Medical Microbiology

CONTENTS
Section GENERAL MICROBIOLOGY
1. Subject, tasks, historical development and achievements of microbiology (I. Hajdushka).....10
1.1. Main stages in the development of microbiology……………………………………………………..10
1.2. Development of microbiology in Bulgaria………………………………………………………………13
2. Introduction to general microbiology (I. Hajdushka)……………………………………………………..14
2.1. Taxonomy of microorganisms…………………………………………………………………………15
2.2. Numerical taxonomy……………………………………………………………………………………16
3. Morphology and structure of microorganisms (I. Hajdushka)…………………………..16
3.1. Shape and mutual arrangement of bacterial cells………………………………16
3.2. Cell wall ………………………………………………………………………………………………….19
3.3. Outer membrane of Gram-negative bacteria …………………………………………..20
3.4. Capsule…………………………………………………………………………………………………………………….. 21
3.5. Fringes ……………………………………………………………………………………………………………………22
3.6. Pili ……………………………………………………………………………………………………………………23
3.7. Spores…………………………………………………………………………………………………………………….. 24

Microbiology

4. Physiology of microorganisms (V. Kirina, M. Atanasova)……………………………….24
4.1. Chemical composition (V. Kirina)…………………………………………………………………………………….25
4.2. Metabolism of bacteria (B. Kirina)……………………………………………………………….27
4.2.1. Catabolite processes (V. Kirina)………………………………………………………………28
4.2.2. Anabolic processes (M. Atanasova)……………………………………………………………….29
4.3. Nutrition of bacteria (M. Atanasova)…………………………………………………………………….30
4.4. Bacterial enzymes (M. Atanasova)…………………………………………………………………………32
5. Growth and reproduction in bacteria (M. Atanasova)………………………………………………33
6. Effect of physical and chemical factors on microorganisms (I. Hajdushka)……34
6.1. Effect of physical factors…………………………………………………………………………34
6.2. Effect of chemical factors……………………………………………………………………………38
7. Microbial genetics (I. Hajdushka)…………………………………………………………………………..40
7.1. Bacterial chromosome…………………………………………………………………………………………41
7.2. Extrachromosomal DNA - plasmids………………………………………………………………………….41
7.3. Transposable elements…………………………………………………………………………………….42
7.4. Genotype and phenotype in viruses, phages and bacteria……………………………………………………42
7.5. Heredity and changeability of microorganisms………………………………………….42
7.6. Types of genetic mutations and mutants…………………………………………………………………………44
8. Antibiotics (I. Hajdushka)…………………………………………………………………………………….47
8.1. Mechanism of resistance…………………………………………………………………………48
8.2. Cell wall synthesis inhibitors. β-lactam antibiotics………………..49
8.3. Inhibitors of protein synthesis…………………………………………………………………….51
8.4. Nucleic acid synthesis inhibitors……………………………………………….54
8.5. New antibiotics………………………………………………………………………………………………57

Medical Microbiology, 9th Edition

Section INFECTION AND IMMUNITY
1. Infection (I. Hajdushka) ………………………………………………………………………………………………58
1.1. Relationship between microorganisms and macroorganism…………………………….58
1.2. Infection. Infectious process. Infectious disease. Necessary conditions for the development of an infectious process……59
1.3. Properties of infectious agents. Pathogenicity. Virulence………………….61
1.4. Factors of the macroorganism relevant to the development of infection………………65
1.5. Role of the external environment and social conditions for the development of infection……………..66
1.6. Development of an infectious process. Front door. Distribution and localization of the causative agents……….66
1.7. Ways of spread of infectious agents in the macroorganism…….68
1.8. Sources and distribution of infectious agents…………………………..69
1.9. Routes of transmission of infectious agents…………………………………………70
1.10. Forms of infection……………………………………………………………………………………………….72
2. Immunity (I. Hajdushka)……………………………………………………………………………………………….73
2.1. Natural resistance……………………………………………………………………………………..74
2.1.1. Mechanical barriers……………………………………………………………………………………75
2.1.2. Humoral factors of natural resistance…………………………………….76
2.1.3. Cellular factors of natural resistance. Phagocytosis………………………78
2.1.4. Natural killer cells (NK cells)……………………………………………………81
2.1.5. Acute phase proteins………………………………………………………………………………….81
2.1.6. Inflammation………………………………………………………………………………………………..82
2.2. Structure and function of the immune system………………………………………………………………..84
2.3. Antigens. Types and properties. Antigenicity and immunogenicity. Superantigens………….87
2.4. Antibodies. Structure and function………………………………………………………………………………90
2.4.1. Structure of immunoglobulins……………………………………………………………………..90
2.4.2. Immunoglobulin classes…………………………………………………………………………..93
2.5. Dynamics of the immune response. Primary and secondary immune response……………………96
2.6. Genetic control of the immune system. HLA system………………………………………….97
2.7. Cell-mediated immunity………………………………………………………………………………99
2.8. Antigen presentation and recognition. Cell cooperative……………………………100
2.9. Interleukin………………………………………………………………………………………………………….103
3. Antigen-antibody reactions (B. Kirina)…………………………………………………………………………105
3.1. Agglutination reaction……………………………………………………………………………………105
3.2. Precipitation reaction……………………………………………………………………………………107
3.3. Neutralization reaction. Toxin - antitoxin……………………………………………………111
3.4. Complement-dependent reactions…………………………………………………………………………..111
3.5. Marked immune reactions………………………………………………………………………………..113
4. Immunopathology (I. Hajdushka)………………………………………………………………………………..116
4.1. Allergy……………………………………………………………………………………………………………………116
4.1.1. Type I. Anaphylaxis………………………………………………………………………………..117
4.1.2. II type. Cytotoxic hypersensitivity………………………………………..118
4.1.3. Type III. Allergic reactions due to antigen-antibody complex….119
4.1.4. Type IV. Hypersensitivity of funny type………………………………………….120
4.2. Immunodeficiency conditions (V. Kirina)………………………………………………………………..121
4.3. Autoimmune reactions and diseases (V. Kirina)……………………………………………………..123

Basic Medical Microbiology

Section SPECIAL MICROBIOLOGY
1. Genus Staphylococcus (I. Hajdushka)………………………………………………………………………………126
2. Genus Streptococcus (I. Hajdushka)…………………………………………………………………………..130
2.1. Streptococci of group A…………………………………………………………………………………….132
2.2. Group B Streptococci…………………………………………………………………………………….133
3. Genus Enterococcus (I. Hajdushka)……………………………………………………………………………………136
4. Pneumococci. Streptococcus pneumoniae (I. Hajdushka) ………………………………………….136
5. Genus Neisseria (I. Hajdushka)…………………………………………………………………………………….138
5.1. Neisseria meningitidis…………………………………………………………………………………………138
5.2. Neisseria gonorrhoeae…………………………………………………………………………………………..141
6. Gram-negative rods (I. Hajdushka)………………………………………………………………..143
6.1. Family Enterobacteriaceae…………………………………………………………………………143
6.1.1. Genus Escherichia………………………………………………………………………………………………144
6.1.2. Genus Klebsiella………………………………………………………………………………………………146
6.1.3. Genus Enterobacter……………………………………………………………………………………………….148
6.1.4. Genus Serratia………………………………………………………………………………………………149
6.1.5. Tribus Proteae…………………………………………………………………………………………..150
6.1.6. Genus Shigella………………………………………………………………………………………………151
6.1.7. Genus Salmonella………………………………………………………………………………………………154
6.1.8. Genus Pasteurella (Yersinia)…………………………………………………………………………158
6.1.8.1. Yersinia pestis…………………………………………………………………………………………..158
6.1.8.2. Yersinia enterocolitica…………………………………………………………………………..162
6.2. Genus Pseudomonas…………………………………………………………………………………………….163
6.3. Genus Burkholderia………………………………………………………………………………………………..165
6.4. Haemophilus influenzae…………………………………………………………………………………………165
6.5. Genus Bordetella………………………………………………………………………………………………167
6.5.1. Bordetella pertussis……………………………………………………………………………………167
6.5.2. Bordetella parapertussis…………………………………………………………………………..170
6.6. Under Brucella…………………………………………………………………………………………………………170
6.7. Sem. Legionellaceae………………………………………………………………………………………………..172
6.8. Genus Francisella………………………………………………………………………………………………..174
6.9. Vibrio cholerae……………………………………………………………………………………………………..176
7. Gram-positive rods (I. Hajdushka)…………………………………………………………………….180
7.1. Genus Corynebacterium………………………………………………………………………………………………180
7.1.1. Corynebacterium diphtheriae…………………………………………………………………………180
7.2. Genus Mycobacterium……………………………………………………………………………………185
7.2.1. Mycobacterium tuberculosis…………………………………………………………………………185
7.2.2. Atypical Mycobacteria…………………………………………………………………………188
7.2.3. Mycobacterium leprae………………………………………………………………………………………….189

Microbiology for the Healthcare…

8. Anaerobic non-sporing bacteria (I. Hajdushka)…………………………………………191
8.1. Anaerobic Gram-positive bacteria………………………………………………………………191
8.1.1. Genus Peptostreptococcus…………………………………………………………………………191
8.1.2. Genus Propionibacterium……………………………………………………………………………………192
8.1.3. Genus Mobiluncus………………………………………………………………………………………………192
8.1.4. Genus Lactobacillus………………………………………………………………………………………….192
8.1.5. Under Bifidobacterium, Eubacterium and Rothia……………………………………………………192
8.2. Anaerobic Gram-negative bacteria……………………………………………………………………193
8.2.1. Genus Bacteroides………………………………………………………………………………………………193
8.2.2. Fusobacterium and Leptotrichia………………………………………………………………193
9. Listeria genus. Listeria monocytogenes (I. Hajdushka)……………………………………………………194
10. Anaerobic spore-bearing bacteria (bacilli). Bacillus anthracis (I. Hajdushka)…………196
11. Aerobic spore-forming microorganisms (I. Hajdushka)……………………………….200
11.1. Genus Clostridium…………………………………………………………………………………………..200
11.1.1. Clostridium tetani…………………………………………………………………………………….200
11.1.2. Clostridium botulinum………………………………………………………………………………..203
11.1.3. Causes of gas gangrene……………………………………………………………….204
11.1.3.1. Clostridium perfringens…………………………………………………………………………204
11.1.3.2. Clostridium novyi………………………………………………………………………………206
11.1.4. Pseudomembranous colitis caused by Clostridium difficile……………………….206
12. Sem. Spirochaetaceae………………………………………………………………………………………………208
12.1. Genus Treponema. Treponema pallidum…………………………………………………………………………208
12.2. Genus Borrelia………………………………………………………………………………………………………….212
12.2.1. Borrelia recurrentis……………………………………………………………………………………..212
12.2.2. Borrelia burgdorferi…………………………………………………………………………………….214

Medical Microbiology 19th Edition

12.3. Genus Leptospira………………………………………………………………………………………………215
13. Genus Campylobacter (I. Hajdushka) …………………………………………………………………………..217
14. Genus Helicobacter (I. Hajdushka)…………………………………………………………………………..218
15. Mushrooms (V. Kirina)…………………………………………………………………………………………………………220
15.1. General characteristic…………………………………………………………………………………………..220
15.2. Dermatomycoses…………………………………………………………………………………………………….225
15.3. Genus Candida……………………………………………………………………………………………….227
15.4. Genus Aspergillus………………………………………………………………………………………………..229
15.5. Genus Cryptococcus……………………………………………………………………………………………….231
15.6. Mucormycoses (Phycomycoses)…………………………………………………………………………232
15.7. Histoplasmosis……………………………………………………………………………………………….234
15.8. Blastomycosis…………………………………………………………………………………………………….235
15.9. Coccidioidomycosis…………………………………………………………………………………………..236
15.10. Paracoccidioidomycosis……………………………………………………………………………….238
15.11. Pneumocystosis………………………………………………………………………………………………..240
15.12. Genus Actinomyces……………………………………………………………………………………………….241
15.13. Genus Nocardia…………………………………………………………………………………………………….243
16. Sem. Chlamydiaceae (I. Hajdushka)………………………………………………………………………….244
17. Mycoplasma. Ureaplasma (I. Hajdushka)……………………………………………………………….249
18. Rickettsiae and rickettsioses (Z. Kalvachev)…………………………………………………………………………250
18.1. Epidemic spotted typhus………………………………………………………………………………252
18.2. Endemic spotted typhus……………………………………………………………………………………..253
18.3. Rocky Mountain Spotted Fever………………………………………………………………254
18.4. Marseille (Mediterranean) fever…………………………………………………………………….255
18.5. Coxiella burnetii and Whooping cough………………………………………………………………………….256
19. Normal microflora of the human body (I. Hajdushka)……………………………….259

Medical Microbiology

Section VIRUSOLOGY
1. General characteristics of viruses (M. Atanasova)…………………………………………………….262
2. Taxonomy and classification of viruses (Z. Kalvachev)………………………………………….271
3. Picornaviridae (Family Picornaviridae) (M. Atanasova, Z. Kalvachev)………………..277
3.1. Enteroviruses (Genus Enterovirus)…………………………………………………………………………277
3.1.1. Poliomyelitis viruses (Human polioviruses)………………………………………….277
3.1.2. Coxsackieviruses and Echoviruses (Coxsackieviruses, Echoviruses)………………………….279
3.1.3. Other enteroviruses……………………………………………………………………………………279
3.2. Rhinoviruses (Genus Rhinovirus)………………………………………………………………………….281
4. Caliciviruses (Family Caliciviridae) (Z. Kalvachev)………………………………………….282
5. Family Reoviridae (Z. Kalvachev, M. Atanasova)……………………………………………………..283
5.1. Orthoreoviruses (Genus Orthoreovirus, Reovirus)……………………………………………………..283
5.2. Rotaviruses (Genus Rotavirus)………………………………………………………………………………..284
6. Togaviruses (Family Togaviridae) (Z. Kalvachev)……………………………………………………..286
6.1. Rubella virus (Rubella virus)…………………………………………………………………………..286
7. Flaviviruses (Family Flaviviridae) (Z. Kalvachev)………………………………………………..288
8. Bunyaviruses (Family Bunyaviridae) (Z. Kalvachev)……………………………………………………289
9. Filoviruses (Family Filoviridae) (Z. Kalvachev)………………………………………………………….291
10. Arenaviruses (Family Arenaviridae) (Z. Kalvachev)………………………………………………293
11. Coronaviruses (Family Coronaviridae) (Z. Kalvachev)………………………………………….295
12. Orthomyxoviruses (Family Orthomyxoviridae) (M. Atanasova)………………………….297
12.1. Influenza viruses (Influenza virus A, B, C)……………………………………………………………….297
13. Paramyxoviruses (Family Paramyxoviridae) (M. Atanasova)…………………………..302
13.1. Parainfluenza viruses (Parainfluenza viruses)………………………………………………………….303
13.2. Epidemic mumps virus (Virus parotitidis, Mumps virus)…………………………..305
13.3. Smallpox virus (Morbillivirus, Measles virus)……………………………………………….307
13.4. Respiratory syncytial virus (Respiratory syncytial virus, RSV)…………………….309

Medical Microbiology

14. Rhabdoviruses (Family Rhabdoviridae) (M. Atanasova, Z. Kalvachev)……………………310
14.1. Rabies virus………………………………………………………………………….311
15. Adenoviruses (Family Adenoviridae) (Z. Kalvachev, M. Atanasova.)…………………….313
16. Herpes viruses (Family Herpesviridae) (M. Atanasova, Z. Kalvachev)………………315
16.1. Human herpes simplex virus (Herpes simplex virus 1, 2)…………………….316
16.2. Varicella and herpes zoster virus (Varicella-zoster virus, VZV)…………………….318
16.3. Infectious mononucleosis virus (Epstein-Barr virus, EBV)…………………….319
16.4. Cytomegalovirus (Cytomegalovirus, CMV)……………………………………………….321
16.5. Other herpes viruses (Human herpes virus 6,7,8)………………………………………………323
17. Human polyoma viruses (Family Polyomaviridae) (Z. Kalvachev)………………….324
18. Human papillomaviruses (Family Papillomaviridae) (Z. Kalvachev)………………325
19. Parvoviruses (Family Parvoviridae) (Z. Kalvachev, M. Atanasova………………………327
20. Poxviruses (Family Poxviridae) (M. Atanasova, Z. Kalvachev)…………………………329
21. Retroviruses (Family Retroviridae) (M. Atanasova)………………………………………………331
21.1. AIDS viruses (HIV-1 and HIV-2)…………………………………………………………………………332
22. Hepatitis viruses (M. Atanasova)…………………………………………………………………………..338
22.1. Hepatitis A virus (Hepatitis A virus, HAV)…………………………………………………………..339
22.2. Hepatitis B virus (Hepatitis B virus, HBV)……………………………………………………..342
22.3. Hepatitis D virus (Hepatitis D virus, HDV)…………………………………………………….346
22.4. Hepatitis C virus (Hepatitis C virus, HCV)……………………………………………………..347
22.5. Hepatitis E virus (Hepatitis E virus, HEV)…………………………………………………………349
23. Bacteriophages (M. Atanasova)…………………………………………………………………………………….351
24. Viroids, viroids, prions (Z. Kalvachev)………………………………………………………………..354