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Course, academic year 2023/2024
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Microbiology 2 - B83163 (General Medicine - English parallel)
Title: Microbiology 2
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: winter
Points: 5
E-Credits: 5
Examination process: winter s.:
Hours per week, examination: winter s.:2/2, C+Ex [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, PhD.
Guarantor: prof. RNDr. Libuše Kolářová, CSc.
Comes under: Compulsory for GM 3.y._23/24
Attributes: Lékařství
Teoretický předmět
Pre-requisite : {Prerekvizity pro zápis Mikrobiologie 2 pro ALEK}, B83122
Interchangeability : B80382
Is co-requisite for: B80033, B80121
Is interchangeable with: B80382
Files Comments Added by
download Requirements for the Practical Part Medical Microbiology Exam (1).docx Practical classes contents Mgr. Kateřina Petříčková, Ph.D.
Annotation
Provides information on special clinical microbiology, virology, and parasitology. Reviews the most important pathogens of particular body systems and particular patient`s groups. Reviews related pathogenesis, diagnostics and therapy. During the practicals, reviews already acquired laboratory skills. Based on typical patient case reports and prepared samples, provides the opportunity to go through complete laboratory and diagnostic process and recommend the optimal treatment.
Last update: Kolářová Jana (12.02.2020)
Aim of the course

Students have to learn specialized microbiology and guidlines for effective anti-microbial therapy. In their written thesis they should provide ability to study in depth from different information sources and comprehensively summarize and explain knowledge obtained.

During practicals they learn diagnostics algorithm used in a routine laboratory for investigation of infectious agent and make familiar with routine tests.

Last update: Kolářová Jana (12.02.2020)
Literature - Czech

Doporučená:

  • Richard Goering, Hazel Dockrell, Mark Zuckerman, Ivan Roitt, Peter L. Chiodini. Mims' Medical Microbiology (5th ed.). : Elsevier Health Sciences,, 2012, s. ISBN 9780702050299.
  • Kayser, F. H.. Medical microbiology. Stuttgart ; New York: Thieme, 2005, 698 s. ISBN 1588902455.
  • Patrick Murray, Ken Rosenthal, Michael Pfaller. Medical Microbiology. 8th Edition. : Elsevier, 2015, s. ISBN 9780323359528.

Last update: Petříčková Kateřina, Mgr., Ph.D. (07.09.2022)
Teaching methods

A. Lectures

  • if not changed due to Covid-19-related restrictions, lectured in presence
  • attendance is registered via ISIC reader - sufficient attendance on lectures will free the student from the final credit test duty.


 B. Practicals (one week, teaching laboratories of the Dept. Microbiology and immunology, Studničkova 7, Ground Floor, Back Entrance.):

  • Please review the knowledge from the Micro I practical class before coming, it is required in the Micro II week!
  • Lab coat and shoes required, otherwise students are not allowed to enter the labs
  • Please come in time, delayed students interfere with the lab programme and disturb the others. Late comers will be recorded as absent for the entire day after the first 15 mins with all the consequences!!!
  • Students obtain a set of coded patients’ samples: urine, stool, wound swab, blood culture, BAL/sputum.
  • The aim is to identify the microbial species in the sample, evaluate the findings from the clinical point of view and suggest the treatment, if relevant.
  • Additionaly, students practise collection of their own samples: throat swab, nose swab, or urine.
  • During the week they follow algorithm of a routine bacteriological laboratory work-flow with using cultivation, microscopy, basic diagnostic tests and antibiotic-sensitivity tests.

 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 9:00and finish before the Integrated Block: Microbiology/Pathology.
  • Switches between the lab groups are allowed only due to serious reasons - illness, hospitalization, VISA issues. Please address your requests to Dr. Tibor Moško (tibor.mosko@lf1.cuni.cz).
Last update: Petříčková Kateřina, Mgr., Ph.D. (14.09.2023)
Entry requirements

All students should have credit for B83122 Microbiology 1.

Last update: Kolářová Jana (12.02.2020)
Requirements to the exam -

I. CREDIT REQUIREMENTS

1.     Lectures - Attendance is not compulsory, but please register it via ISIC readers in the lecture hall. If you attend 10 of 14 lectures at least you do not need to pass a final credit test. The optional credit test will review the knowledge from the lectures 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 reasons only (illness, injury, VISA issues) can be tolerated, please discuss the matter with your class supervisor in advance. In such case the student must learn the content of the missing lesson – the knowledge will be checked by the teacher.

3.     Laboratory protocols. Write down the workflows and results obtained during the processing of individual materials. It is checked by the teacher during the practical lessons. In the end of the week, students report orally on the results of their identification experiments based on the protocols.

4.     Seminar work. Within the scope of Microbiology 1+2, the topic is chosen by the student himself/herself, the thesis should contain a theoretical ("textbook") introduction to the topic and, above all, a new knowledge from scientific or medical sources (e.g. new epidemiological data, therapeutic and preventive procedures, novel knowledge about known or new infectious agents, interesting clinical cases, etc.).

    • Preferred formshort PowerPoint presentation (8 min + 2 min discussion) presented at the end of the practical week.
    • Alternatively, 4 standard A4 pages of text.
    • Both with appropriately cited sources.

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. 

 

 

II. EXAM: LIST OF EXAMINATION QUESTIONS (valid from 2022/23):

 

I. PRACTICAL PART - 1 question - topics covered by microbiology practicals + following fields:

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 parasitary 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 (preanalytical 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

 

II. THEORETICAL PART - 3 questions:

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

A4.     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-haemolytic streptococci (Streptococcus pyogenes, S. agalactiae and other)

B4.      α-haemolytic 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 diarrhoeas

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.    Arboviroses and arbovirus encephalitis

B50.    Causative agents of viral haemorrhagic fevers

B51.    Rabies virus

B52.    Poxviruses

B53.    Prion diseases

B54.    Trypanosomes (African trypanosomes 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.    Malaric plasmodia

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.      Exanthematous diseases of viral origin; 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.    Fetal 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. (14.09.2023)
Education plan -
Schedule by date
Day Date Description Teacher Files Note Hodnocení
Thursday05.10.2023HIV, Viral Hepatitis, Antiviral Therapy MUDr. Zora Mělková, Ph.D. 
průměr: 3, hodnoceno: 1x
Thursday12.10.2023Antimicrobial agents and antimicrobial therapy.prof. Ing. Jaroslav Hrabák, Ph.D. 
Thursday19.10.2023Principles of Anti-microbial Therapy. Antibiotic Centre. MUDr. Václava Adámková, Ph.D. 
Thursday26.10.2023Agents of Gastrointestinal Tract Infections Mgr. Marta Chanová, Ph.D. 
Thursday02.11.2023Selected Agents of Respiratory Tract InfectionsMgr. Kateřina Petříčková, Ph.D. 
Thursday09.11.2023Agents of Abdominal Infections. Infections during pregnancy. MUDr. Václava Adámková, Ph.D. 
Thursday16.11.2023Clinical Microbiology of Skin, Soft Tissue, Bone and Joints Infections. MUDr. Václava Adámková, Ph.D. 
Thursday23.11.2023Neuroinfections. Infectious Agents in Bloodstream. RNDr. Jan Novák, Ph.D. 
Thursday30.11.2023Agents of Urinary Tract Infections. Sexually Transmitted Infections. MUDr. Václava Adámková, Ph.D. 
Thursday07.12.2023Fetal and neonatal infections.Lectured by Dr. Soňa Mečířová
Thursday14.12.2023 Integrated Block Microbiology/Pathology/Infection Medicine  
Thursday21.12.2023Infections in Immunocompromised Patients (Opportunistic Infections) RNDr. Jan Novák, Ph.D. 
Thursday04.01.2024Microbiology of Imported Infections RNDr. MUDr. František Stejskal, Ph.D. 
Thursday11.01.2024Community Infections Tending to Epidemies. Hospital - acquired Infections. RNDr. Tibor Moško, Ph.D. 
Thursday18.01.2024Emerging Infectious AgentsMUDr. Emil Pavlík, CSc. 
 
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