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Course, academic year 2022/2023
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Microbiology 2 - B80382 (General Medicine - English parallel)
Title: Mikrobiologie 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 2021
Semester: winter
Points: 4
E-Credits: 4
Examination process: winter s.:
Hours per week, examination: winter 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: not taught
Language: English
Teaching methods: full-time
Explanation: Mgr. Kateřina Petříčková, Ph.D.; katerina.petrickova@lf1.cuni.czWhite-coat and/or white shirt (T-shirt) and trousers.Seminar Thesis required for credit
Additional information: http://uim.lf1.cuni.cz
Old code: 382
Guarantor: prof. RNDr. Libuše Kolářová, CSc.
Attributes: Lékařství
Teoretický předmět
Pre-requisite : {Prerekvizity pro zápis Mikrobiologie 2 pro ALEK}, B83122
Co-requisite : B83121, B83123
Interchangeability : B83163
Is pre-requisite for: B80134
Is interchangeable with: B83163
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)

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.

Syllabus -
Last update: Mgr. Kateřina Petříčková, Ph.D. (23.05.2019)

Lectures Microbiology 2 (3rd year, Winter Term)

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




Practicals (one week, total 25 hours):

Students practisize collection of their own samples: throat swab, nose swab, urine and transport them to the laboratory.
During the week they follow algorithm of routine bacteriological laboratory work-flow hands-on.
Additionaly they obtain coded patiens samples: urine, stool, vaginal swab and blood culture.
They investigate each sample making different tests. At the end they have to provide results for each sample:
Determined pathogen and its sensitivity to antibiotics
Additionaly they perform Immunocard tests for different agents: viral or bacterial. They interpret serological tests and detect genome of EBV or CMV using PCR

 

Literature -
Last update: Mgr. Kateřina Petříčková, Ph.D. (15.09.2021)

Recommended:

  • MURRAY P.R., ROSENTHAL K.S., PFALLER M.A. eds. Medical Microbiology, 8th edition. : Elsevier, 2015, s. ISBN 9780323359528.
  • Richard Goering, Hazel Dockrell, Mark Zuckerman, Ivan Roitt, Peter L. Chiodini. Mims' Medical Microbiology (5th ed.). : Elsevier Health Sciences, 2012, s. ISBN 9780702050299.

Learning resources
Last update: Mgr. Kateřina Petříčková, Ph.D. (25.09.2020)

MS Teams: Microbiology 2 20/21 B83163

Teaching methods
Last update: Mgr. Kateřina Petříčková, Ph.D. (15.09.2021)

.A. Lectures

  • Covid epidemics-related update (Sep 15, 2021): Lectures given in presence according to current legal rules. Please follow the guidelines in the www.lf1.cuni.cz webpage for updates.


 
C. 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
  • 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 practical week starts with a short test of knowledge acquired during Microbiology 1 practicals/lectures
    • 30 questions, multiple choice, 15 correct answers required to pass
    • major topics: sterilisation and disinfection, cultivation techniques (aerobes, anaerobes, basic cultivation media, bacteria, yeast, viruses), staining and microscopy techniques, identification techniques (bacteria, yeast, viruses, parasites), antibiotic sensitivity-related terms and assays, basic characteristics of the most important pathogens presented during Microbiology I
  • 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 and 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 or Dr. Jan Novák.



 

Entry requirements
Last update: Mgr. Kateřina Petříčková, Ph.D. (23.05.2019)

All students should have credit for B80035 Microbiology 1.


Requirements to the exam
Last update: Mgr. Kateřina Petříčková, Ph.D. (07.11.2019)

CREDIT requirements

  • Practical class attendance
  • Successful identification of 80 % of microbes in the clinical samples provided. Written protocols reviewing the findings.
  • Seminar thesis (4 x A4 pages in minimum) or seminar talk (10 mins including a space for questions) on a selected topic.

 

 

LIST OF EXAMINATION QUESTIONS valid from the winter semester 2019/2020:

 

I. PRACTICAL PART - 1 question - topics covered by microbiology practicals(cultivation, staining, direct and indirect diagnostic techniques, clinical specimen collection, transport and processing, personnel and environment hygiene, disinfection and sterilisation, basis of aseptic work)

II. THEORETICAL PART - 3 questions:

 

A. GENERAL MICROBIOLOGY

A1.         Bacterial cell structure (bacterial cell wall, superficial structures, spores)

A2.         Types and end products of bacterial metabolism

A3.         Growth and proliferation of the bacterial population

A4.         Genetic information of bacteria and its transfer

A5.         Biofilms and regulation of bacterial flora

A6.         Physiological bacterial flora of the human body and its clinical significance

A7.         Pathogenicity and virulence factors of bacteria; bacterial toxins and superantigens

A8.         Medically important yeasts and moulds

A9.         Mycotoxicosis

A10.       Characteristics of medically important parasites

A11.       Viruses: Structure, growth cycle, replication strategies, and classification

A12.       Interactions between viruses and cells: Types of infection, cytopathogenic effects of viruses

A13.       Genetics of viruses, frequency of mutations, use of attenuated strains, recombination, reassortment

A14.       Virus and host organism: Types of infection courses.

A15.       Induction and function of interferons and their use in therapy

A16.       Viral mechanisms of immune evasion

A17.       Principles of collection of clinical specimens

A18.       Principles and mechanisms of specific, non-specific and antitoxic immunity

A19.       Transmission of infections: ways and mechanisms

A20.       Principles of vaccination, immunoprophylaxis, passive immunization. Compulsory and on-demand vaccinations; evaluation of vaccination efficiency

A21.       Diagnosis of bacterial infections

A22.       Examination of clinical specimens by cultivation

A23.       Anaerobic bacteria: properties and cultivation

A24.       Serological examination of clinical specimens

A25.       Diagnosis of viral infections

A26.       Diagnosis of parasitic infections

A27.       Diagnosis of mycotic infections

 

B. SPECIAL MICROBIOLOGY AND PARASITOLOGY

B1.         Staphylococcus aureus

B2.         Coagulase negative staphylococci

B3.         Streptococcus pyogenes, S. agalactiae and other β-hemolytic streptococci

B4.         Viridans streptococci, Streptococcus bovis and other rare streptococci

B5.         Streptococcus pneumoniae

B6.         Enterococci

B7.         Corynebacterium spp and other coryneform gram-positive rods

B8.         Listeria spp., Erysipelothrix spp.

B9.         Bacillus spp., Nocardia spp., Rhodococcus spp.

B10.       Enterobacteriaceae - Escherichia coli

B11.       Enterobacteriaceae - Salmonella spp.,  Shigella spp.

B12.       Yersinia spp.

B13.       Enterobacteriaceae - Klebsiella spp., Enterobacter spp., Serratia spp., Proteus spp. and other facultatively pathogenic species

B14.       Vibrio spp., Aeromonas spp. and Plesiomonas spp.

B15.       Pseudomonas aeruginosa and other pseudomonades

B16.       Gram-negative non-fermenting rods: Burkholderia spp., Stenotrophomonas spp., Acinetobacter spp. and others

B17.       Neurotoxic clostridia species

B18.       Histotoxic clostridia species

B19.       Gram-positive non-sporulating anaerobes

B20.       Gram-negative anaerobic rods and cocci

B21.       Legionella spp.

B22.       Neisseria spp., Moraxella spp.

B23.       Genera Francisella, Bartonella, Afipia, Pasteurella, Brucella

B24.       HACEK group (genera Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, and Kingella)

B25.       Haemophilus spp., Bordetella spp.

B26.       Campylobacter spp., Helicobacter spp.

B27.       Borrelia spp., Leptospira spp.

B28.       Treponema spp. and other spirochetes

B29.       Mycoplasma spp. and Ureaplasma spp.

B30.       Chlamydia spp. Chlamydophilla spp.

B31.       Rickettsia spp., Coxiella spp., Anaplasma spp., Ehrlichia spp.

B32.       Classical and atypical mycobacteria

B33.       Candida spp. - localized and systemic infections

B34.       Cryptococcus spp. and other (non-Candida) pathogenic yeasts (Saccharomyces spp., Malassezia spp., Trichosporon spp.)

B35.       Aspergillus spp.

B36.       Dermatophytes (Trichophyton spp., Microsporum spp., Epidermophyton spp.)

B37.       Mucorales (Rhizopus spp., Rhizomucor spp., Absidia spp., Mucor spp.)

B38.       Dimorphic fungi (Histoplasma spp., Blastomyces spp., Penicillium marneffei, etc)

B39.       Pneumocystis jirovecii and mycotic infections in AIDS patients

B40.       Herpes Simplex and Varicella zoster (alpha-herpesviruses)

B41.       CMV other beta-herpesviruses

B42.       EBV and KSHV (gamma-herpesviruses)

B43.       Human papillomaviruses and polyomaviruses

B44.       Rotaviruses, noroviruses and other agents of viral diarrheas

B45.       Fecal-orally-transmitted hepatitis viruses

B46.       Sexually-transmitted hepatitis viruses

B47.       HIV virus

B48.       Influenza viruses

B49.       Rhinoviruses, coronaviruses, paramyxoviruses (Parainfluenza and RS virus)

B50.       Adenoviruses

B51.       Enteroviruses (Polio and others)

B52.       Paramyxoviruses and parvoviruses

B53.       Rubella Virus

B54.       Arbovirosis and arbovirus encephalitis

B55.       Causative agents of viral hemorrhagic fevers

B56.       Rabies virus

B57.       Poxviruses

B58.       Prions

B59.       African  trypanosomes and Trypanosoma cruzi

B60.       Leishmania spp.

B61.       Entamoeba histolytica and other intestinal amoebae

B62.       Giardia intestinalis, Balantidium coli and non-pathogenic intestinal protozoa (e.g. Chilomastix mesnili)

B63.       Trichomonas vaginalis

B64.       Amphizoic amoebae (Naegleria fowleri, Acanthamoeba spp., Balamuthia mandrillaris)

B65.       Toxoplasma gondii

B66.       Malaria parasites (genus Plasmodium)

B67.       Intestinal coccidia

B68.       Human and animal schistosomes

B69.       Hepatic, intestinal and pulmonary flukes

B70.       Tapeworms of the genera Taenia, Diphyllobothrium, Spirometra, and Hymenolepis

B71.       Echinococcus granulosus and E. multilocularis

B72.       Strongyloides spp., Ancylostoma spp., Necator spp.

B73.       Ascarids (roundworms)

B74.       Filariae

B75.       Trichinella spp., Trichuris spp.

B76.       Pinworms, Anisakis spp., Pseudoterranova spp.

B77.       Lice, fleas, bedbugs and itch mites

               

C. CLINICAL MICROBIOLOGY

C1.         Basic rules for the correct use of antibiotics in community and hospital

C2.         Basic pharmacodynamic and pharmacokinetic parameters of antibiotics (MIC, MBC distribution of MIC in bacterial population, antibiotic boundary concentration, maximum concentration, maximum dose, AUC/MIC, T above MIC, possibility to increase antibiotic activity - dose, interval)

C3.         Genetic backgrounds of bacterial antibiotic resistance, conditions preserving the resistance in a bacterial population

C4.         Antibiotic susceptibility testing: common methods (principles of disc and dilution methods, conditions for reliability of results, limitations, interpretations)

C5.         Antibiotic susceptibility testing: special methods (detection in fastidious bacteria, slow growing bacteria, and anaerobes; typical examples of poorly verifiable resistance)

C6.         Bacterial resistance caused by the production of inactivating enzymes: β-lactam antibiotics, hyperproduction of β-lactamases, chromosomal/plasmid β-lactamases, main producers in clinically relevant bacteria, differences in resistance to aminoglycosides in cocci and enterobacteria (associated resistance); interpretation of the results

C7.         Resistance to macrolides and lincosamides (main causes of resistance, efflux)

C8.         Main mechanisms of resistance to antibiotics of choice in clinically relevant bacteria (staphylococci, pneumococci, streptococci, haemophili, gonococci, meningococci, E. coli, Salmonella spp., Klebsiella spp., pseudomonads)

C9.         Inflammation and sepsis

C10.       Causative agents of epidemiologically significant autochthonous infections

C11.       Causative agents of the most important infections imported to Europe; assessment of their epidemiological significance

C12.       Causative agents of highly infectious diseases and prevention of their spread

C13.       The most significant agents of nosocomial infections

C14.       Causative agents of the upper respiratory tract infections: Methods of identification, appropriate clinical specimens, therapy

C15.       Causative agents of the ear infections: Methods of identification, appropriate clinical specimens, therapy

C16.       Causative agents of the lower respiratory tract infections: Methods of identification, appropriate clinical specimens, therapy

C17.       Causative agents of the Skin and soft tissue infections: Methods of identification, appropriate clinical specimens, therapy

C18.       Causative agents of the post-surgery infections: Methods of identification, appropriate clinical specimens, therapy

C19.       Causative agents of the eye infections: Methods of identification, appropriate clinical specimens, therapy

C20.       Causative agents of the CNS infections: Methods of identification, appropriate clinical specimens, therapy

C21.       Causative agents of the urinary tract and kidney infections: Methods of identification, appropriate clinical specimens, therapy

C22.       Causative agents of the male genital tract infections: Methods of identification, appropriate clinical specimens, therapy

C23.       Causative agents of the female genital tract infections: Methods of identification, appropriate clinical specimens, therapy

C24.       Causative agents of the heart and blood vessels infections: Methods of identification, appropriate clinical specimens, therapy

C25.       Causative agents of the bloodstream infections and sepsis: Methods of identification, appropriate clinical specimens, therapy

C26.       Causative agents of the gastrointestinal infections: Methods of identification, appropriate clinical specimens, therapy

C27.       Causative agents of the intra-abdominal infections (peritonitis, intra-abdominal abscesses and empyemas): Methods of identification, appropriate clinical specimens, therapy

C28.       Causative agents of the bone and joint infections: Methods of identification, appropriate clinical specimens, therapy

C29.       Causative agents of the zoonotic infections: Methods of identification, appropriate clinical specimens, therapy

C30.       Causative agents of the sexually transmitted infections: Methods of identification, appropriate clinical specimens, therapy

C31.       Mechanisms of antibiotic action, significance and examples of bactericidal effect, possible consequences of narrow/broad-spectrum antibiotics, toxicity

C32.       Basic principles of antimicrobial therapy (crucial information for initiation of treatment, antibiotic treatment strategies prior to the agent identification)

C33.       Antibiotic treatment (initial treatment: routes and duration of administrations, and intensity of treatment; targeted treatment - routes and duration of administrations, intensity of treatment; supportive measures: pus drainage, etc.)

 
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