Download MICROBIOLOGY, GENERAL MEDICINE

MICROBIOLOGY, GENERAL MEDICINE - SYLLABUS
First semester:
Second semester:
practical courses - 2 hrs/week
lectures – 3 hrs/week
practical courses – 2 hrs/week
Lectures, Clinical microbiology:
1. Introduction, history of clinical microbiology, evolution of microbes, bacterial
genetics (viruses, bacteria, parasites, mechanisms of horizontal gene transfer –
transformation, transduction, conjugation, specific genetic elements – insertion
sequences, transposons, integrons, etc.)
2. Principles of general microbiology, factors responsible for virulence,
pathogenesis of infectious diseases (structure of virus, virus living cycle, basic
knowledge of immunity response, barriers, bacterial toxins, adhesins, mechanisms of
escape against immunity, etc.)
3. Review of clinically important G+ bacteria (characteristics, factors responsible for
virulence, diseases, diagnostics, epidemiology, antibiotic therapy; Streptococcus spp.,
Enterococcus spp., Staphylococcus spp., Bacillus spp., Corynebacterium spp., etc.)
4. Review of clinically important G- bacteria (characteristics, factors responsible for
virulence, diseases, diagnostics, epidemiology, antibiotic therapy; Neisseria spp.,
Haemophilus spp., Enterobacteriaceae, Vibrio spp., Campylobacter spp.,
Helicobacter spp., Pseudomonas and other non-fermenting rods, Legionella spp.)
5. Review of clinically important bacteria (characteristics, factors responsible for
virulence, diseases, diagnostics, epidemiology, antibiotic therapy; Mycobacterium
spp., Nocardia spp., Actinomyces spp., Chlamydia spp., Mycoplasma spp., Rickettsia
spp., anaerobic bacteria – review of the most important species, e.g. Clostridium
difficile, C. perfringens, C. tetani, C. botulinum, Peptostreptococcus spp.,
Fusobacterium spp.)
6. Review of clinically important parasites 1 (physiology of parasite, living cycle,
vectors, diseases, diagnostics, treatment; protozoology, Trypanosoma spp.,
Leishmania spp., Trichomonas vaginalis, Giardia intestinalis, Entamobea histolytica,
Plasmodium spp., Toxoplasma gondii, Balantidium coli, Cryptosporidium parvum)
7. Review of clinically important parasites 2 (physiology of parasite, living cycle,
vectors, diseases, diagnostics, treatment; helminthology, medical entomology,
Fascilopsis buski, Paragonimus westermani, Clonorchis sinensis, Schistosoma, spp.,
Taenia spp., Echinococcus spp., Hymenolepis nana, Nematodes)
8. Review of clinically important fungi (characteristics, factors responsible for
virulence, diseases, diagnostics, epidemiology, therapy; Candida spp., Craptococcus
spp., Aspergillus spp., Penicillium spp., dermatomycoses, Hystoplasma spp.,
Pneumocystis jirovecii)
9. Antibiotics (basic groups of antibiotics, mechanism of action, molecules; betalactams, glycopeptides, polymyxins, amynoglykosides, quinolones, sulfonamides,
chloramphenicol, etc.)
10. Mechanisms and epidemiology of antibiotic resistance (mechanisms of bacterial
resistence, clonal spread of resistant bacteria, horizontal transfer of genes –
mobilisation of genes, mobile genetic elements, integrons, co-resistnace, crossresistance)
11. Hospital-acquired infections (definition, examples of the most important pathogens,
resistence bacteria as a causative agents of hospital-acquired infections – MRSA,
VRE, resistant Gram-negative rods – production of extended-spectrum betalactamases, carbapenemases)
12. Review of viral diseases 1 (structure of virus, pathogenesis, epidemiology,
diagnostics, prevention, therapy; papillomaviruses, polyomaviruses, adenovirus,
herpesviruses, poxviruses, picornaviruses, coronaviruses, paramyxoviruses, influenza
virus, rhabdoviruses, filoviruses, reoviruses, togaviruses and flaviviruses, togaviruses,
bunyaviridae)
13. Review of viral diseases 2 (structure of virus, pathogenesis, epidemiology,
diagnostics, prevention, therapy; retroviruses – HIV, hepatitis viruses)
14. Indication, limitations, and interpretation of microbiological diagnostics methods
Microbiology exercises for general medicine I. (summer semester)
1) Introduction – safety, classification of microbes, characterization of main groups of
microbes
2) Dizinfection and sterilization – fyzical and chemical methods and agents, indication and
quality control, laboratory equipment and its application
3) Cultivation I. – specimens collection, processing and storage, culture media characteristics
4) Cultivation II. – seeding of culture media, characteristics of microbial growth
5) Microscopy I. – Gram stain, bacterial morphology
6) Microscopy II. – Acid-fast stain, negative stain, slides of clinical specimens, host cells
identification
7) Cultivation III. – Biochemical and additional tests
8) Cultivation IV. – Antibiotic susceptibility testing
9) Immunological methods I.– terms definition, polyclonal and monoclonal antibodies
charteristics, production and application,
10) Immunological methods II. – Principles of direct and indirect immunological methods
11) Immunological methods III. – Main assays, its characteristics, application and limits in
diagnostics
12) Identification of medically important microbes – main groups of microbes in cultures
and microscopy slides
Microbiology exercises for general medicine II. (winter semester)
1) Normal microflora, laboratory diagnoses of anaerobes - normal microflora on culture
media and microscopy slides, primocultures of various sites with fyziological colonization,
Methods of anaerobic cultivation, genus Clostridium, non-spore-forming anaerobes
2) Laboratory diagnosis of skin mucosae and soft tissue infections, sexually transmited
diseases –diagnostic strategies, collection of specimens, causative agent detection and
identification: Staphylococcus aureus, Streptococcus pyogenes, Pseudomonas aeruginosa,
Clostridium sp. (histolytic), non-spore-forming anaerobes, diagnostic methods of bacterial
STD: Treponema pallidum, Neisseria gonorrhoeae, Chlamydia trachomatis
3) Laboratory diagnosis of intestinal and urinary tract infections - diagnostic strategies,
collection of specimens, causative agent detection and identification: Salmonella sp., Shigella
sp., Yersinia enterocolitica, Escherichia coli, Vibrio cholera, Campylobacter jejuni,
Helicobacter pylori, Proteus sp., Klebsiella sp., Staphylococcus sp., Enterococcus sp.
4) Laboratory diagnosis of respiratory tract infections - diagnostic strategies, collection of
specimens, causative agent detection and identification: Streptococcus pyogenes,
Streptococcus pneumonie, Haemophilus influenzae, Bordetella pertussis, Pseudomonas
aeruginosa, Chlamydia pneumoniae, Mycoplasma pneumoniae, Mycobacterium tuberculosis,
Corynebacterium diphteriae
5) Laboratory diagnosis of zoonotic diseases - diagnostic strategies, collection of
specimens, causative agent detection and identification: Leptospira sp., Borrelia burgdorferi,
Chlamydia psittaci, Francisella tularensis, Pasteurella multocida, Listeria monocytogenes,
Salmonella sp., non-tuberculous mycobacteria
6) Laboratory diagnosis of CNS infections, sepsis - diagnostic strategies, collection of
specimens, causative agent detection and identification: Haemophilus influenzae,
Streptococcus pneumoniae, Neisseria meningitides, Streptococcus agalactiae,
haemocultivation – collection of blood specimen, set up rules
7) Antimicrobial therapy – case reports
8) Laboratory diagnosis of parasites I. – coprology - methods of concentration, blood
smears, vaginal smears, protozoan parasites - diagnostic strategies, collection of specimens,
causative agent detection and identification: Trichomonas vaginalis, Giardia intestinalis,
Leishmania sp., Entamoeba sp., Toxoplasma gondii, Plasmodium falciparum, Plasmodium
vivax,
9) Laboratory diagnosis of parasites II. – parasitic helminth and parasitic arthropods diagnostic strategies, collection of specimens, causative agent detection and identification:
Ascaris lumbricoides, Enterobius vermicularis, Taenia saginata, Toxocara sp., Trichuris
trichiura, Pediculus humanus, Ixodes ricinus
10) Laboratory diagnosis of fungi I. Specific diagnostic methods in mycology. Yeastsdiagnostic strategies, collection of specimens, causative agent detection and identification:
Candida albicans, Candida sp., Cryptococcus neoformans, Malassezia furfur
11) Laboratory diagnosis of fungi II. Molds - diagnostic strategies, collection of specimens,
causative agent detection and identification: Aspergillus sp., Mucor sp., Trichophyton sp.,
Microsporum sp.,
12) Laboratory diagnosis of viruses I. Specific diagnostic methods in virology. Diagnostic
strategies, collection of specimens, causative agent detection and identification.
13) Laboratory diagnosis of viruses II Excursion to the Department of Virology