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The new zoonoses Directive 2003/99/EC gives the opportunity for an improvement in the harmonization of antimicrobial resistance testing of zoonotic agents. The current reporting system under Council Directive 92/117/EEC was a voluntary approach leading to a limited comparability of the data. In the directive 2003/99/EC, inforced since June 2004, antimicrobial susceptibility testing is part of the legislation. The benchmarks, the zoonotic agents Salmonella spp. and Campylobacter spp., the animal species cattle, pigs and poultry, as well as products thereof are fixed. In this paper details for a harmonized monitoring scheme are proposed. The draft specifies in more detail the animal species, the production lines and the locations of the sampling. The sampling frame should ensure a representative number of isolates to meet the objectives, these are detection of occurrence of resistance patterns, estimation of the prevalence of resistance to an antimicrobial substance, and assessment of changes in the prevalence of antimicrobial resistance. Apart from isolates from monitoring schemes reflecting the healthy animal population, clinical isolates should be included to detect new emerging resistance genes. The comparability of the methods applied has to be ensured by an external quality assurance system. As the monitoring of antimicrobial resistance should be closely linked to the monitoring programs laid down in the directive 2003/99/EC to estimate the prevalence of zoonotic agents along the food chain. A stepwise implementation in accordance with the other monitoring programs is suggested. In order to support management decisions to limit the emergence and spread of resistance additional information has to be collected, i.e. resistance in animal pathogens, usage of antimicrobials, or the relevance of the import of animals or products of animal origin.