Metagenomics Adoption in EFSA Risk Assessment

The tenderer must have generated an overall annual turnover of at least 1.000.000 € in each of the last 3 closed financial years (2023, 2024 and 2025).

The tenderer overall must have extensive and demonstrable experience in: a) Metagenomics for microbiological characterisation of complex microbial communities/microbiomes; b) Development of harmonised laboratory protocols and Standard Operating Procedures (SOPs) in the fields of food and/or feed safety or related microbiological domains; c) Bioinformatics analysis of metagenomics data, including taxonomic profiling, genome-level reconstruction (e.g., metagenome-assembled genomes - MAGs), and detection of safety-relevant genomic features (e.g., antimicrobial resistance genes, virulence factors); d) Regulatory science or microbiological research with regulatory relevance, including: · Reviewing and synthesising data and information from various sources · Interpreting findings in regulatory science contexts · Understanding of regulatory frameworks or quality standards for risk microbiological assessment · Writing scientific reports and publications in English for regulatory and/or scientific audiences; e) Project management dealing with multidisciplinary teams combining wet-lab microbiology and bioinformatics experts.

The tenderer shall provide a team of at least 4 experts compliant with the following requirements. One expert can cover more than one area: a) One expert with at least 5 years of experience in metagenomics laboratory methods, including: · Sample preparation and DNA extraction from complex microbial communities · Library preparation and sequencing strategies for shotgun metagenomics · Quality control and harmonisation/standardisation of DNA extraction and sequencing protocols; b) One expert with at least 5 years of experience in metagenomics bioinformatics, including: · Assembly, binning, and reconstruction of metagenome-assembled genomes (MAGs) · Taxonomic classification and microbial community composition analysis · Functional annotation for detection of safety-relevant genomic features (e.g. antimicrobial resistance genes, virulence factors, pathogen-associated sequences); c) One expert with at least 5 years of experience in microbiology including: · Culture-based methods for microbial characterisation or experience working with difficult-to-culture organisms, with experience working with multi-species communities · Understanding of microbiological challenges in complex multi-species products (e.g., difficult-to-culture organisms, community interactions); d) One expert with at least 3 years of experience in method standardisation/validation, and/or quality assurance/control for laboratory methods; e) One expert with at least 5 years of experience in microbiological risk assessment or applied microbiological research with regulatory relevance, in the context of food safety or feed safety, or related regulatory science domains, including knowledge of current regulatory frameworks (e.g., EFSA or equivalent regulatory science organisations); f) One expert acting as project leader with at least 5 years of experience in project management in the area of food/feed safety or related microbiological domains, who will manage the coordination of the project development and be responsible for the overall contract and for the implementation of all services requested by EFSA in this call for tender. The project leader will be the contact point for the services requested by EFSA and must update regularly EFSA on the progress of work.

The project leader (profile f) and the regulatory science specialist (profile e) listed above in section 2.4.B.2 must each have individually a very good level of spoken and written standard UK English. For non-native speakers, this shall be demonstrated by: (i) experience (minimum three years) in international projects or activities where English is the working language (e.g., international research collaborations, participation in scientific working groups or expert panels, international professional activities); OR (ii) at least two years of work/study in an English-speaking environment; OR (iii) certificate of English proving at least a C1 level; OR (iv) at least 3 publications written in English. Other team members should have a working knowledge of English sufficient to participate in project meetings and contribute to technical documentation.

The tenderer must: a) Have the technical equipment, resources and tools needed to perform the required metagenomics work, including: · Laboratory facilities and equipment for sample preparation, DNA extraction, and library preparation for metagenomics · Access to high-throughput sequencing platforms (either in-house or through project partners/subcontractors with sequencing facilities) · Computational infrastructure for bioinformatics analysis of metagenomics data, including adequate data storage and processing capacity and workflow management systems (e.g., Docker, Nextflow, Snakemake, or equivalent); b) Have access to or capability to obtain the samples required for the work described in this tender; c) Have access to scientific literature databases for literature review (e.g., institutional library access); d) Have infrastructure for digital collaboration, including video conferencing and document sharing capabilities (e.g., Office 365 or equivalent).

a) Signed declaration on honour.

a) Signed declaration on honour.