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Course, academic year 2022/2023
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Microbiology 1 - B80035 (General Medicine - English parallel)
Title: Mikrobiologie 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 2018
Semester: summer
Points: 4
E-Credits: 4
Examination process: summer s.:
Hours per week, examination: summer s.:2/2 [hours/week]
Extent per academic year: 60 [hours]
Capacity: unlimited
Min. number of students: unlimited
Virtual mobility / capacity: no
State of the course: taught
Language: English
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
Guarantor: prof. RNDr. Libuše Kolářová, CSc.
Attributes: Lékařství
Teoretický předmět
Pre-requisite : {Anatomy as a requisite}, {General Histology as a pre-requisite}, B80005
Is interchangeable with: B83122
Annotation -
Last update: Mgr. Kateřina Petříčková, Ph.D. (23.05.2019)
Provides basic information on general and specialised human medical microbiology, virology, mycology and parasitology. Describes important human pathogens, their characteristic properties, pathogenicity mechanisms of the diseases they induce, and basics of the antibiotic, antifungal, antiviral and antioparasitic therapy of the diseases. In practical hands-on learning provides important skills for bacteriological investigation of selected samples. The student will learn technics for clinical specimen collection, strategy of microbial identification and anti-microbial therapy.
Aim of the course
Last update: Mgr. Kateřina Petříčková, Ph.D. (23.05.2019)

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: Mgr. Kateřina Petříčková, Ph.D. (04.02.2019)

Lectures Microbiology 1 (2nd year, Summer Term)

Lectures in 2 hour units 30 hours of lectures/term
Week Lecturer Theme

  1. Kolářová: Introduction to Medical Microbiology, Basic Disciplines. Role in Health Care System. Characteristics of microorganisms- bacteria, viruses, fungi and parasites
  2. Pavlik: Identification Techniques for Microbes
  3. Paetříčková: Morphology and Physiology of Bacteria, Bacterial Genetics
  4. Holada: Disinfection and Sterilisation Technics, Methods of Sterility Control
  5. Pavlik: Interaction of bacteria and the host - Pathogenicity and Virulence,
  6. Adámková: Antimicrobial agents and antimicrobial therapy.
  7. Pavlík: Review of Medical Bacteriology. Gram-positive bacteria
  8. Pavlík: Gram-negative Bacteria, Spirochets and Mycoplasma
  9. Pavlík: Mycobacteria, Chlamydiae, Rickettsiae
  10. Mělková: Viruses. Taxonomy. pathogenesis and intracellular parasitism in the host cell
  11. Mělková:  Selected DNA Viruses
  12. Holada Prions and prionic infections
  13. Mělková: Selected RNA Viruses
  14. Skořepová: Medical Mycology
  15. Chánová: Parasitology

Seminars (Attendance Compulsory, within the lectures, indicated in the Education Plan):

  1. Diagnostic Techniques in Medical Microbiology (3 hours)
  2. Rational antimicrobial therapy (3 hours)


Practicals (one week, total 24 hours):

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. (23.05.2019)

MURRAY P.R., ROSENTHAL K.S., PFALLER M.A. eds.: Medical Microbiology fifth edition, Mosby Inc. St. Louis 2006.

Teaching methods
Last update: Mgr. Kateřina Petříčková, Ph.D. (23.05.2019)

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).
Additional 2 seminars on Modern diagnostic techniques in medical microbiology and Strategies of antimicrobial therapy.
Lectures cover basic topics on general microbiology and first 4 topics on specialised medical microbiology.
Students are provided a selection of themes for their seminar thesis required for B 80372 Microbiology 2 credit

Entry requirements
Last update: Mgr. Kateřina Petříčková, Ph.D. (17.01.2019)

All students should have credit for B80005 Biology and Genetics 1 + Anatomy [B80598, B82239],

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.
  • 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.

Requirements to the exam
Last update: Mgr. Kateřina Petříčková, Ph.D. (18.02.2022)

 

Credits will be awarded on the basis of a credit test, the practical week active attendance, protocols and announcement of topic chosen for seminar thesis.

 

 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: 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 Bacterial cell structure (bacterial cell wall, superficial structures, spores)
A2 Growth and proliferation of the bacterial population. Types and end products of bacterial metabolism
A3 Natural bacterial flora and its regulation. Biofilms
Pathogenicity and virulence factors of bacteria; bacterial toxins and superantigens
A5 Genetic information of bacteria and its transfer
A6 Mechanisms of intrinsic and acquired antibiotic resistance in clinically relevant bacteria
A7 Structure of viruses and viral particles
A8 Genetic information of viruses and their classification
A9 Viral infection of a host cell and its cytopathic effects
A10 Virus and host organism: Pathogenesis of viral infections, interferons. Ways of viral infection transmission.
A11 Structure of an infectious prion particle, mechanism of prion propagation
A12 Fungal cell structure
A13 Medically important micromycetes - characteristics, transmission, mycotoxicoses
A14 Medically important Protozoa - characteristics, transmission
A15 Medically important helminths - characteristics, transmission
A16 Basic rules for clinical specimen collection
A17 Principles and mechanisms of specific and non-specific immunity
A18 Transmission of infections: ways and mechanisms
A19 Cultivation of bacteria and diagnosis of bacterial infections, limitations and examples of application
A20 Antibiotic susceptibility assays, interpretation of results. Basic pharmacodynamic and pharmacokinetic parameters of antibiotics (MIC, MBC, AUC/MIC, T above MIC...)
A21 Diagnosis of viral infections
A22 Diagnosis of mycotic infections
A23 Diagnosis of parasitic infections
A24 Serological examination of clinical specimens. Basic techniques, their advantages and limitations
A25 Methods for direct proofs of infectious agents in 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 Antiviral drugs. Classification, mechanisms of action and resistance
A32 Antiviral drugs - inhibitors of entry and initial phases of viral replication cycle
A33 Antiviral drugs - inhibitors of the nucleic acid synthesis
A34 Antiviral drugs - inhibitors of proteases and the virus release from cells
A35 Antifungal drugs
A36 Antiparasitic drugs
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 trypanosomas and Trypanosoma cruzi)
B55 Leishmania spp.
B56 Amoebae (Entamoeba histolytica and other)
B57 Intestinal Protozoa (Giardia intestinalis and other)
B58 Trichomonas vaginalis
B59 Toxoplasma gondii
B60 Malaria plasmodia species
B61 Schistosomas
B62 Intestinal cestodes (Taenia, Hymenolepis, Diphylbothrium and other)
B63 Tissue cestodes
B64 Ascarids, pinworms and other intestinal nematodes
B65 Strongyloides 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.

 
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