TEMA

Alimentazione, nutrizione e sicurezza degli alimenti

Sicurezza microbiologica degli alimenti

La sicurezza microbiologica degli alimenti comprende tutte le attività collegate alla identificazione e caratterizzazione dei pericoli microbiologici (sia batteri che virus patogeni per l’uomo), quali lo sviluppo delle metodologie analitiche, dei piani di campionamento e l’adeguatezza dei piani di autocontrollo degli operatori del settore alimentare.

Queste attività vengono sviluppate e garantite dall'Istituto Superiore di Sanità (ISS), in particolare attraverso le attività di centri e laboratori nazionali di riferimento.

L’ISS ha anche la missione di valutare il rischio microbiologico nelle diverse filiere produttive degli alimenti e garantire un giudizio terzo nel caso di controversie sulla conformità degli alimenti ai criteri microbiologici prescritti dalla normativa.



Indietro E. coli Genomics: Next Generation Sequencing (NGS) applied to the study of pathogenic E. coli

The E. coli genomics section of the previous website is meant to give the user access to information related with the E. coli genomics and Next Generation Sequencing (NGS) applied to the study of pathogenic E. coli. Efforts will be done to maintain the section constantly updated with the latest releases in the sector.
Information on the updates available will be pushed to all the EU NRL through the “Focus on” mailing list and to any other user via the RSS channel, upon subscription.
This section may also feature downloadable material, including documents related with the EURL for E. coli initiatives in the field, as well as link to usable tools to perform local analyses of NGS data.
All the software and tools included in the list are freeware and are made available directly from the authors’ websites.
Additional links are provided that direct the user to the web environments where it is possible to remotely run analyses using NGS data.
This section is also the portal to access the EURL VTEC-managed Galaxy platform ARIES. It contains tools and workflows developed by the EURL for E. coli and specifically intended for analysing E. coli genomes, as well as other bioinformatics, available on the Galaxy tool shed, for a standard QC and analysis of NGS data.

Related links

Center for Genomic Epidemiology (Technical University of Denmark)
Multi Locus Sequence Typing of E. coli at the University of Warwick (Sanger sequencing)
E. coli reference genomes at NCBI
VelvetOptimizer de novo assembler by Victorian Bioinformatics Consortium for genome annotation
Sequence assembly with MIRA 4
PROKKA by Victorian Bioinformatics Consortium for genome annotation
RAST Rapid Annotation using Subsystem Technology
MAUVE Multiple Genome Alignment
BLAST Ring Image Generator (BRIG)
Galaxy CRS4 Orione (data intensive biology)
Tablet: A high-performance graphical viewer for NGS assemblies and alignments
Integrated Genome Browser (IGB). A piece of software to browse genomic data.


• Basic Course on Bioinformatics tools for NGS data mining (Rome, 11-12 June 2015)
• 2nd Course on Bioinformatics Tools for Next Generation Sequencing data mining: use of bioinformatics tools for typing pathogenic E. coli (Rome, 16-17 June 2016)
• 3rd Course on Bioinformatics Tools for Next Generation Sequencing data mining: use of bioinformatics tools for typing pathogenic E. coli (Rome, 18-19 June 2018)


Dipartimenti/Centri/Servizi

Dipartimenti Sicurezza Alimentare, Nutrizione e sanità pubblica Veterinaria

Target

Operatore Sanitario

Tipologia

Documenti

Tematica

Alimentazione, Nutrizione e Sicurezza degli alimenti Malattie a trasmissione alimentare Sicurezza microbiologica degli alimenti Sanità pubblica veterinaria Zoonosi