MICROBIOLOGIA MOLECOLARE APPLICATA E MICROBIOLOGIA CLINICA

12 CFU - 2° Semester

Teaching Staff

STEFANIA STEFANI - Module Applied Molecular Microbiology - BIO/19 - 6 CFU
VIVIANA CAFISO - Module Applied Molecular Microbiology
PIO MARIA FURNERI - Module Clinical Microbiology - MED/07 - 6 CFU
ALDO STIVALA - Module Clinical Microbiology

Learning Objectives

Applied Molecular Microbiology
With the course of Applied Molecular Microbiology, students will broaden and deepen the basic knowledge in the biomolecular field captured with the first degree. The course explores the molecular aspects of pathogenicity, virulence and antibiotic resistance of the major human pathogens, and their clonal relationship. The new identification technologies and study of microorganisms are also addressed (genomes, metagenomes, proteomes etc) as well as the basics of the interaction host parasite including immunological aspects. From the application point of view, they are taken into consideration the vaccine preparations (both traditional and recombinant) as well as some examples of microbial products produced with advanced technologies. The students then, will possess an integrated understanding of biological phenomena and advanced scientific training in morphological / functional level, chemical / biochemical, cellular / molecular and evolutionary aspects of the microbial world.
Clinical Microbiology
Acquire knowledge of the applicative basis of clinical microbiology in the various fields of interest for health;

Acquire knowledge of the major microbial identification techniques and skills to apply the same in health care

Know the principles of quality control in clinical microbiology

Course Structure

Applied Molecular Microbiology
Three main parts:

1) Study of microrganisms of bio-medical interest; Taxonomy and identification; Host-pathogen relationship interactions; molecular mechanisms of pathogenicity; Genetic and genomic analysis; phylogenetic reconstruction; What a microbial genome is teaching us; Bacteriocins, RNA and transcriptomic

2) Pharmaceutical compounds, antibodies; Vaccins (traditional and molecular-based preparations)

3) Applied medical microbiology, examples
Clinical Microbiology
Lectures (5 UFCs) and Laboratory (1 UFC)

Detailed Course Content

Applied Molecular Microbiology
Study of microrganisms involved in bio-medical and industrial applications.

Overview of taxonomy and identification of microrganisms. Host-parasite relationships. Molecular mechanisms of pathogenicity.

Molecular biotechnology of microbial systems. Phylo-genomics: the benefit between phylogeny reconstruction and genomic analyses.

Genetic and genomic application in the study of new molecular targets for therapeutic agents.

Screening for microbial Products: potential bacteriocins,.

sRNA regulators reprogram bacteria Enzymes, monoclonal and polyclonal antibodies, nucleic acids as therapeutic agents.

Study of molecular mechanisms of antibiotic-resistance. Vaccines. Traditional and recombinant technologies in medical microbiology.
Clinical Microbiology
1. Humand microbiota - The different possibilities of infection and spread of infectious diseases
  1. The normal human microbiota.
    1. Microbiota models for apparatuses
    2. The role of microbiota
    3. Dysbiosis and loss of resilience
  2. Epidemiology of infectious diseases
    1. General aspects and Epidemiological terminology
    2. The infectious cycle: history of a disease
      
      Carriers and reservoirs
2. The infection control and general knowledge on the prevention of infectious diseases
  1. Sterilization and disinfection techniques
    1. Sterilization by physical methods
    2. Sterilization by chemical methods
    3. Preparation of culture media in the microbiology laboratory
    4. Sterilization of the workplace
    5. Disinfectants
      
      Objectives and methods of carrying out disinfection
      
      Targets and mechanisms of action of disinfectants
      
      Types of disinfectants
      
      Methods for assessing the effectiveness and activity of disinfectants
  2. Biosafety
    1. Legislative decree 81/2008 and the management of microbiological risk
  3. The bioassay in the clinical microbiology laboratory
    1. Susceptibility tests
      
      Classical methods
      
      Automated methods
    2. The biological dosage of antibiotic concentrations in various organs and apparatuses
    3. Non-biological techniques for the biological dosage of antibiotic concentrations in various organs and apparatuses
  4. Procedures for the storage of microorganisms
3. Diagnosis of bacterial, fungal, viral and parasitic diseases.
  1. Clinical microbiology laboratory
  2. Cultivation methods
    1. Bacteria
    2. Viruses
    3. Fungi
    4. Protozoa
  3. Independent culture techniques
    1. Histological techniques
    2. Molecular techniques
      
      Amplification of the target
      
      Amplification of the probe
      
      Amplification of the signal
      
      Hybridization
      
      Sequencing
      
      Proteomics (MALDI-TOF etc.)
  4. Chromatographic techniques
  5. Other techniques
  6. Serological techniques
    1. Fluorescent assay
    2. Immunoassay
    3. Immunochromatografic assay
  7. Specific diagnostic procedures for:
    1. Staphylococcus, Streptococcus, Enterococcus, Neisseria, Branhamella, Mycobacterium, Streptomyces, Nocardia, Actinomyces, Corynebacterium, Lactobacillus, Bartonella, Listeria, Gardnerella, Bacillus, Clostridium, Enterobacteriaceae, Haemophilus, Pasteurella, Vibrio, Legionella, Brucella, Bordetella, Acinetobacter, Pseudomonas, Bacteroides, Campylobacter, Helicobacter, Mycoplasma, Ureaplasma, Chlamydiaceae, Rickettsiales, Spirochetales.
    2. Poxviridae, Herpesviridae, Adenoviridae, Papillomavirus e Polyomavirus umani, Parvoviridae, Paramyxoviridae, Orthomyxoviridae, Picornaviridae, Arenaviridae, Bunyaviridae, Caliciviridae, Coronaviridae, Filoviridae, Flaviridae, Reoviridae, retrovirus umani, Togaviridae, Rhabdoviridae, virus delle epatiti (HAV, HBV, HCV, HDV, HEV, HGV).
    3. Fungi
      
      Dimorphic primary pathogens responsible for systemic mycoses:
      
      Histoplasma capsulatum var. capsulatum, Histoplasma capsulatum var. duboisii, Blastomyces dermatitidis, Coccidioides immits , Paracoccidioides brasiliensis .
      
      Superficial Mycoses:
      
      Aspergillus spp., Rhizopus spp., Scopulariopsis spp., Mucor spp., Penicillium spp., Malassezia furfur, Exophiala werneckii, Trichosporon beigelii, Piedraia hortae, Candida spp.
      
      Cutaneus mycoses:
      
      Dermatophytoses: Microsporum spp., Trichophyton spp., Epidermophyton spp.
      
      Dermatomycoses:
      
      Candida albicans, Hendersonula toruloidea, Scytalidium hyalium (Natrassia spp.), Scopulariopsis brevicaulis.
      
      Main agents of Subcutaneous mycoses
      
      Opportunistic pathogens responsible for various forms of mycosis:
      
      Candida spp., Cryptococcus neoformans (Systemic mycoses), Trichosporon spp., Fusarium spp., Penicillium spp., Talaromyces spp.
      
      Notes on Microsporidiosis and Pneumocystis spp
      
      Parasites
      
      Protozoa:
      
      Sarcomastigophora: flagellated (Giardia intestinalis, Trichomonas spp.); haemoflagellates (Trypanosoma spp., Leishmania spp.); amoebas (Entamoeba histolytica, Acanthamoeba spp).
      
      Apicomplexa: Plasmodium spp., Toxoplasma gondii, Criptosporidium parvum, Isospora (notes), Eimeria (notes)
      
      Ciliophora: Balantidium coli
      
      Helminths:
      
      Cestoda:
      
      Echinococcus spp., Taenia spp.
      
      Trematoda:
      
      Schistosoma spp., Paragonimus spp., Fasciola hepatica, Opistorchis spp.
      
      Nematoda:
      
      Ancylostoma duodenale, Necator americanus, Ascaris lumbricoides, Enterobius vermicularis, Trichinella spp., Filarie (Brugia malayi, Onchocerca volvulus , Wuchereria bancrofti, Loa loa)
4. The microbiological quality control, diagnostic principles for food microbiology and environmental microbiology in health care (0.5 CFU).
  1. The microbiological quality control, diagnostic principles for food microbiology and environmental microbiology in health care
    1. ISO and UNI EN procedures
  2. Procedures for microbiological food control
    1. Risk and risk management
    2. The HACCP system
    3. The concept of limit
    4. Current legislation
  3. Environmental control in the healthcare environment
    1. Application scope
    2. Sampling techniques
      
      Air
      
      Surfaces
      
      Water
      
      Others
    3. Microbiological evaluation of samples
      
      Cultivation techniques
      
      Independent culture techniques
      
      Molecular independent culture techniques
      
      Current legislation
5. Diagnostic models applied to infections
  1. of the respiratory system
  2. of the cardiovascular system
  3. of the integumentary apparatus
  4. of the digestive system
  5. of the urinary system
  6. of the reproductive system
  7. of the muscular system
  8. of the skeletal system
  9. of the nervous system and sense organs
6. New and old integrated diagnostic methods and polyphasic approaches
  1. Rapid methods in clinical microbiology
  2. Methods in human microbial ecology
    1. Cultivation techniques
    2. Methods to evaluate microbial diversity
    3. Methods to evaluate microbial community activities
  3. Chemotaxonomic methods
  4. Omic applications in clinical microbiology
    1. Microbiomics
    2. Metagenomics
    3. Metabolomics
    4. Other “omics”
  5. The polyphasic methods in clinical microbiology

Textbook Information

Applied Molecular Microbiology
1. Deho' Galli - Biologia dei Microrganismi - Casa editrice EA
2. Brock – Biologia dei Microrganismi – vol. 2 Casa Editrice CEA
3. Perry JJ et al – Microbiologia vol 2 – Casa Editrice Zanichelli
4. Sherris - Microbiologia Medica - Edizione EMSI
5. https://onlinelibrary.wiley.com/doi/book/10.1002/9780470688618 (free for all students)
Da consultare:
1. Glick et al – Molecular Biotechnology 3th ed. ASM
2. Brodgen KA et al – Virulence mechanisms of bacterial pathogens 3th ed ASM
3. Lavori in lingua Inglese
Clinical Microbiology
1) Koneman's - Color Atlas and textbook of Diagnostic Microbiology 7ed. Wolters Kluver - International Edition ISBN-13: 978-1-4511-8935-3

2) Persing et Al. MOLECULAR MICROBIOLOGY Diagnostic Principles and Practice 2 nd Ed. ASM Press. ISBN 978-1-55581-497-7

Further resources

Topley & Wilsons' su: https://onlinelibrary.wiley.com/doi/book/10.1002/9780470688 (the link must be used within University of Catania network)

Open in PDF format Versione in italiano