SubjectsSubjects(version: 945)
Course, academic year 2023/2024
   Login via CAS
Microbiology 1 - B83122 (General Medicine - English parallel)
Title: Microbiology 1
Guaranteed by: Institute of Immunology and Microbiology First Faculty of Medicine and General University Hospital in Prague (11-00351)
Faculty: First Faculty of Medicine
Actual: from 2023
Semester: summer
Points: 6
E-Credits: 6
Examination process: summer s.:
Hours per week, examination: summer s.:2/2, C [HT]
Extent per academic year: 60 [hours]
Capacity: unlimited
Min. number of students: unlimited
4EU+: no
Virtual mobility / capacity: no
State of the course: taught
Language: English
Teaching methods: full-time
Teaching methods: full-time
Explanation: Mgr. Kateřina Petříčková, Ph.D.; katerina.petrickova@lf1.cuni.czwhite-coat selected for this course only
Additional information: http://uim.lf1.cuni.cz
Old code: 35
Note: prefer medical statement
enabled for web enrollment
Guarantor: prof. RNDr. Libuše Kolářová, CSc.
Comes under: Compulsory for GM 2.y._23/24
Attributes: Lékařství
Teoretický předmět
Pre-requisite : {Anatomy as a requisite}, {General Histology as a pre-requisite}
Interchangeability : B80035
Is pre-requisite for: B80054, B83163, B80382
Files Comments Added by
download Organizace_Rozpis_Praktika_LS_2024_20240214.xls RNDr. Tibor Moško, Ph.D.
Annotation
Last update: Jana Kolářová (10.02.2020)
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.
Aim of the course
Last update: Ing. Vladislava Kohútová (07.01.2019)

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.

Syllabus
Last update: Jana Kolářová (10.02.2020)
  • 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):

    1. Diagnostic Techniques in Medical Microbiology
    2. 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.

    Literature -
    Last update: Mgr. Kateřina Petříčková, Ph.D. (11.02.2022)

    Obligatory:

    • Murray, Patrick R., Rosenthal, Ken S. Pfaller, Michael A.. Medical microbiology. : , 2021, s. ISBN 978-0-323-67450-8.

    Teaching methods
    Last update: Mgr. Kateřina Petříčková, Ph.D. (11.02.2022)

    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.

     

    Requirements to the exam
    Last update: Mgr. Kateřina Petříčková, Ph.D. (20.02.2024)

    CREDIT REQUIREMENTS

    1.     Lectures

    • Attendance is not compulsory, but please register it via ISIC readers in the lecture hall.
    • If you attend 10 lectures at least you do not need to pass 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., Acinetobacter spp. 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.

    Education plan -
    Schedule by date
    Day Date Description Teacher Files Note Hodnocení
    Monday19.02.2024Introduction to Medical Microbiology, Basic Disciplines. Role in Health Care System. Characteristics of microorganisms- bacteria, viruses, fungi and parasites prof. RNDr. Libuše Kolářová, CSc. 
    průměr: 3, hodnoceno: 2x
    Monday26.02.2024Disinfection and Sterilisation Technics, Methods of Sterility Control. doc. Ing. Karel Holada, Ph.D. 
    průměr: 4, hodnoceno: 2x
    Monday04.03.2024Morphology And Physiology Of Bacteria, Bacterial Genetics. Mgr. Kateřina Petříčková, Ph.D. 
    průměr: 5, hodnoceno: 2x
    Monday11.03.2024Interaction Of Bacteria And The Host - Pathogenicity And Virulence Mgr. Kateřina Petříčková, Ph.D. 
    průměr: 5, hodnoceno: 2x
    Monday18.03.2024Identification Techniques for Microbes. Correct Sampling and Transport of Material RNDr. Jan Bobek, Ph.D. 
    průměr: 3, hodnoceno: 2x
    Monday25.03.2024Normal human microbiota. Interpretation of laboratory data. MUDr. Jana Kudláčková 
    průměr: 3, hodnoceno: 2x
    Monday01.04.2024Public holiday 
    průměr: 5, hodnoceno: 2x
    Monday08.04.2024Review of Medical Bacteriology. Gram-positive bacteria. Ing. Gabriela Kroneislová 
    Monday15.04.2024Review of Medical Bacteriology: Gram-negative Bacteria. RNDr. Jan Novák, Ph.D. 
    Monday22.04.2024Review of Medical Bacteriology: Spirochaetes, Mycoplasmas, Chlamydiae, MycobacteriaMgr. Kateřina Petříčková, Ph.D.Mycobacteria lectured by Mgr. Kateřina Svobodová, Ph.D.
    Monday29.04.2024Viruses. Taxonomy. Pathogenesis And Intracellular Parasitism In The Host Cell. Selected RNA Viruses. MUDr. Zora Mělková, Ph.D. 
    Monday06.05.2024 Selected DNA Viruses.MUDr. Zora Mělková, Ph.D. 
    Monday13.05.2024Medical Mycology Lectured by Mgr. Kateřina Svobodová, Ph.D
    Monday20.05.2024Parasitology Mgr. Marta Chanová, Ph.D. 
    Monday27.05.2024Antiinfectives And Mechanisms Of ResistanceMUDr. Václava Adámková, Ph.D. 
     
    Charles University | Information system of Charles University | http://www.cuni.cz/UKEN-329.html