Genomcis Wageningen Food Safety Research

Genomics

Genomics, the study of heritability and genes (DNA) in a cell or organism, plays a significant role in the microbiological research of WFSR. A great deal of attention is paid to Genomics in researching bacteria. Virology research also increasingly makes use of Genomics applications.

At Genomics, we work for example on mapping the complete DNA of bacteria: whole genome sequencing (WGS). This research provides a rich store of information. WGS allows the comparison of strains from different food products. Has a genome sequence been encountered previously? Do they have a shared origin?

Whole genome sequencing and metagenomics

Useful genome information is shared in a database and is compared with human data in collaboration with the RIVM (National Institute for Public Health and the Environment). The information can also be used to predict the functional properties of bacteria, such as resistance to antibiotics.

We carry out WGS on the bacteria listeria, STEC, Salmonella and Campylobacter (‘Big Four’) among others. We also work with metagenomics, a development that allows not only a specific search for a particular bacterium, but also much broader measurement. In this way, Wageningen Food Safety Research pioneers research into safe and reliable food in the future.

Sign up and send bacterial isolates

If you have an arrangement to sign up and send bacterial isolates to Wageningen Food Safety Research, you can do so using this form.

We share WGS data with WFSR in real-time to more quickly identify potential sources of disease outbreaks. The independent bioinformatic analyses pose a valuable peer-check for our analyses.

Eelco Franz - RIVM - Head of Department Epidemiology and Surveillance Enteric Infections & Zoonoses

Leading the way in research into safe and reliable food

Below you will find out more about our varied work and how we make a contribution through them to food safety:

Molecular typing

Research into the genome sequencing of bacteria is also conducted for listeria, STEC, Salmonella, Campylobacter, Vibrio and B. cereus. Molecular typing is carried out for these bacteria. Molecular typing is a relationship analysis used to determine the origin of an isolate. Determining the relationship (clustering) of these isolates assists in tracing the source.

Whole Genome Sequencing analysis and Multilocus Sequence Typing (MLST)

Functional typing

Functional typing is recording the various properties of a bacterium. By this means, the resistance to antibiotics can be predicted and linked to the phenotypic resistance (phenotypic and genotypic characterisation). In addition, we also analyse the virulence (degree of pathogenicity) and persistence, the extent to which a bacterium can survive. This is done for example by coding the genes that are resistant to cleaning agents. The techniques that we use for this include comparative genomics, CRISPR analysis and methylation typing.

Metagenomics

Current investigation frequently looks for a single bacterium isolate from a single sample. In future, it will increasingly be possible to measure much more broadly, rather than to search for a particular species. This is done by immediately isolating the DNA of the sample to be investigated and sequencing it. This use of genomics, which is still under rapid development, is referred to as metagenomics.

ICT and software

The Genomics reseachers strives to be fully up-to-date on the technical methods of research - certainly in the area of computer technology and software. In practice, this means that we conduct our analysis on the High Performance Computing Cluster (HPC) of Wageningen University & Research (WUR).

Read more about our microbiology expertises virology, bacteriology and A ntimicrobial Resistance Research (AMR).

Publications

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