Analysis of isolate based data on antimicrobial resistance collected from volunteer Member States for the year 2010
The European Food Safety Authority (EFSA) is charged with coordinating the annual reporting of zoonoses, zoonotic agents, antimicrobial resistance (AMR) and food-borne outbreaks in the European Union under the Directive 2003/99/EC as well as analysing and summarising the data collected. Until the year 2010, data on antimicrobial resistance (AMR) in animals and food were submitted by the reporting countries and analysed by EFSA on an aggregated level (i.e. as numbers of isolates resistant to a given antimicrobial substance out of the total number of isolates tested). However, data at bacterial isolate level enable more in-depth analysis of resistance, including multi-resistance patterns of isolates and description of clonal spreading of resistant strains. A pilot project for the collection of isolate based AMR data from volunteering reporting countries was carried out in 2011. Data were successfully collected from eleven Member States and one reporting country. This report focuses on the analysis of multi-resistance, co-resistance and complete susceptibility patterns in these isolate-based AMR data, containing information on Salmonella, Campylobacter, indicator E. coli and indicator enterococci isolates from food and animal samples for the year 2010. In addition, attention is paid to the study of the quantitative association between resistance to different antimicrobials in the dataset. Finally, several methods to identify possible clusters of similar multi-resistance patterns are described and exemplified based on selected subsets. Results are shown through specific summary tables as well as graphical representations.