Event information

Unit

Contents

Unit 1.1

Introduction to Bacteria and Viruses

Learning objectives

At the end of the unit, the student will be able to understand:

• basic concepts of structure of Bacteria cells (cytoplasm, nucleoid, wall, capsule, ribosomeetc..)
• the Bacteria DNA replication and extrachromosomal elements (transposons, plasmids, etc..) and the different ways for Bacteria to acquiring or loosing geneticmaterials
  • microbiology and mechanism of DNA and  RNA virusesreplication
  • viralpathogenesis

Topics

Index Intro

Description of bacterial structure Bacteria DNA replication

DNA replication of extrachromosomal elements Bacteria evolution

Viruses Morphology and classification

Viruses Replication (DNA viruses replication and RNA viruses replication)

In depth contents Summary

Test

Unit 1.2

Food Microbiology Lab

Learning objectives

At the end of the unit, the student will be able to understand:

• the basis of laboratory routine for conventional typing (Gram staining, biochemical tests, serotyping etc..), molecular typing (PCR, MLVA, MLST, PFGE etc..) and MALDI-TOF mass spectrometry for bacterialidentification
  • the use of WGS in Food Microbiologylab
• the principles and procedures of Antibiotic Susceptibility Test (AST) (i.e. Disk diffusion, Agar dilution, Broth dilution…) and molecular methods for detecting AMRgenes
• the basis of laboratory routine for Food Virology and methods for viruses cultivation, identification methods and  the use of WGS in Foodvirology

Topics

Index Intro

Bacterial culture Bacterial typing

Proteomics MALDI-TOF for bacterial identification WGS in Food Microbiology lab

Antibiotic susceptibility test Viral Culture

Virus Identification WGS in Food virology In depth contents Summary

Test

Unit 1.3

Molecular microbiology

Learning objectives

At the end of the unit, the student will be able to understand:

- fundamental principles guiding molecular genetics approaches and genetic processes

• principles and procedures of Bacteria moleculartyping
• the mechanisms that lead to genetic variability during DNA and RNAvirus replication and the molecular methods to identifythem
  • the main uses of Genetic-engineering in FoodLab

Topics

Index Intro

Genetic variation in bacteria

Bacteria molecular typing methods (MLVA, MLST, PFGE, etc..) DNA viruses (Genetic variability & molecular typing)

RNA viruses (Genetic variability & molecular typing) Genetic-engineering

In depth contents Summary

Test

Units 1.4

Introduction to Genomics

Learning objectives

At the end of the unit, the student will be able to understand:

• basic concepts of DNA sequencing and itsevolution
• the differences between short read and long reads platforms (cost, technical specifications, outputs, advantages anddisadvantages)
  • how WGS can be used as an epidemiologicaltool
  • basic concepts of different NGS platforms and the workflow ofNGS
  • the methods for DNA extraction, quantification and qualitycontrol
• the methods for libraries preparation and sequencing with different NGS platforms
  • the principles for validation of wet labprocedures
  • principles of targetedampliseq
  • the methods for sequencing of bacterial 16SrRNA
  • principles and workflow of ShotgunMetagenomics
  • application of shotgun metagenomics in AMRsurveillance
  • the Transcriptomicsworkflow
  • the Proteomicsworkflow

Topics

Index Intro

WGS-basic concepts NGS platforms

Wet Lab workflow Metagenomics 16S

Targeted ampicon sequencing

Characterisation of microbiome using 16S rRNA metagenomics Shotgun Metagenomics

Transcriptomics of microrganisms Proteomics

In depth contents Summary

Test