36. Zoonotic and Vector-Borne Infections
Zoonotic infections

• Epidemiology, classification, factors influencing the emergence of zoonotic diseases, laboratory diagnosis of zoonotic infections
• Plague
• Tularemia

• Infections following bite of animals: Pasteurella multocida infection, Capnocytophaga infections, cat scratch disease, rat bite fever (RBF)

Vector-borne infections

Control of zoonotic and vector-borne infections

37. Opportunistic Infections

• Characteristics of opportunistic pathogens
• Opportunistic bacterial infections
• Opportunistic viral infections
• Opportunistic fungal infections
• Opportunistic parasitic infections
• Laboratory diagnosis of opportunistic infections

38. Emerging Infections

• Emerging infectious diseases
• Infections leading to public health emergencies
• Factors contributing to emerging diseases
• Re-emerging infections
• Emerging infections in the Indian scenario
• Antibiotic resistance

39. Oncogenic Viruses

• Mechanisms of viral oncogenesis
• Oncogenic DNA viruses
• Oncogenic RNA viruses

40. National Health Programmes, Disease Detection, and Reporting

• National TB Elimination Programme (NTEP)
• National Leprosy Eradication Programme (NLEP)
• National Vector-Borne Disease Control Programme (NVBDCP)
• National AIDS Control Programme (NACP)
• Integrated Disease Surveillance Project (IDSP)
• National Viral Hepatitis Control Programme (NVHCP)
• National Programme on Containment of Antimicrobial Resistance (NPCAR)
• Response to COVID-19 pandemic in India

PART V PRACTICAL MICROBIOLOGY

I. Grand Viva Questions
II. Reasoning Questions
III. SPOTs and Objective Structured Practical Examination (OSPE) Questions

Annexures
I. AETCOM
II. Bioterrorism
III. Pandemic Management
Index