National Study Centre for Sequencing in Risk Assessment

Recent advances in microbial whole genome sequencing and metagenome analysis using next generation sequencing are playing an increasingly important role in the assessment of microbial risks. For example, food-borne disease outbreaks can be more safely tracked, documented and clarified by using new high-resolution technology.

Whole genome sequencing will also offer significant advantages in the characterisation of food-borne pathogens. Conventional typing methods, such as serotyping, target-gene amplification of specific genes (e.g. toxin genes), antibiotic resistance gene determination, pulsed-field gel electrophoresis (PFGE) and "multiple-locus variable-number tandem repeats analysis" (MLVA) can either be replaced by whole genome sequencing or the analysis options can be expanded.

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 for harmonisation and standardisation, across multiple disciplines, as a diagnostic investigation technique, which would also enable comparison of results from the various areas of specialisation.

At the BfRshort forGerman Federal Institute for Risk Assessment, the National Study Centre for Sequencing in Risk Assessment brings together expertise in second and third generation microbial Next Generation Sequencing (NGS) processes. It supports the BfR’s laboratories in planning and implementing projects using the technology. In addition, since September 2021, the Federal Ministry of Food and Agriculture (BMELshort forGerman Federal Ministry of Food and Agriculture) has assigned the National Study Centre the task of supporting the official food monitoring testing laboratories in establishing whole genome sequencing of bacterial isolates. It proposes data management concepts that contribute to an efficient cross-border solution for typing bacterial isolates as part of the investigation of food-borne outbreaks. The study centre also carries out its own research projects in the field of genomics (the entirety of the isolate genome) and metagenomics (the entirety of all genomes of a sample) and is actively involved in procedural harmonisation at national and international level.

The study centre has a large number of technology platforms available for its activities. It operates devices that can be used for high-throughput sequencing of isolates as well as for complex metagenome samples. For the creation of closed reference genome sequences and plasmids, devices are also used that can generate long-read lengths.

The tasks of the study centre include:

• Development, validation and standardisation of laboratory experiments and bioinformatics solutions for isolate typing using next generation sequencing
• Coordination of genome sequencing for the microbiological national reference laboratories at the BfRshort forGerman Federal Institute for Risk Assessment according to Control Regulation (EU) 2017/625
• Support of the national reference laboratories in organising interlaboratory testing on behalf of official inspection laboratories for the purpose of method validation
• Creation and provision of bioinformatic pipelines for the evaluation of microbial sequence data
• Provision of evaluation software for the official inspection laboratories involved in food monitoring
• Technical support in conducting investigations of cross-regional food-borne outbreaks and food-borne risk assessments associated with genome sequence data
• Third-party funded research in the field of genomics, metagenomics and transcriptomics
• Participation in national and international bodies for the standardisation of genome sequencing
• Training courses and seminars

The study centre has a large number of second and third generation sequencing platforms available for its tasks. It operates devices that can be used for high-throughput sequencing of isolates as well as for complex metagenome samples (second generation Illumina technology). For the creation of closed reference genome sequences and plasmids, third generation devices (Oxford Nanopore or Pacific BioSciences technology) that can generate long-read lengths are also used. The following sequencers are currently in operation:

Illumina Technology (short-read):
iSeq100
MiSeq
NextSeq500

Oxford Nanopore Technology (long-read):
MK1B
MK1C
Flongle

Pacific BioSciences (long-read):
Sequel I