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
- Dengue fever—Dengue virus
- Chikungunya—Chikungunya virus
- Kyasanur Forest disease—KFD virus
– Crimean Congo hemorrhagic fever—CCHF virus
– Rodent-borne hemorrhagic fevers
- South American hemorrhagic fevers—Junin and Machupo viruses
- Lassa fever—Lassa virus
- Hemorrhagic fever with renal syndrome
- Hanta pulmonary syndrome (HPS)
– Filoviral hemorrhagic fevers
- Ebola virus disease—Ebola virus
- Marburg disease—Marburg virus
• Fungal bloodstream infections
– Candidiasis—Candida
• Parasitic infections of the bloodstream
– Malaria—Plasmodium
– Kala-azar/Visceral leishmaniasis—Leishmania
– Trypanosomiasis—Trypanosoma
- African trypanosomiasis (sleeping sickness)—T. brucei complex
- American trypanosomiasis (Chagas disease)—T. cruzi
– Babesiosis—Babesia
– Lymphatic filariasis
- Wuchereria bancrofti
- Brugia malayi
– Schistosomiasis
- Schistosoma mansoni
- Schistosoma japonicum
- Schistosoma haematobium
• 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
- Cytomegaloviral infection—CMV
- Epstein–Barr virus (EBV) disease—EBV
• Infections in the oral cavity
– Oral candidiasis—Candida
– Periodontal infection
– Dental caries
• Lower respiratory tract infections
– Lung abscess, empyema, pneumonia
– Bacterial pneumonia
- Pneumococcal pneumonia—Streptococcus pneumoniae
- Haemophilus influenzae pneumonia—H. influenzae
- Whooping cough—Bordetella pertussis
- Nosocomial bacterial pneumoniaxii
- Klebsiella pneumoniae pneumonia
- Pseudomonas aeruginosa pneumonia
- Acinetobacter pneumonia
- Atypical bacterial pneumonia
- Mycoplasmal pneumonia
- Chlamydial pneumonia
- Legionellosis—Legionella maltophilia
– Viral pneumonia
– Fungal pneumonia
- Aspergillosis—Aspergillus species
- Penicillosis—Penicillium species
- Mucormycosis—Rhizopus spp., Mucor spp., Absidia
- Cryptococcosis (torulosis)—Cryptococcus neoformans
- Histoplasmosis—Histoplasma capsulatum
- Blastomycosis—Blastomyces dermatitidis
- Coccidioidomycosis—Coccidioides immitis
- Paracoccidioidomycosis—Paracoccidioides
– Parasitic lung infections
- Paragonimiasis—Paragonimus westermanii
• 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
- Poliomyelitis—Polio virus
- Coxsackievirus diseases—Coxsackie viruses A and B
- Echoviral diseases—Echoviruses
– Rabies—Rabies virus
• Slow viral diseases
– Subacute sclerosing panencephalitis (SSPE)
– Progressive multifocal leukoencephalopathy (PML)
– Prion diseases
• Arboviral diseases
– Encephalitis
- Japanese encephalitis (JE) virus
- Tick-borne encephalitis—Russian spring–summer encephalitis (RSSE) complex
- West Nile virus
- Zika virus
• 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
- Cryptosporidiosis—Cryptosporidium
- Cystoisosporaiasis—Cystoisospora
- Sarcocystosis—Sarcocystis
- Cyclosporiasis—Cyclospora
– Parasitic dysentery
- Entamoeba histolytica
- Balantidium coli
– Helminthiasis
- Ascariasis—Ascaris lumbricoides
- Hookworm infestation—Necator americanus and Ancylostoma duodenale
- Trichuriasis—Trichuris trichuria
- Enterobiasis—Enterobius vermicularis
- Strongyloidiasis—Strongyloides spp.
– Visceral larva migrans
- Angiostrongylus cantonensis
- Gnathostoma spinigerum and Anisakis species
– Intestinal cestode infections
- Taenia saginata
- Taenia solium
- Hymenolepis nana and H. diminuta
- Diphyllobothrium
– Intestinal trematode infestation
- Fasciolopsiasis—Fasciolopsis buski
- Intestinal schistosomiasis—Schistosoma
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
- Chlamydia trachomatis serovar D-K
- Mycoplasma genitalium and M. hominis
- Ureaplasma urealyticum
– 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
- Clostridium perfringens
- Clostridium septicum
- Clostridium novyi
- Clostridium histolyticum
– Bacterial mycetoma
- Actinomycosis—Actinomycetes
- Nocardiosis—Nocardia
- Botryomycosis
– Melioidosis—Burkholderia pseudomallei
– Glanders—Burkholderia mallei
– Lyme disease—Borrelia burgdorferi
– Skin diseases by non-tuberculous mycobacteria
- Buruli ulcer—M. ulcerans
- Swimming pool granuloma—M. marinum
- Leprosy—M. leprae
• 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
- Amoebiasis cutis—Entamoeba histolytica
- Post-kala-azar dermal leishmaniasis—Leishmania donovani
- Cutaneous leishmaniasis—Leishmania spp.
– Nematodes affecting the skin
- Cutaneous larva migrans—Hookworms
- Larva currens—Strongyloides stercoralis
- Guinea worm disease or dracunculiasis—Dracunculus medinensis
- Trichinellosis—Trichinella
- Onchocerciasis/River blindness—Oncocerca volvulus
- Loiasis—Loa loa
- Mansonellosis—Mansonella spp.
- Dirofilariasis—Dirofilaria immitis
– Cestodes affecting the skin
- Cercarial dermatitis—Schistosoma
– Trematodes affecting the skin
- Cysticerci—T. solium
- Subcutaneous hydatid cysts
– Ectoparasites
• Fungal infections of the skin
– Superficial mycoses
- Pityriasis versicolor
- Dermatophytosis
- Tinea unguium
- Dermatophytid reaction
- Onchomycosis
– Subcutaneous mycoses
- Mycotic mycetoma
- Rhinosporidiosis
- Subcutaneous phycomycosis
- Blastomycosis
- Coccidiodomycosis
- Cutaneous candidiasis
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)