SECTION I General Microbiology
1 Introduction and History of Microbiology
Amita Jain
Classification and Nomenclature of Microbes
History of Microbiology
2 Microbial Genetics
Amita Jain
Structure of Nucleic Acids
Genetic Elements Present in Bacterial Cells
DNA Replication
Transfer of Genetic Material
Mutations
Gene Expression
3 Basics of Immunology
Amita Jain
Important Terminology
Innate Immunity
Adaptive Immune Response
Hypersensitivity
Immune System Disorders
Video: Principle of Enzyme Linked Immunosorbent Assay
4 Host-Pathogen Interaction
Amita Jain
Classifi cation of Diseases
Classifi cation of Pathogens
Modes of Disease Transmission
Phases of Disease Development
Development of Disease
5 Normal Flora of Human and Microbiome
Amita Jain
Microbial Flora of Human Body
6 Sterilisation and Disinfection
Parul Jain and Atin Singhai
Importance of Cleaning
Spaulding’s Classification
for Instruments
Sterilisation Methods
Disinfection of Surfaces
Video: Dry Heat Sterilisation
Video: Moist Heat Sterilisation
SECTION II Aetiological Agents
PART A: Bacterial Pathogens
7 Introduction to Bacterial Pathogens
Parul Jain
Classification
Nomenclature
Morphology
Structure
Physiology (Growth and Multiplication)
Bacterial Metabolism
Video: Types of Motility
Video: Basic Steps in PCR
Video: Biochemical Reactions for Laboratory Diagnosis of Enteric Fever
8 General Principles of Laboratory Diagnosis of Bacterial Pathogens
Amita Jain
Approach to a Case of Bacterial Infection
9 Gram-Positive Cocci
Parul Jain
Staphylococcus species
Streptococcus species
Gram-positive Anaerobic Cocci
10 Gram-Positive Bacilli
Parul Jain
Aerobic Gram-Positive Bacilli
Corynebacterium diphtheriae
Other Coryneform Bacteria
Listeria monocytogenes
Erysipelothrix rhusiopathiae
Bacillus anthracis
Bacillus cereus
Clostridium tetani
Clostridium perfringens
Clostridium botulinum
Clostridium difficile
Anaerobic Non-Spore-Forming Gram-Positive Bacilli
11 Mycobacteria, Actinomycetes and Nocardia
Amita Jain
Mycobacterium tuberculosis
Atypical Mycobacteria
Leprosy
Actinomycetes
Nocardia species
12 Gram-Negative Cocci
Parul Jain
Neisseria meningitidis
Neisseria gonorrhoeae
Moraxella catarrhalis
Kingella species
Acinetobacter species
Anaerobic Gram-Negative Cocci
13 Gram-Negative Rods: Enterobacteriaceae
Parul Jain
Escherichia coli
Citrobacter
Edwardsiella
Klebsiella
Enterobacter
Hafnia
Serratia
Salmonella
Shigella
Proteus, Providencia and Morganella
Yersinia
Miscellaneous Members
of Enterobacteriaceae
14 Gram-Negative Rods: Other than Enterobacteriaceae
Parul Jain
Pasteurellaceae
Haemophilus infl uenzae
Haemophilus infl uenzae
Biogroup aegyptius
Haemophilus ducreyi
Other species of Haemophilus
HACEK Group of Bacteria
Pasteurella
Actinobacillus
Vibrionaceae
Vibrio cholerae
Halophilic vibrios
Aeromonas
Psedomonadaceae
Pseudomonas aeruginosa
Stenotrophomonas
Burkholderia cepacia
Burkholderia pseudomallei
Burkholderia mallei
Legionella Pneumophila
Bordetella pertussis
Bordetella parapertussis
Fransicella tularensis
Bartonella
Brucella
Campylobacter
Helicobacter
Anaerobic Gram-Negative Rods
15 Spirochaetes
Amita Jain
Spirochaetes of Oral Cavity
T. pallidum Subspecies pallidum
Treponema Other Than T. pallidum
Leptospira
Borrelia
16 Chlamydia
Amita Jain
Chlamydia Trachomatis
Chlamydia Pneumoniae
Chlamydia Psittaci
17 Rickettsia
Amita Jain
Rickettsia
Ehrlichia
18 Mycoplasma
Amita Jain
Important Mycoplasma Species Affecting Human
PART B: Viral Pathogens
19 Introduction to Viral Pathogens
Amita Jain
Historical Milestones
Properties of Viruses
The Viral Structure
Virus Nomenclature
Classification of Viruses
Transmission and Replication of Viruses
Diagnosis of Viral Infections
Video: Methods of Identification of Viral Infection
20 Herpesviruses
Amita Jain
Herpes Simplex Viruses
Varicella-Zoster Virus
Cytomegalovirus
Epstein–Barr Virus
Human Herpesvirus 6
Human Herpesvirus 7
Human Herpesvirus 8
21 Poxviruses
Amita Jain
Smallpox, 155
Orf, Cowpox and Monkeypox Virus
Molluscum Contagiosum Virus
Vaccinia Virus
22 Hepatitis Viruses
Amita Jain
Hepatitis A virus (HAV)
Hepatitis B virus (HBV)
Hepatitis C virus (HCV)
Hepatitis D Virus (HDV)
Hepatitis E Virus (HEV)
23 Orthomyxoviruses and Paramyxoviruses
Amita Jain
Orthomyxoviruses (Influenza Viruses)
Paramyxoviruses
Parainfluenza Viruses
Mumps Virus
Respiratory Syncytial Virus
Measles Virus
Human Metapneumovirus
Nipah and Hendra Viruses
24 Arboviruses
Amita Jain
Dengue Virus (DENV)
Yellow Fever Virus
Zika Virus
Japanese Encephalitis Virus
Chikungunya Virus
West Nile Virus
Kyasanur Forest Disease Virus
Crimean–Congo Haemorrhagic Fever Virus
Hantavirus
25 Enteroviruses and Rhinoviruses
Amita Jain
Polioviruses
Coxsackieviruses
Echoviruses (Entero Cytotoxic Human Orphan)
Newly Identified Picornaviruses
Parechovirus
Rhinoviruses
26 Human Immunodeficiency Virus
Amita Jain
HIV types, Subtypes and Sub-Subtypes
Opportunistic Infections
Diagnosis
Prevention and Control
Dos and Don’ts in Case of Exposure
27 Rabies Virus
Amita Jain
Structure and Classification of Rabies Virus
Laboratory Diagnosis, Prophylaxis, Treatment of Rabies
28 Miscellaneous DNA Viruses
Amita Jain
Adenoviruses
Human Parvoviruses
Polyomaviruses
29 Miscellaneous RNA Viruses
Amita Jain
Rotavirus
Caliciviruses
Adenoviruses
Astroviruses
Coronaviruses
Ebola Virus
Marburg Virus
Lassa Fever Virus
South American Haemorrhagic Fevers Virus
Lymphocytic Choriomeningitis Virus
30 Other Miscellaneous Viruses
Amita Jain
Mechanism of Viral Oncogenesis
Human T-Lymphotropic Virus (HTLV-1)
Polyomaviruses
Papillomavirus
Slow Virus Infections and Prion Diseases
Subacute Sclerosing Panencephalitis
Progressive Multifocal Leukoencephalopathy
PART C: Parasitic Pathogens
31 Introduction to Parasites
Parul Jain
Glossary of Terms
Sources of Infection
Routes of Entry Into Body
Pathogenicity
Classification
Laboratory Diagnosis of Parasites
Video: Direct Detection of Parasites
Video: Concentration of Stool
32 Protozoa
Parul Jain
Entamoeba species
Free-Living Amoebae
Leishmania species
Trypanosoma species
Giardia
Trichomonas
Other Flagellates
Plasmodium
Babesia
Toxoplasma
Cryptosporidium
Cyclospora
Cystoisospora (Formerly Called Isosporiasis)
Sarcocystis
Balantidium
Chromista
33 Helminths
Parul Jain
Nematodes
Ascaris lumbricoides
Trichuris trichiura
Ancyclostoma duodenale, Necator americanus
Strongyloides stercoralis
Enterobius vermicularis
Trichinella
Dracunculus medinensis
Filarial Worm
Cestodes
Taenia saginata and Taenia solium
Hymenolepis
Diphyllobothrium latum
Echinococcus granulosus and Echinococcus multilocularis
Taenia multiceps, T. serialis
Trematodes
Schistosoma
Clonorchis and Opisthorchis
Fasciola
Fasciolopsis buski and Heterophyes hetrophyes
Paragonimus
34 Ectoparasites
Parul Jain
Medically Important Ectoparasites
PART D: Fungal Pathogens
35 Introduction to Fungal Pathogens
Suruchi Shukla
Historical Milestones
Classification
Fungal Vegetative Structures
Laboratory Diagnosis
Antifungal Agents
Video: Appearances of Different Fungi
36 Fungi Causing Superficial and Cutaneous Infections
Suruchi Shukla
Piedra
Tinea
Malassezia Infection
Dermatophytoses
37 Fungi Causing Subcutaneous Infections and Mycetoma
Suruchi Shukla
Sporothrix schenckii
Chromoblastoma
Phaeoid Fungi
Rhinosporidium seeberi
Mycetoma
38 Yeasts Causing Human Infections
Suruchi Shukla
Candida
Cryptococcus
39 Dimorphic Fungi Causing Human Infections
Suruchi Shukla
Paracocciodioides
Coccidioides
Histoplasma
Blastomycetes
40 Opportunistic Fungal Infections and Miscellaneous Fungal Diseases
Suruchi Shukla
Hyaline Moulds
Aspergillus
Zygomycetes
Penicillium
Pseudallescheria boydii
Fusarium
Acremonium
Paecilomyces spp.
Pigmented Moulds (Phaeoid Fungi)
Yeast-Like Fungi
Candida spp. Other Than Candida albicans
Trichosporon spp.
Rhodotorula spp.
Geotrichum spp.
Saccharomyces cerevisiae
Pneumocystis jirovecii
Fungi causing Allergic Diseases
Fungi Producing Toxins
Miscellaneous Fungal Infections
Oculomycoses
Otomycosis
SECTION III Laboratory Approach to Common Clinical Syndromes
41 Laboratory Approach to Common Clinical Syndromes
Amita Jain
Pyrexia of Unknown Origin
Respiratory Tract Infections
Urinary Tract Infection
Meningitis and Encephalitis
Food-Borne Illnesses
Sexually Transmitted Infections and Reproductive Tract Infections
Skin and Soft Tissue Infections
Prevention of Hospital-Acquired and Blood-Borne Infections
Video: Sample Collection for Pyrexia of Unknown Origin
Video: Microscopic Examination for Laboratory Diagnosis of Diarrhoea and Dysentery
Video: Culture Methods for Laboratory Diagnosis of Food Poisoning
Video: Antimicrobial Susceptibility Testing for Urinary Tract Infection
Multiple Choice Questions
Further Reading
Index
