Commission Implementing Regulation (EU) 2025/179

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THE EUROPEAN COMMISSION,Having regard to the Treaty on the Functioning of the European Union,Having regard to Directive 2003/99/EC of the European Parliament and of the Council of 17 November 2003 on the monitoring of zoonoses and zoonotic agents, amending Council Decision 90/424/EEC and repealing Council Directive 92/117/EEC^note, and in particular Article 8(3) thereof,Whereas:

(1)Article 8(2) of Directive 2003/99/EC requires the competent authority of the respective Member State to investigate food-borne outbreaks in cooperation with the competent authorities responsible for addressing serious cross-border threats to human health and the consequences thereof pursuant to Decision No 2119/98/EC of the European Parliament and of the Council^note. That Decision was repealed by Decision No 1082/2013/EU of the European Parliament and of the Council^note, which was later repealed and replaced by Regulation (EU) 2022/2371 of the European Parliament and of the Council^note. Those investigations are to provide data on the epidemiological profile, the foodstuffs potentially implicated, the potential causes of the outbreaks, as well as to include adequate epidemiological and microbiological studies.

(2)The efficiency and the cross-sectorial cooperation between public health and food safety authorities in such investigations is essential to limit the public health impact of an outbreak and to minimize the economic impact linked to recalls and withdrawal of unsafe or potentially unsafe food. For this purpose, the quick and reliable identification of batches and lots or consignments containing contaminated food and the cause of the outbreak is necessary.

(3)Whole genome sequencing (WGS) is a modern molecular analytical technique for microbiological studies which facilitates greatly the swift identification of clusters of microorganisms, supporting the epidemiological investigations. It enables to establish links between isolates of food-borne pathogens recovered from humans, food, animals, feed and the related environment during the outbreak investigation.

(4)To substantially facilitate food-borne outbreak investigations and the timely detection of the sources of those outbreaks, Member States should be required to collect Salmonella enterica, Listeria monocytogenes, Escherichia coli, Campylobacter jejuni and Campylobacter coli isolates derived from food, animal, feed and related environmental samples from food and feed business operators and during official controls, where those isolates are associated or suspected to be associated with a food-borne outbreak. Member States should also be required to carry out WGS on those isolates.

(5)The Member States should transmit the results from WGS on isolates of those pathogens from food, animals, feed and the related environment to the European Food Safety Authority (the ‘Authority’) that developed a joint One Health system together with the European Centre for Disease Prevention and Control (ECDC). Within the joint One Health system, the Authority can compare the results from WGS on isolates of those pathogens collected in accordance with this Regulation with the results from WGS in human isolates communicated to ECDC in accordance with Article 13(3), point (d), of Regulation (EU) 2022/2371. Such comparison allows the identification of the source of an outbreak and of the affected consignments when used in combination with data from epidemiological investigations. When transmitting the results of the WGS to the EFSA Authority, additional related data, essential for the investigation of foodborne outbreaks, should be included.

(6)It is appropriate to grant to Member States and the Authority sufficient time to adapt to the new requirements on collecting isolates derived from food, animal, feed and related environmental samples, the WGS of those isolates and the transmission of the related data in order to provide for the necessary technical applications and financial means. The requirements in this Regulation should therefore start to apply 18 months from the date of entry into force of this Regulation.

(7)The measures provided for in this Regulation are in accordance with the opinion of the Standing Committee on Plants, Animals, Food and Feed,

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Commission Implementing Regulation (EU) 2025/179

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