LEARNING OUTCOMES
The aim of course is to enable the students to understand:
1) The basic concern of Bacteriology and the systematic study of bacteria
2) Interactions between bacteria and human and their effects and factors influencing the onset and manifestation of the disease
3)Τhe basic biological and genetic characteristics that contribute to and are involved in their pathogenesis and their association with the disease they cause
4) The principles of laboratory diagnosis of bacterial infections and methodologies for isolation, culture, detection, identification / standardization, as well as the interpretation and evaluation of laboratory findings and
5)Τhe mechanisms of sensitivity and resistance to antibiotics that will enable them to use the appropriate antibiotics in the laboratory
The scope of the course is to introduce students to the principles of Bacteriology and their applications in laboratory and clinical practice. The general characteristics, the structure, the classification, the pathogenic action of the bacteria, but also the laboratory diagnosis, the epidemiology, the treatment and the prevention are presented in detail. The course additionally covers the branches of bacterial genetics, standardization and phylogenetic study of their population
SYLLABUS
Theory
1. Introduction to Bacteriology: Definitions. Ecology of bacteria. Bacterial symbiotic relationships and habitats. Physicochemical functions of bacteria. Presence of pathogens and non-bacteria in a variety of aquatic and solid ecosystems / food. Biofilms- biofilm formation, properties, pathogenesis.
2. Structure and classification of bacteria: Bacterial cell structure. Bergey classification. Molecular classification. Bacterial evolution and diversity. Phylogeny. Proteobacteria. Archaebacteria
3. Bacterial genetics: Bacterial genome (Core and Accessory genome). Genetically transmissible elements. Pathogenicity genes. Plasmids / resistance genes. Introduction to genetic processes such as transformation, bacterial conjugation, mutagenesis. Recombinant DNA techniques.
4. Bacterial metabolism: Microbial growth in closed and open environment-continuous culture. Growth curves / liquid cultures. Energy and enzymes. Synthesis of nucleic acids and proteins. Gene regulation.
5. Archaebacteria (Archaea): Classification. Habitats. Structure and metabolism. Genetics of Archaea. Applications, his example of Thermus aquaticus.
6. Proteobacteria: Gram negative α-, β-, γ-, δ- και ε- proteobacteria. Characteristics, metabolism, participation in biochemical cycles. Classification: Neisseriales, Enterobacterialles, Pseudomonadales, Vibrionales, Campylobacterales, Chlamydiaceae.
7. Enterobacteralles: Escherichia coli, Klebsiella, pneumonia, Yersinia pestis, Proteus mirabilis, Salmonella spp., Shigella spp. General characteristics. Infectious agents. Pathogenic action-epidemiology. Laboratory diagnosis (phenotypic – molecular techniques).
8. Pseudomonadales: General characteristics. Infectious agents. Pathogenic action-epidemiology. Laboratory diagnosis (phenotypic – molecular techniques). The example of Pseudomonas aeruginosa.
9. Neisseriales/Vibrionales: Neisseria gonorrhoeae, Neisseria meningitidis, Vibrio cholerae, Vibrio parahaemolyticus, Vibrio vulnificus. General characteristics. Infectious agents. Pathogenic action-epidemiology. Laboratory diagnosis (phenotypic – molecular techniques).
10. Campylobacterales/Chlamydiaceae: Campylobacter jejuni, Campylobacter coli, Helicobacter pylori, Chlamydia trachomatis, Chlamydophyla pneumonia. General characteristics. Infectious agents. Pathogenic action – epidemiology. Laboratory diagnosis (phenotypic – molecular techniques).
11. Gram positive coccus: Staphylococcus (Staphylococcus aureus), Streptococcus (Streptococcus pyogenes) and Enterococcus (Enterococcus faecalis). General characteristics. Infectious agents. Pathogenic action-epidemiology. Laboratory diagnosis (phenotypic – molecular techniques).
12. Gram positive coccus (Clostridia, Mollicutes, Bacilli): Clostridium tetani, Clostridium botulinum, Clostridium perfrigens, Bacillus anthacis, Bacillus subtillis, Bacillus influenzae, Mycoplasma hyopneumoniae, Ureoplasma urealyticum. General characteristics. Infectious agents. Pathogenic action-epidemiology. Laboratory diagnosis (phenotypic – molecular techniques).
13. Gram positive coccus (Actinobacteria): Corynebacterium diphtheriae, Mycobacterium tuberculosis, Mycobacterium leprae. General characteristics. Infectious agents. Pathogenic action-epidemiology. Laboratory diagnosis (phenotypic – molecular techniques).
14. Antimicrobial susceptibility to antibiotics: Resistant bacteria in primary / secondary care facilities and environmental habitats. Classes of antibiotics per group of bacteria and their genetic basis. Antibiogram. Recording and control of microbial resistance
15. Bacterial standardization and phylogeny: Definition of standardization and its importance in the monitoring of bacterial infections. Phylogenetic studies of bacteria and modern methods for detecting the phylogenetic course of a bacterial population. The role of phylogeny in the development of the epidemiology of bacterial infections.
Laboratory
1. Laboratory safety / Biosafety levels: Safe laboratory handling, collective and individual protection measures. Bio-safety levels of bacterial infection testing laboratories (BSL).
2. Nutrient substrates: preparation of basic nutrient substrates, sterilization, storage.
3. Culture of samples in nutrient substrates: incubation, culture of Staphylococci, Streptococci, Enterobacteriaceae.
4. Bacterial identification Part 1: Colony study, preparation and microscopy of fresh samples.
5. Bacterial identification Part 2: Preparation staining and microscopy
6. Identification of bacteria Part 3: Study of biochemical properties of Staphylococci and Streptococci. Molecular identification
7. Identification of bacteria Part 4: Study of biochemical properties of Enterobacterial. Molecular identification.
8. Identification of bacteria Part 5: Study of biochemical properties of Pseudomonas. Molecular identification.
9. Pharyngeal, ear sample culture: Identification of microbes (evaluation of colonies, staining of microbes, study of biochemical properties).
10. Blood cultures: Identification of microbes (evaluation of colonies, staining of microbes, study of biochemical properties).
11. Urine culture: Identification of microbes (evaluation of colonies, staining of microbes, study of biochemical properties).
12. Antibiogram: diffusion on agar by the Kirby-Bauer method. Selection and evaluation of appropriate antibiotics.
13. Antibiogram evaluation: Application of the limits according to the international standards of Clinical and Laboratory Standards Institute (CLSI), European Committee on Antimicrobial Susceptibility Testing – EUCAST and Epidemiological Cut-Off Values (ECOFFs).
14. Bacterial standardization: Differences in standardization identification. Phenotypic and Molecular standardization (serotyping, pcr-based techniques). Evaluation of standardization results.