Study Centre for Genome Sequencing and Analysis

Recent advances in microbial whole genome sequencing and metagenome analysis using next generation sequencing play an increasingly important role in the assessment of microbial risks. Using this new high-resolution technology foodborne disease outbreaks can be tracked, documented and resolved more reliably, for example.

Whole genome sequencing also offers major benefits for the future characterisation of foodborne disease pathogens. Conventional typing techniques such as serotyping, target gene amplification of specific genes (e.g. toxin genes), antimicrobial resistance gene determination, pulsed-field gel electrophoresis (PFGE) and "multiple-locus variable-number of tandem repeats analysis" (MLVA) can be replaced by whole genome sequencing or the analytical options can be extended.

Across all fields of public healthcare, from animal health and food safety through to the environment ("One Health" concept), microbial whole genome analysis has the potential to become interdisciplinarily harmonised and standardised as a diagnostic investigation technique and therefore to render results from the various areas of speciality comparable.


The Study Centre for Genome Sequencing and Analysis pools the expertise of the BfR in the field of microbial next generation sequencing (NGS) techniques of the 2nd and 3rd generation. It supports the laboratories at the BfR in the planning and implementation of projects using this technology. Alongside this, the Study Centre conducts its own research projects in the field of genomics (entire genome of an isolate) and metagenomics (all genomes of a sample) and is actively involved in the national and international harmonisation of the relevant techniques.

In its activities, the Study Centre can draw on a wide range of technology platforms. It operates equipment that can be used both for high-throughput sequencing of isolates as well as for complex metagenome samples. In order to create closed reference genome sequences and plasmids, the Study Centre also makes use of devices that can generate long read lengths.

The work of the Study Centre focuses on the following topics:

  • Development, validation and standardisation of laboratory experiment and bioinformatic solutions for the typing of isolates using next generation sequencing
  • Coordination of genome sequencing activities for the microbiological National Reference Laboratories at the BfR appointed pursuant to the Official Control Regulation (EU) 2017/625
  • Creation and provision of bioinformatic pipelines for the evaluation of microbial sequence data
  • Expert support in the identification of transregional foodborne outbreaks and foodborne risk assessments in relation to genome sequence data
  • Third party-funded research in the area of genomics, metagenomics and transcriptomics
  • Involvement in national and international bodies tasked with the standardisation of genome sequencing
  • Training courses and seminars

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