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Microbiology 1 - B83122 (General Medicine - English parallel)
Provides basic information on clinical microbiology, virology, and parasitology. Based on the recent classification,
reviews the most important bacteria, fungi, and parasites of humans, their features, pathogenesis, diseases.
Reviews microbiological diagnostic techniques, prevention, vaccination, and therapeutic methods. During the
practicals, provides the opportunity to test correct sampling, subsequent basic laboratory diagnostic methods,
pathogen identification, and antibiotics sensitivity testing, and strategy of ATB therapy.
Last update: Kolářová Jana (10.02.2020)
Aim of the course
The aims of the subject: to provide knowledge on general microbiology, teach students , how to behave in an infectious area, how to deal with infectious material, how to prevent spread of infection. Students should understand interactions of infectious agents and the host, pathogenetic and immune mechanisms in the disease. They obtain basic laboratory skills and get guidlines for taking proper samples.
Last update: Kohútová Vladislava, Ing. (07.01.2019)
Syllabus
Introduction to Medical Microbiology, Basic Disciplines. Role in Health Care System. Characteristics of microorganisms- bacteria, viruses, fungi and parasites
Identification Techniques for Microbes
Morphology and Physiology of Bacteria, Disinfection and Sterilisation Technics, Methods of Sterility Control
Interaction of bacteria and the host - Pathogenicity and Virulence,
Antimicrobial agents and antimicrobial therapy.
Review of Medical Bacteriology.Bacterial Genetics
Gram-negative Bacteria, Spirochets and Mycoplasma
Mycobacteria, Chlamydiae, Rickettsiae
Viruses. Taxonomy. pathogenesis and intracellular parasitism in the host cell
Selected DNA Viruses
Prions and prionic infections
Selected RNA Viruses
Medical Mycology
Parasitology
Seminars (Attendance Compulsory):
Diagnostic Techniques in Medical Microbiology
Rational antimicrobial therapy
Practicals:
Microscopy in medical bacteriology, mycology and parasitology. Native, fixed and stained slide. Staining techniques (Gram. Ziehl-Nielsen, Buri, Giemsa, immunofluorescence). Bacterial culture media, cultures and macroscopic morphology. Metabolic Tests (API, Pliva Staphytest, Streptotest, Enterotest) Toxin detection. Antigen detection, Typing. Antibiotic susceptibility tests (diffusion/disc tests, E-tests, MIC, MBC-testing) Serologic reactions( agglutination, precipitation, immunodiffusion, immunofluorescence, ELISA, immunoblot). Genome detection techniques ? hybridisation, PCR. Horizontál electrophoresis, real-time PCR. Urine culture and interpreting of the test. Yeast culture (Sabouraud) and GT-test. Sample collection techniques and Kits, documentation, transport requirements. Disinfection and Sterilisation techniques and Sterility control. Blood cultures ? proper taking of samples, culture systéme icl. BacTec, BactAlert. Anearobic Culture. Anaerostat.
Last update: Kolářová Jana (10.02.2020)
Literature -
Obligatory:
Murray, Patrick R., Rosenthal, Ken S. Pfaller, Michael A.. Medical microbiology. : , 2021, s. ISBN 978-0-323-67450-8.
Recommended:
Melter, Oto, Castelhano, Rute (eds.). The MicroBook : clinical microbiology for medical students. Prague: Univerzita Karlova, Nakladatelství Karolinum, 2019, 326 s. ISBN 978-80-246-3871-3.
Last update: Petříčková Kateřina, Mgr., Ph.D. (29.08.2024)
Povinná:
Murray, Patrick R., Rosenthal, Ken S. Pfaller, Michael A.. Medical microbiology. : , 2021, s. ISBN 978-0-323-67450-8.
Goering, Richard V. Dockrell, Hazel M. Zuckerman, Mark A. Chiodini, Peter L. (eds.). Mims' medical microbiology. : , 2013, 565 s. ISBN 978-0-8089-2440-1.
Last update: Petříčková Kateřina, Mgr., Ph.D. (11.02.2022)
Teaching methods
The course consists of one week block of practical training (hands-on) focused on microscopy and culture of bacteria and fungi, staining techniques, desinfection and sterilizing techniques, antibiotic susceptibility tests(disc, MIC, MBC), sterility control techniques, basic defense immunity mechanisms, toxin detection, serological reactions, microscopic parasitology, and proper specimen collection and transport (teaching laboratories of the Dept. Microbiology and immunology, Studničkova 7, Ground Floor, Back Entrance).
Organization of the Practicals:
The students are divided into groups of 12 based on the capacity of laboratories.
The list of students assigned to particular groups and dates will be available in the SIS as soon as the list of all registered students is ready - shortly before the beginning of the semester.
The practical classes will start in the 2nd week of the semester (Monday 9:00)
Switches between the lab groups are allowed only due to serious reasons - illness, hospitalization.
Students should bring their own signed white coat, a pair of lab shoes and a small pendant lock for the garderobe locker. We cannot allow students without the coat and shoes in the laboratories! Thanks for understanding.
Last update: Petříčková Kateřina, Mgr., Ph.D. (11.02.2022)
Requirements to the exam
CREDIT REQUIREMENTS
1. Lectures
Attendance is not compulsory, but please register it via ISIC readers in the lecture hall.
If you attend10 lectures at leastyou do not need topass a final credit test.
The optional credit test will review the knowledge from the lectures and practical classes only (PC room, Moodle-based, 30 MCQs for 36 minutes, evaluated percentually, 60 % at least needed to pass, 3 attempts available, credit week primarily).
2. Attendance at the laboratory week
A single day absence due to serious and documented reasons only (illness, injury, VISA issues) can be tolerated, please discuss the matter with your class supervisor in advance. This, however, does not apply to the Friday parasitology training.
If you miss the parasitology part, please contact dr. Vladimir Skala z NRL (Vladimir.Skala@vfn.cz) in advance to set an alternative date to pass the parasitology practice.
In case of missing one of the days, please make sure to catch up with all the relevant knowledge, as the practical teachers may check it.
3. Laboratory protocols.
Please document all the techniques and results obtained during the class. The protocols will be checked by the teachers and you will use your notes during the Microbiology 2 practical week, too, where the acquired knowledge is essential.
NON-COMPLETION OF THE PRACTICAL WEEK IN JUSTIFIED CASES: The student may be moved to a substitute week. This option is quite extraordinary, and each application will be strictly controlled. The application shall be sent to the tibor.mosko@lf1.cuni.cz and shall be approved by the Head of the Institute.
Credits will be awarded by the practical labs’ supervisors in the credit week after passing all the above-listed tests and duties.
LIST OF EXAMINATION QUESTIONS valid from the winter semester 2022/2023 (Microbiology 2):
PRACTICAL PART - knowledge from the practical laboratory weeks plus the following topics
1. Microbiological diagnosis: indications, risks and effectiveness 2. Diagnosis of bacterial infections 3. Diagnosis of viral infections 4. Diagnosis of mycotic infections 5. Diagnosis of parasitic infections 6. Direct proof methods of microbial agents identification, interpretation of results 7. Indirect proof methods of microbial agents identification, interpretation of results; antibodies titre and its relevance 8. Cultivation media types and their applications 9. Anaerobic culture 10. Staining techniques for bacteria, micromycetes and parasites 11. Methods of toxin production proof 12. Interaction of bacterial hemolysins 13. Antibiotic susceptibility assessment: principles of disc-based and dilution methods, factors affecting reliability, limitations, interpretation of results 14. Identification based on phenotypic markers 15. Molecular techniques in identification: material, typical indications, results interpretation 16. Vaginal swab image (vaginal wet mount): interpretation of results 17. Basic rules for microbial specimen collection 18. Transport of clinical specimens (pre-analytical phase). 19. Infections of blood stream and systemic infections: valid material for microbiological diagnosis 20. Respiratory tract, oral cavity and ear infections: valid material for microbiological diagnosis 21. Gastrointestinal tract infections: valid material for microbiological diagnosis 22. Urinary tract infections: valid material for microbiological diagnosis 23. Genital tract infections: valid material for microbiological diagnosis 24. CNS infections: valid material for microbiological diagnosis 25. Eye infections: valid material for microbiological diagnosis 26. Skin infections: valid material for microbiological diagnosis 27. Microbiological examination of biopsy, punctate and section materials 28. Microbiological control of environment and sterility 29. Methods of decontamination 30. Methods of sterilization and the process control 31. Safety rules in the environment with risks of professional infections
A. GENERAL MICROBIOLOGY
A1 Structure of a bacterial cell (cell wall, external structures, spores). A2 Growth and multiplication of bacterial population. Products of bacterial metabolism. A3 Natural bacterial flora and its regulation. Biofilms. A4 Bacterial pathogenicity and virulence factors; bacterial toxins and superantigens. A5 Genetic information in bacteria and its transfer. A6 Mechanisms of natural and acquired antibiotic resistance in clinically important bacteria. A7 Structure of viruses and viral particles. A8 Genetic information of viruses and their classification. A9 Course of viral infection of the host cell and its cytopathic effects. A10 Virus and host: pathogenesis of viral infections, interferons. Modes of transmission of viral infections. A11 Structure of the infectious prion particle, mechanism of prion propagation. A12 Cell structure of yeasts and fungi. A13 Medically important micromycetes - characteristics, transmission, mycotoxicoses. A14 Medically important Protozoa – characteristics and transmission. A15 Medically important helminths – characteristics and transmission. A16 Basic rules of collection of clinical materials. A17 Principles and mechanisms of specific and non-specific immunity. A18 Transmission of diseases: modes and mechanisms of spread of microbial agents. A19 Bacterial culture and diagnosis of bacterial infections, their limitations and examples of use. A20 Antibiotic susceptibility testing, interpretation of results. Basic pharmacodynamic and pharmacokinetic parameters of antibiotics. A21 Diagnosis of viral infections. A22 Diagnosis of mycotic infections. A23 Diagnosis of parasitic infections. A24 Serological examination of clinical materials, principles of basic methods, their advantages, and limitations. A25 Methods for direct detection of agents in the diagnosis of microbial infections. A26 Beta-lactam antibiotics. Classification, mechanisms of action and resistance. A27 Macrolides, lincosamides, tetracyclines, chloramphenicol. Classification, mechanisms of action and resistance. A28 Quinolones. Classification, mechanisms of action and resistance. A29 Aminoglycosides. Classification, mechanisms of action and resistance. A30 Glycopeptide antibiotics. Classification, mechanisms of action and resistance. A31 Antivirals. Classification, mechanisms of action and resistance. A32 Antivirals - inhibitors of entry and initial phases of viral replication cycle. A33 Antivirals - inhibitors of the nucleic acid synthesis. A34 Antivirals - inhibitors of proteases and viral release from cells. A35 Antifungals. A36 Antiparasitics. A37 Cotrimoxazole, metronidazole, nitrofurantoin. Classification, mechanisms of action and resistance.
B. SPECIAL MICROBIOLOGY AND PARASITOLOGY B1 Staphylococcus aureus B2 Coagulase negative staphylococci B3 β-hemolytic streptococci (Streptococcus pyogenes, S. agalactiae and other) B4 α-hemolytic streptococci (Streptococcus pneumoniae, viridans and other) B5 Enterococci B6 Corynebacterium spp and other coryneform gram-positive rods B7 Listeria spp., Erysipelothrix spp. B8 Bacillus spp., Nocardia spp., Rhodococcus spp. B9 Enterobacteria - Escherichia coli B10 Enterobacteria - Salmonella spp., Shigella spp., Yersinia spp. B11 Enterobacteria - Klebsiella spp., Enterobacter spp., Serratia spp., Proteus spp. and other facultatively pathogenic species B12 Vibrio spp., Aeromonas spp., Plesiomonas spp. B13 Pseudomonas aeruginosa and other pseudomonades B14 Gram-negative non-fermenting rods: Burkholderia spp., Stenotrophomonas spp., Acinetobacterspp. and other B15 Neurotoxic clostridia species B16 Histotoxic clostridia species B17 Gram-positive non-sporulating anaerobes B18 Gram-negative anaerobic rods and cocci B19 Legionella spp. B20 Gram-negative aerobic cocci (Neisseria spp., Moraxella spp.) B21 Haemophilus spp., Bordetella spp. B22 Campylobacter spp., Helicobacter spp. B23 Borrelia spp., Leptospira spp. B24 Treponema spp. B25 Mycoplasma spp., Ureaplasma spp. B26 Chlamydia spp., Chlamydophilla spp. B27 Rickettsia spp., Coxiella spp., Anaplasma spp., Ehrlichia spp. B28 Classical and atypical mycobacteria B29 Candida spp. B30 Cryptococcus spp. and other (non-Candida) pathogenic yeasts B31 Aspergilli and Zygomycetes B32 Dermatophytes B33 Mucorales (Rhizopus spp., Rhizomucor spp., Absidia spp., Mucor spp., etc) B34 Dimorphic fungi (Histoplasma spp., Blastomyces spp., Penicillium marneffei, etc) B35 Pneumocystis jirovecii and mycotic infections in AIDS patients B36 Herpes Simplex and Varicella zoster virus B37 Herpesviruses - CMV, EBV. HHV-6,7,8 B38 Human papillomaviruses and polyomaviruses B39 Rotaviruses, noroviruses and other agents of viral diarrheas B40 Fecal-orally-transmitted hepatitis viruses B41 Sexually- or blood-transmitted hepatitis viruses B42 HIV virus B43 Influenza viruses B44 Rhinoviruses, coronaviruses, paramyxoviruses (Parainfluenza and RS virus) B45 Adenoviruses B46 Enteroviruses (Polio and others) B47 Paramyxoviruses and parvoviruses B48 Rubella virus B49 Arboviruses and arbovirus encephalitis B50 Causative agents of viral haemorrhagic fevers B51 Rabies virus B52 Poxviruses B53 Prion diseases B54 Trypanosomas (African trypanosomes and Trypanosoma cruzi) B55 Leishmania spp. B56 Amoebae (Entamoeba histolytica and others) B57 Intestinal Protozoa (Giardia intestinalis and others) B58 Trichomonas vaginalis B59 Toxoplasma gondii B60 Malaria plasmodia species B61 Schistosomas B62 Intestinal cestodes (Taenia, Hymenolepis, Diphyllobothrium and others) B63 Tissue cestodes B64 Roundworms, pinworms and other intestinal nematodes B65 Strongyloides spp. and hookworms B66 Trichinella spp. and other tissue nematodes B67 Lice, fleas and bedbugs B68 Itch mites and other skin-associated mites
C. CLINICAL MICROBIOLOGY C1 Pathogens of skin and soft tissue infections; microbiological diagnosis; therapy. C2 Viral exanthemas; microbiological diagnosis; therapy. C3 Surgical site infections; causative agents and microbiological diagnosis; therapy. C4 Neuroinfections - aseptic infections and suppurative meningitis; causative agents and microbiological diagnosis; therapy. C5 Causative agents of upper respiratory tract infections; microbiological diagnosis; therapy. C6 Causative agents of lower respiratory tract infections; microbiological diagnosis; therapy C7 Causative agents of urinary tract and kidney infections; microbiological diagnosis; therapy. C8 Sexually transmitted infections; causative agents and microbiological diagnosis; therapy. C9 Causative agents of heart and blood vessels infections; microbiological diagnosis; therapy. C10 Causative agents of bloodstream infections and sepsis; microbiological diagnosis; therapy. C11 Intra-abdominal infections; causative agents and microbiological diagnosis; therapy. C12 Pathogens of diarrhoeal infections; microbiological diagnosis; therapy. C13 Pathogens of bone and joint infections; microbiological diagnosis; therapy. C14 Foetal and neonatal infections; causative agent and microbiological diagnosis; therapy. C15 Basic principles of antimicrobial therapy (essential information for initiating and selecting an anti-infective treatment strategy when the causative agent is unknown). C16 Basic tools and methods for influencing appropriate antibiotic use in the community and hospital. C17 Treatment with antibiotics and other anti-infective drugs (initial and targeted treatment - choice of route and duration of administration, intensity of treatment; supportive measures: drainage of pus, etc.). C18 Principles of vaccination, immunoprophylaxis, passive immunization. C19 Mandatory vaccination and vaccination on request; evaluation of vaccination effectiveness. C20 Causative agents of the most important imported infections and assessment of their epidemiological significance in the Czech Republic. C21 Pathogens of highly dangerous infections and ways of preventing their spread. C22 The most important agents of nosocomial infections; multiresistant strains. C23 Zoonotic agents, principles of transmission, microbiological diagnosis, therapy and prophylaxis.
Last update: Petříčková Kateřina, Mgr., Ph.D. (20.02.2024)
