With Regulation (EU) 2025/179, the European Union mandates the use of Whole genome sequencing (WGS) for several foodborne pathogens originating from food starting on 23 August
- Listeria monocytogenes
- Salmonella enterica
- E. coli bacteria
- Campylobacter jejuni
- Campylobacter coli bacteria
- This applies when these pathogens are linked to a foodborne disease outbreak that must be investigated or controlled.
- The goal is to establish a Europe-wide molecular early-warning system that can detect and trace the source of outbreaks quickly, precisely, and consistently.
- While WGS becomes the new standard for traceability, Real-Time PCR remains the backbone of routine testing in every control laboratory.
🧬WGS technology – the new reference technology for traceability
- WGS (Whole Genome Sequencing) technology – whole genome sequencing – is a technology for analyzing the entire DNA sequence of an organism (for example: bacteria, viruses, molds) in a sample.
- Unlike traditional techniques that identify only a few genes or characteristic gene segments, WGS reads the whole genome, allowing organisms to be distinguished at strain level and their evolutionary relationships to be recognized.
* Basic principle
- The sample (food, water, environment, clinical specimen…) has its DNA extracted.
- The DNA is fragmented, tagged with indices (barcodes), and loaded into a next-generation sequencing instrument (Next Generation Sequencing - NGS).
- The machine decodes the entire genome → millions of reads are obtained.
Bioinformatics software assembles, compares, and analyzes the data against reference databases to:
- Identify the species, strain, and lineage of the microorganism.
- Detect virulence genes, antibiotic resistance genes, and genetic relationships between samples.
- Whole genome sequencing analyzes the entire DNA of the microorganism, detecting even the smallest differences between strains – something conventional techniques cannot do.
- Result: the fingerprint of each pathogen. This data allows regulators and testing laboratories to detect outbreaks, determine the source of contamination, and verify whether pathogens from different samples share the same origin.
WGS technology is gradually replacing traditional microbiological analysis methods, opening up full traceability across the entire production and supply chain.
* Application in traceability
- WGS is considered the "new gold standard" for tracing the origin of disease outbreaks and food contamination because:
- It distinguishes precisely down to strain level – helping determine whether microbial samples in the factory or from the product are the same strain or different.
- It identifies transmission routes and contamination sources (for example: the same Listeria monocytogenes strain detected in the product and in a point in the processing line).
- Global data integration: many countries (such as the US, EU, and Japan) are building shared WGS data banks, which are extremely valuable and enable international tracing.
- It supports investigation far faster and more accurately than traditional methods (such as PFGE, MLST…) or culture-based serotyping.
* Global trends
- The FDA (US), EFSA (Europe), and CFIA (Canada) have deployed WGS as the reference standard in food-safety surveillance and outbreak response.
- FAO & WHO recommend WGS as the primary tool for a modern food traceability system, especially for pathogens transmitted through food.
* Practical application in the food industry
- Regulators: used to trace and investigate outbreaks.
- Food manufacturers: use it to monitor and control microorganisms in the production line and to detect contamination sources early.
- Testing labs: used as a confirmation tool for positive samples, helping certify results quickly and with a valid legal basis.
🌍 What will the EU require from 2026?
Under Regulation (EU) 2025/179, member states must use WGS when:
- A foodborne outbreak is suspected or confirmed
- Strains isolated from food, animals, animal feed, or the environment are linked to human cases of illness
* This mainly affects:
- National reference laboratories.
- Food and veterinary laboratories.
- Government food inspection agencies
Food businesses are not required to carry out WGS themselves – but they must supply the isolated strains and related data to the authorities when it is requested.
EFSA requires the submission of specific data along with the WGS sequence. This data includes a reference identifier, isolation date, sample type, production context (batch, processing line), and the epidemiological information needed for tracing.
🧪 Real-Time PCR – the working backbone of food safety
Despite the technological advances, Real-Time PCR remains the essential tool for routine testing and day-to-day food control in industrial plants and labs:
- Results in hours rather than days
- High sensitivity
- Standardized protocols
- Automated workflows for large sample volumes
Practical applications include:
- Release testing (for example, for fresh products or ready-to-eat products)
- Environmental and hygiene monitoring (CIP, surfaces)
- Raw material control and supplier evaluation
🧭 From testing to strategy | WGS and Real-Time PCR working together
Modern testing systems combine Real-Time PCR and WGS in a tiered workflow:
- Screen with Real-Time PCR: early detection of pathogens.
- Isolate positive samples: the basis for deeper analysis.
- WGS analysis of relevant isolates: for traceability, clustering, and outbreak investigation.
- This ensures WGS is used only when needed and Real-Time PCR remains the cost-saving decision-making tool in every testing step.
👉 For more information on pathogen testing – visit
👉 Sources
https://eur-lex.europa.eu/eli/reg_impl/2025/179/oj
https://food.ec.europa.eu/document/download/bb6b197a-cce2-4ebf-aca2-ebb6696c803f_en
Source: food.r-biopharm.com