Essentials of Microbiology

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