Regulatory-ready genomic characterization of microbial strains for EFSA, FDA, and global submissions.
WGS is a key requirement for the safety assessment of microbial production strains used in food, feed, and biotechnology applications. BaseClear delivers high-quality WGS integrated with advanced bioinformatics analysis to enable comprehensive genome characterization, including taxonomic identification, genetic modification (GM) confirmation, and the detection of genes of concern such as antimicrobial resistance (AMR), virulence factors, toxins, and mobile genetic elements.
This service is designed for companies developing microbial products requiring regulatory approval across different regulatory pathways, including novel foods, food enzymes, and feed additives, as well as probiotic and biotechnology applications. It is particularly relevant for applicants preparing dossiers for EFSA and/or other authorities, where genomic data is required to demonstrate strain identity and safety.
We apply state-of-the-art sequencing technologies and bioinformatics workflows to generate accurate and complete genome assemblies. Our approach focuses on data quality, robust analysis pipelines, and regulatory alignment, ensuring that results are reliable and suitable for safety assessment and regulatory submission.
Clients receive a comprehensive, dossier-ready report including genome assembly metrics, taxonomic identification, detailed gene screening results, and regulatory interpretation supported by targeted literature review where necessary. The report is structured in line with EFSA and international guidance, allowing seamless integration into regulatory submissions. Raw sequencing data, annotated genome files, and complete bioinformatics analysis outputs are also provided.
We define project scope, regulatory requirements, and sequencing strategy based on client’s product and target market.
The test strain is processed using optimized DNA extraction methods and is sequenced using appropriate short- and/or long-read technologies.
We perform genome assembly, annotation, and screening for genes of concern using validated pipelines, along with additional custom analyses where relevant.
A structured, dossier-ready report with clear interpretation aligned to EFSA and international guidelines will be delivered.
We support you throughout the EFSA evaluation phase, including responding to questions, preparing additional data, and guiding communication with the authority.
End-to-end microbial safety assessment capabilities
Regulatory-ready data generation and interpretation
Integrated wet-lab and bioinformatics expertise
Structured support for EFSA and global submissions
Hybrid sequencing approaches combining short-read and long-read technologies are recommended for regulatory whole genome sequencing. For bacterial strains and viruses with genomes ≥20 kb, the use of long-read sequencing or hybrid assembly methods is required to ensure accurate genome reconstruction. This approach is also strongly recommended for yeasts and filamentous fungi. Integrating short- and long-read data provides improved genome completeness, including detection of extra-chromosomal elements, and increases the reliability of genome assembly.
High-quality genome assembly and annotation are essential for regulatory acceptance of WGS data. Assemblies should meet defined quality metrics, including sufficient sequencing depth, high completeness, and low fragmentation, supported by parameters such as N50, total genome size, and contig number. In addition, all bioinformatics tools used for assembly and annotation must be fully documented, including software name, version, and parameters, as well as the databases used (with version and access date where available). This information ensures reproducibility and enables regulatory authorities to assess the robustness and reliability of the analysis.
Taxonomic identity must be unambiguously established at the species level using genome-wide approaches such as Average Nucleotide Identity (ANI) and/or phylogenomic analysis. The genome of the strain under assessment should be compared against the type strain of the claimed species and multiple type strains of closely related species. If a genome sequence of the type strain is not available, publicly available genomes of well-characterised reference strains may be used.
AMR genes are evaluated by screening the complete genome sequence, including chromosomal and extrachromosomal elements, against curated antimicrobial resistance databases. Comparison against at least two maintained databases is recommended to ensure robust identification. When a match to a known AMR gene is identified, its relevance is assessed by determining whether the gene represents intrinsic or acquired resistance in the species of the production strain, in line with regulatory guidance.
A regulatory-ready WGS report delivers comprehensive, validated genomic analysis with clear regulatory interpretation. It includes genome quality metrics, taxonomic identification, and systematic screening for genes of concern, combined with transparent methodology and alignment with current regulatory guidance. The report is structured to support safety conclusions and enable direct inclusion in regulatory dossiers, minimizing the need for additional clarification.
SERVICES
Phenotypic assessment of antimicrobial resistance aligned with EFSA guidelines
SERVICES
Phenotypic assessment of antimicrobial and cytotoxic production
Speak with our experts to design a WGS strategy aligned with your regulatory needs. Your first consultation is free and without obligation.
