Whole genome sequencing has transformed foodborne outbreak investigation. A bacterial isolate recovered in one country can now be compared, at extraordinarily high resolution, with isolates recovered from patients, food, animals or environments elsewhere. But a genome does not arrive with its history attached. Who collected the sample? What was sampled? When and where was it collected? Which isolate produced the sequence, which laboratory performed the sequencing, and which outbreak investigation does it belong to? Ultimately, how confidently can that genomic observation be connected to the biological and supply-chain events investigators are trying to reconstruct?
Those questions have become particularly timely in Europe. On 2–3 September 2026, the European Food Safety Authority (EFSA) and the Inter-European Union Reference Laboratories Working Group on Next Generation Sequencing brought regulators, laboratories and food-industry representatives together in Rome for Science Meets Policy: From Regulation to Practice – Turning WGS into Action for Foodborne Outbreak Investigation. The timing was significant: just days earlier, on 23 August 2026, Commission Implementing Regulation (EU) 2025/179 became applicable, establishing new requirements for the collection, sequencing and transmission of molecular analytical data during investigations of foodborne outbreaks. Europe has therefore crossed an important threshold. The question is no longer simply whether genomic information should be shared across food-safety systems — increasingly, the question is how genomic evidence can be made useful, trustworthy and interpretable once it is shared.
Regulation 2025/179 concerns five important bacterial foodborne pathogens: Salmonella enterica, Listeria monocytogenes, Escherichia coli, Campylobacter jejuni and Campylobacter coli. When these organisms are associated, or suspected to be associated, with a foodborne outbreak, competent authorities must collect relevant isolates derived from suspected food, animals, feed or related environments. At least one isolate of each relevant serovar, biotype or molecular type must undergo whole genome sequencing in an official laboratory accredited for the method under ISO 17025, and the resulting WGS information must then be transmitted to EFSA without undue delay. That is already a substantial step towards making genomics a routine component of European foodborne outbreak infrastructure. But one of the most interesting parts of the regulation is not the genome itself — it is what must accompany it.
Article 2 of the regulation requires WGS results to be accompanied by defined contextual information: a unique reference number for the genome sequence, a unique reference number for the sample, the pathogen species, a description of the food, animal, feed or environment from which the isolate originated, the sampling date, the Member State of sampling, a RASFF reference where applicable, and a unique reference number for the national foodborne outbreak investigation.
That list illustrates something fundamental about genomic surveillance: sequence without provenance has limited investigative value. A genome can establish that two bacterial isolates are genetically extremely similar, but it cannot, by itself, tell an investigator what happened. The biological interpretation depends on the evidence surrounding it — a sequence needs to remain connected to an isolate, the isolate to a sample, the sample to its source, and the source to place, time and investigation. Eventually those observations may need to be connected to epidemiological evidence, food traceability information and regulatory action. In other words, the useful unit in an outbreak investigation is not simply a genome; it is something closer to an unbroken chain running from outbreak, through sample, isolate, sequence, analysis and comparison, to epidemiological interpretation and action. The genome is extraordinarily powerful evidence inside that chain, but it is still one link in it.
It is important not to imply that Europe is beginning from scratch. EFSA and the European Centre for Disease Prevention and Control (ECDC) have operated a joint One Health WGS system since 2022, and the architecture is particularly interesting because it already recognises the institutional boundaries inherent in One Health surveillance. Rather than placing everything into one undifferentiated database, the system consists of two interconnected platforms: EFSA operates the food-safety side and ECDC operates the public-health side, each collecting genomic information from its respective sector, with the systems exchanging genomic profiles to support cross-sector analysis. When ECDC detects a cluster of human isolates, its system can request a search against relevant food-sector genomic profiles held through EFSA; the EFSA platform can then identify closely matching profiles and return defined genomic and contextual information. That enables investigators to ask one of the central questions in foodborne epidemiology — does the genomic signal observed in human disease match something already seen in food, animals or the food-production environment? — and EFSA and ECDC then combine those genomic observations with epidemiological and traceability evidence when assessing multi-country outbreaks. This is already a significant One Health data infrastructure. The new regulation strengthens the data feeding into it.
This is where the discussion becomes particularly relevant to The BioChain. The BioChain is not part of the EFSA–ECDC WGS system, and we are not suggesting that the European system needs replacing — it does not, and nor have we deployed The BioChain for European foodborne outbreak surveillance. What interests us is the architectural problem revealed by the direction Europe is taking: as biological information moves between organisations, how do we preserve evidence about where it came from and what happened to it?
Consider a simplified outbreak workflow: a food sample yields a bacterial isolate, which receives a laboratory accession and undergoes DNA extraction and a sequencing run, producing raw reads that pass through a quality-control pipeline into a genomic profile, which is then used for cluster comparison, epidemiological interpretation and, ultimately, a regulatory decision. Different stages can involve different organisations, systems and jurisdictions. A sequence identifier tells us which sequence we are discussing; a sample identifier tells us which sample it relates to. But identifiers alone do not necessarily constitute a complete history of how one became the other — and that distinction matters increasingly as genomic evidence begins informing consequential decisions.
Traditional data provenance asks where data came from. A stronger evidence-provenance model asks what happened to it, who performed each step, what evidence supports that claim, and whether another authorised party can verify that history. For genomic surveillance, that might mean being able to establish that a particular sample was collected by an authorised organisation at a recorded time, that a particular isolate genuinely originated from that sample, that a particular sequencing run generated the underlying reads, that a particular analytical workflow — and the reference data it used — transformed those reads into a genomic profile, that the resulting profile was subsequently associated with a particular investigation, and that none of those historical records has silently changed since the events occurred.
This does not necessarily require exposing the underlying data publicly; in many cases that would be inappropriate. Instead, it requires mechanisms through which organisations can make verifiable claims about biological evidence while retaining control of the underlying information. That distinction sits at the centre of The BioChain’s architecture.
Suppose Laboratory A generates a sequence associated with an outbreak. It already has laboratory systems recording the sample and result, and there is little value in forcing the laboratory to abandon those systems and enter everything into another central database. A provenance layer can instead create a cryptographic commitment to important events occurring within the existing workflow — a signed, timestamped record that sample S123 was received, another that isolate I456 was derived from S123, another that sequence G789 was generated from I456, and another that analysis A101 was performed against G789 using a specified workflow version. The underlying laboratory records can remain exactly where they are; what becomes portable is the ability to verify the relationships between them, so that the resulting chain — S123 → I456 → G789 → A101 → outbreak investigation O22 — can be traced without requiring every participating organisation to surrender custody of its complete underlying dataset. That is a fundamentally different proposition from building another genomic database. It is an evidence layer between existing systems.
Foodborne outbreaks rarely respect organisational boundaries, and increasingly they do not respect national ones either. A food product might contain ingredients produced in one Member State, processed in another, distributed through several others and eventually associated with human cases across multiple jurisdictions. The biological evidence surrounding that event can consequently exist across public-health laboratories, food-safety laboratories, veterinary laboratories, food businesses, national competent authorities, European agencies and potentially research institutions. Centralising every piece of underlying information is neither realistic nor necessarily desirable, but being able to establish that records held by those organisations refer to the same biological event is extremely valuable. This is where federated provenance becomes interesting: the objective is not that everyone uses the same database, but that everyone can verify the relevant evidence chain.
One of the explicit objectives of this week’s EFSA conference was to bring food businesses into the discussion, because industry is an important holder of potentially relevant data. Regulation 2025/179 provides that, where available and when requested, food and feed business operators must submit relevant pathogen isolates and WGS results from their own investigations, together with associated information. That creates an interesting interface between private operational data and public regulatory infrastructure: businesses may possess valuable information while also having legitimate concerns around commercial confidentiality, access and control. EFSA’s existing WGS architecture already incorporates controls around ownership and visibility — Member States retain ownership of their submitted data, and access to information is governed according to role and context. That principle, sharing what is necessary without unnecessarily surrendering control of everything else, is likely to become increasingly important as genomic surveillance expands, and it is closely aligned with the problem The BioChain is trying to solve.
Perhaps the most significant implication of Regulation 2025/179 is not technical. It is that genomic information is moving further from being an exceptional specialist tool towards becoming part of routine regulatory evidence infrastructure. Once that happens, expectations change: it becomes less acceptable for a genomic result simply to exist. We increasingly need to know where it came from, how it was produced, which biological material it represents, which analytical process generated the interpretation, who made the relevant claims, and whether those claims remain verifiable later. That is the same transition occurring elsewhere in biological research. As sequencing becomes cheaper, automation increases and AI begins participating in biological analysis and design, biological evidence chains become longer rather than shorter. More data does not automatically create more trust — sometimes it simply creates more things whose history needs to be established.
The BioChain should be precise here. We are not proposing an alternative to the EFSA–ECDC One Health WGS system, we are not claiming that Regulation 2025/179 requires blockchain technology (it does not), and we are not claiming that European food-safety authorities currently lack mechanisms for maintaining data integrity, access control or provenance. What the regulation does demonstrate is a broader architectural trend that is highly relevant to our work: biological evidence increasingly has to remain interpretable across organisations, systems, sectors and time. Our proposition is that a shared provenance layer can complement existing scientific and regulatory infrastructure by making important relationships between records independently verifiable, without requiring the underlying systems themselves to become one system. That applies to research collaborations, to livestock-health monitoring, to biobanks and to genomic surveillance — and the more biological evidence crosses institutional boundaries, the more valuable that capability becomes.
Europe has now taken an important step by requiring outbreak-associated genomic evidence to move more systematically between the organisations responsible for protecting public health. The next infrastructure question is not simply whether we can move the genome. It is whether, years later and several systems away from where it originated, we can still prove the history that makes that genome meaningful.
Commission Implementing Regulation (EU) 2025/179 became applicable. It establishes requirements concerning the collection, whole genome sequencing and transmission of molecular analytical information associated with investigations of foodborne outbreaks.
The regulation covers outbreak-associated or suspected outbreak-associated isolates of Salmonella enterica, Listeria monocytogenes, Escherichia coli, Campylobacter jejuni and Campylobacter coli from relevant food, animal, feed and environmental samples.
No. The requirements are considerably more specific. Competent authorities have defined obligations during foodborne outbreak investigations, and food and feed business operators can also be required to provide relevant isolates and available WGS results from their own investigations when associated or suspected to be associated with an outbreak.
No. WGS can provide exceptionally strong evidence that isolates are genetically related, but source attribution depends on combining genomic information with epidemiological, sampling and traceability evidence.
It is an interconnected European infrastructure, operational since 2022, through which genomic information from the food-safety and human-health sectors can be compared to help detect and investigate foodborne outbreaks.
No. The EFSA–ECDC infrastructure performs a different function. The BioChain’s interest is in the provenance layer surrounding biological evidence: preserving verifiable relationships between records held in existing systems and organisations.
An identifier establishes identity; provenance establishes history. A complete evidence chain may need to show how a sample produced an isolate, how the isolate produced sequence data, which analysis generated a result, and how that result subsequently contributed to an investigation or decision.
Cryptographic commitments and digital signatures can allow an organisation to demonstrate that a record existed in a particular state, originated from an identified authority, and has not subsequently been altered — without necessarily publishing all of the underlying sensitive information.
If your organisation generates, manages, analyses or governs biological evidence and would be interested in participating in a UK or European provenance demonstrator, The BioChain would welcome the conversation.
Get in touch
Regulatory developments, technical notes and platform news — sent occasionally, straight to your inbox.