Publication - Advice and guidance


Published: 18 Jan 2019

Guidance on the regulation and monitoring of salmonella in animals.

18 Jan 2019


Salmonellae are a bacterial cause of food-poisoning worldwide, and are common commensals of all animals and birds.

Some types of salmonellae can affect humans as well as animals. Transmission to humans occurs when organisms, introduced into the kitchen in poultry carcasses, meat or unpasteurised milk, then multiply in food because of inadequate cooking, cross-contamination of cooked foods and inadequate storage.

Many of the types of salmonellae which cause human food poisoning do not cause clinical signs in animals so monitoring is necessary to check levels of infection.


The objective of the Zoonoses Directive (2003/99/EC) is to gather information in order to assess the risk to human health from sources of zoonoses and zoonotic agents in the domestic and wild animal populations.

The Directive aims to achieve this objective through enhanced monitoring of the trends and sources of zoonoses and zoonotic agents and related anti-microbial resistance and by ensuring that food-borne disease outbreaks receive proper epidemiological investigation. A further aim of the Directive is to move, when necessary and agreed, towards harmonised monitoring systems, e.g. using the same sampling methods, sample types and laboratory test methods to provide information on the trends and sources of zoonotic agents in the EU as a whole.

The requirements of Directive 2003/99 are implemented by The Zoonoses (Monitoring) (Scotland) Regulations 2007

The Zoonoses Regulation (2160/2003) deals with the management of risk of zoonotic infections in animals and is closely allied to the Directive. It requires that Member States implement national control plans (NCPs) for the reduction of specified zoonoses (currently salmonella) at farm level in certain animal species (currently domestic fowl, turkeys and pigs).

The first stage in the process is to undertake EU-wide surveys to establish the baseline level of salmonella in animal species on farm. These surveys are carried out using predetermined procedures and methods so that the prevalence of salmonella can be determined uniformly in each Member State and in the Community as a whole.

On the basis of the data provided by the baseline surveys, the European Commission sets each Member State a target to reduce the pathogen or infectious agent within a set timescale. Once the baseline figures are established and reduction targets assigned each Member State is then required to develop a National Control Programme (NCP), including details of how this target will be achieved and verified, for approval by the European Commission.

The Zoonoses Monitoring (Scotland) Regulations 2007 provide the legal basis for future sampling work and act as a mechanism for monitoring implementation and progress of the NCPs. Reports on the EU-wide baseline surveys can be obtained on the European Food Safety Authority (EFSA) website.

National Control Plans

Under the Zoonoses Regulation all Member States are required to introduce NCPs as follows:


NCP required by:


Jan 2007


Jan 2008


Jan 2009


Jan 2010

Fattening pigs

Jan 2011

Breeding pigs

Jan 2011

Approved laboratories

NCPs will place an obligation on operators to collect samples at predetermined intervals. These samples will need to be submitted to an approved laboratory for analysis. A list of laboratories approved to conduct this work is available.

Sampling and testing costs

All costs associated with sampling and testing have to be met by operators. Additionally, costs will also be recovered from flock owners for any official sampling work undertaken on behalf of Scottish Ministers by the Animal & Plant Health Agency (APHA).

The APHA deliver a wide range of statutory inspection and certification services for businesses and individuals which support consumer confidence and facilitate the ability to trade. These statutory charges have been updated to align with government policy requiring that services of commercial benefit should be charged at full-cost recovery rate.