I.I. Generalov MEDICAL MICROBIOLOGY, VIROLOGY & IMMUNOLOGY Part 2 Medical Bacteriology & Medical Virology Lecture Course for Students of Medical Universities VITEBSK STATE MEDICAL UNIVERSITY 2016 Ministry of Health of the Republic of Belarus Higher Educational Establishment “Vitebsk State Order of Peoples' Friendship Medical University” I.I. Generalov MEDICAL MICROBIOLOGY, VIROLOGY & IMMUNOLOGY Part 2 Medical Bacteriology & Medical Virology Lecture Course for Students of Medical Universities VITEBSK 2016 2 УДК [579+616.31]=111(07) ББК 52.64 я73+56.6 я73 Г 34 Printed according to the decision of Educational&Methodological Consociation on Medical Education (July 1, 2016) Reviewed by: D.V.Tapalsky, MD, PhD, Head of Microbiology, Virology and Immunology Dpt, Gomel State Medical University Microbiology, Virology and Immunology Dpt, Belarusian State Medical University, Minsk Generalov I.I. Г 34 Medical Microbiology, Virology and Immunology. Part 2. Medical Bacteriology & Medical Virology – Lecture Course for students of medical universities / I.I. Generalov. – Vitebsk, - VSMU. - 2016. - 392 p. ISBN 978-985-466-743-0 The Lecture Course on Medical Microbiology, Virology and Immunology accumulates a broad scope of data covering the most of essential areas of medical microbiology. The textbook is composed according to the educational standard, plan and program, approved by Ministry of Education and Ministry of Health of the Republic of Belarus. This edition encompasses all basic sections of the subject – General Microbiology, Medical Immunology, Medical Bacteriology and Virology. Part 2 of the Lecture Course comprises Medical Bacteriology and Medical Virology sections. The book is directed for students of General Medicine faculties and Dentistry faculties of higher educational establishments. УДК [579+616.31]=111(07) ББК 52.64 я73+56.6 я73 © Generalov I.I., 2016 © VSMU Press, 2016 ISBN 978-985-466-743-0 3 CONTENTS Pages Abbreviation list 5 Section 1. MEDICAL BACTERIOLOGY 8 Chapter 1. Causative agents of suppurative, wound, and hospital-acquired infections 9 Chapter 2. Causative agents of suppurative, wound, and hospital-acquired anaerobic infections 33 Chapter 3. Causative agents of enteric bacterial infections: Escherichia coli and shigellae 52 Chapter 4. Causative agents of enteric bacterial infections: salmonellae and yersiniae 66 Chapter 5. Pathogenic vibrios – causative agents of cholera. Causative agent of botulism. Helicobacter pylori 80 Chapter 6. Causative agents of bacterial respiratory infections: meningococci, Haemophilus influenzae, bordetellae, legionellae, and mycoplasmas 98 Chapter 7. Causative agents of bacterial respiratory infections: pathogenic mycobacteria and corynebacteria 124 Chapter 8. Causative agents of sexually transmitted diseases 145 Chapter 9. Causative agents of bacterial zoonozes:plague, anthrax, brucellosis, and tularemia 163 Chapter 10. Causative agents of leptospirosis and borrelioses 184 Chapter 11. Causative agents of rickketsioses and Q fever 197 Chapter 12. Infection-associated diseases of oral cavity (for students of Dentistry faculty) 208 Section 2. MEDICAL VIROLOGY 232 Chapter 13. General characteristics of viruses 233 Chapter 14. Bacteriophages 250 Chapter 15. Causative agents of viral respiratory infections 257 Chapter 16. Human enteric viruses: rotaviruses, picornaviruses 290 Chapter 17. Hepatotropic viruses 303 Chapter 18. Retroviruses: human immunodeficiency virus (HIV) 322 Chapter 19. Herpesviruses and herpes viral infections 333 Chapter 20. Causative agents of zoonotic viral infections 349 Chapter 21. Prions and prion diseases 372 Chapter 22. Infectious diseases with specific lesions in oral cavity (For students of Dentistry faculty) 377 4 ABBREVIATION LIST Ab – antibody ACE 2- angiotensin- converting enzyme 2 Ag – antigen AIDS – acquired immunodeficiency syndrome ALT – alanine aminotransferase ANUG – acute necrotizing ulcerative gingivitis BCG vaccine – bacillus Calmette-Guerin vaccine BCYE agar – buffered charcoal yeast extract agar BSE – bovine spongiform encephalopathy BSK medium – Barbour-Stoenner-Kelly medium BSL – biosafety level CADIS – candida-associated denture induced stomatitis CagA – cytotoxin-associated gene A cAMP – 3',5'-cyclic AMP cccDNA – covalently closed circular DNA CJD – Creutzfeldt-Jakob disease CMV – cytomegalovirus CNS – central nervous system CRISPR – clustered regularly interspaced short palindromic repeats CRS – congenital rubella syndrome CSF – cerebrospinal fluid DAT – diphtheria antitoxin DFA-TP – direct fluorescent-antibody test for T. pallidum DIC – disseminated intravascular coagulation DPT vaccine – diphtheria, pertussis, and tetanus vaccine DST – Diaskintest DtxR – diphtheria toxin repressor EAEC – enteroaggregative E. coli EBV – Epstein-Barr virus EF – edema factor EHEC – enterohemorrhagic E. coli EIEC – enteroinvasive E. coli ELISA – enzyme-linked immunosorbent assay EMB agar – eosin-methylene blue agar EPEC – enteropathogenic E. coli ESBL – extended-spectrum beta-lactamase ETEC – enterotoxigenic E. coli EVD – Ebola virus disease FFI – fatal familial insomnia GCF – gingival crevicular fluid GPAC – gram-positive anaerobic cocci 5 GSS – Gerstmann-Straussler-Scheinker syndrome HAART – highly active antiretroviral therapy HAV – hepatitis A virus HBsAg – hepatitis B surface antigen HBV – hepatitis В virus HCV – hepatitis С virus HDV – hepatitis D (delta) virus HEV – hepatitis E virus HHV-6 – human herpesvirus type 6 HHV-7 – human herpesvirus type 7 Hib – Haemophilus influenza type b HLA – human leukocyte antigen(s) Hsp – heat shock protein(s) HSV – herpes simplex virus HUS – hemolytic uremic syndrome ICTV – International Committee on Taxonomy of Viruses IGRA – interferon-gamma release assay KSHV – Kaposi’s sarcoma-associated herpesvirus LBAT – liver bile acid transporter protein LCV – legionella-containing vacuole LF – lethal factor LOS – lipooligosaccharide LPS – lipopolysaccharide M cells – microfold cells MAPK kinase – kinase of mitogen-activated protein kinase MAT – microscopic agglutination test MDR M. tuberculosis – multidrug resistant M. tuberculosis MDT – multidrug therapy MERS – Middle East respiratory syndrome MODS – multiple-organ-dysfunction syndrome MOMP – major outer membrane protein MPA – meat peptone agar MPB – meat peptone broth MRSA – methicillin-resistant Staphylococcus aureus MSF – Mediterranean spotted fever NAATs – nucleic acid amplification tests nAChR – nicotinic acetylcholine receptor NP – nucleoprotein NSAID – nonsteroidal anti-inflammatory drug(s) NSP – non-structural protein OMP – outer membrane protein(s) Osp – outer surface protein(s) PA – protective antigen 6 PBP – penicillin-binding protein PCR – polymerase chin reaction PEP – post-exposure prophylaxis PRNP – prion protein gene PRP – polyribosil ribitol phosphate pYV – plasmid of yersinia virulence RDS – respiratory distress syndrome RMSF – Rocky Mountain spotted fever RPR test – rapid plasma reagin test RT-PCR – reverse transcription PCR RV – rubella virus SARS – severe acute respiratory syndrome SFG – spotted fever group SIRS – systemic inflammatory response syndrome SLT – Shiga-like toxin SPI – salmonella pathogenicity island STD – sexually transmitted disease STX toxin – Shiga toxin T3SS – type III secretion system T4SS – type IV secretion system T7SS – type VII secretion system TBEV – tick-borne encephalitis virus TCBS agar – thiosulfate-citrate-bile-sucrose agar TCP – toxin-coregulated pili TSEs – transmissible spongiform encephalopathies TSST – toxic shock syndrome toxin TST – tuberculin skin test UNAIDS – Joint United Nations Programme on HIV/AIDS VacA – vacuolating cytotoxin A VAP – ventilator-associated pneumonia VBNC forms – viable but non-culturable forms VDRL test – Venereal Disease Research Laboratory test VP – viral proteins VPI – Vibrio pathogenicity island VZV – varicella-zoster virus WHO – the World Health Organization XDR M. tuberculosis – extensively drug-resistant M. tuberculosis Yop proteins – yersinia outer proteins 7 MEDICAL BACTERIOLOGY 8 Chapter 1 CAUSATIVE AGENTS OF SUPPURATIVE, WOUND AND HOSPITAL-ACQUIRED INFECTIONS PATHOGENIC STAPHYLOCOCCI The History of Discovery R. Koch discovered staphylococci in 1878. L. Pasteur obtained the pure culture of these bacteria in 1880. Later they were thoroughly studied by F. Rosenbach (1884). Classification of Staphylococci Staphylococci pertain to the family Staphylococcaceae, genus Staphylococcus. The genus Staphylococcus comprises more than 40 species. Three most common species are Staphylococcus aureus, Staphylococcus epidermidis, and Staphylococcus saprophyticus. S. aureus is one of the major human pathogens. It causes suppurative lesions in different tissues, wound infections, food poisoning, septicemia and many other serious disorders. Other staphylococci are usually the representatives of normal human microflora of skin and mucosal tissues. Nevertheless, S. epidermidis affects immunocompromised patients and patients with implanted appliances (intravenous catheters, drains, etc.) The infections of prosthetic devices can be also caused by S. hominis and S. haemolyticus. In rare cases S. saprophyticus is able to cause urinary tract infections predominantly in young women. The rest of staphylococcal species (S. schleifeiri, S. warneri, S. capitis and many others) is not regarded as causing infections in humans. Structure and Properties of Staphylococci Morphology Staphylococci are small spherical microbes, 0.5-1 m in diameter. Microbial cells are usually grouped into irregular grape-like clusters but