Area 1 (‘Economy’): Improve the productivity, resilience and competitiveness of European Animal Production
Effect of antimicrobial agents on the microbial biodiversity and bacterial resistance
DTU is the largest technical university in Denmark with more than 5,000 employees and organized in 19 institutes and 9 centers. DTU covers all technical sciences, including large efforts in health and lifesciences.
DTU-Food employs 420 people working in four departments and two research units and focuses on public health in relation to human nutrition, food safety and environment. In addition to include all aspects of foods and the food chain on health and production, activities include development of methodologies for identification and comparison of microbial organisms, including animal, human and zoonotic pathogens. The Institute is part of the national food safety contingency plan and national reference laboratory for microbial food safety. DTU-Food also serves as an international reference laboratory for the EU, WHO (World Health Organization) and EFSA (European Food Safety Authority) in a number of areas. The Genomic Epidemiology Unit is reference laboratory for EU and WHO on AMR.
DTU and the researchers involved are well-experiences in research and training programs and have successfully supervised several PhD-students, from several different countries. The Genomic epidemiology unit have for more than 20 years combined basic research with producing results of relevance for industry and authorities, especially within food safety. The unit has each year since 2000 conducted several international proficiency tests and development of standard within antimicrobial susceptibility testing and more recently whole genome and whole community sequencing. The group has also been heavily involved in developing bioinformatics pipelines and web-platforms for data upload, analysis and storage.
The research unit headed by Frank Aarestrup is located at the main campus of DTU, with fully equipped microbial class 2, gene class 2 and microbial class 3 laboratories, as well as supporting facilities including PCR, gene detection, micro-array, fermentation, whole genome sequencing, etc. The group (~38 people) has a large collection of well characterized bacterial isolates (>100,000) and reference strains and via international networks (e.g. WHO and EU reference laboratories) assess to bacterial isolates and metagenomics samples from more than 100 laboratories worldwide. The scientific and technical staff has more than 15 years of experience working with molecular typing and antimicrobial resistance and covers very broadly research of resistance in different reservoirs and bacterial species.
Together with DTU-Food CBS has already developed online tools for analysis of both single isolate and metagenomic NGS data including species identification, clonal grouping, detection and quantification of antimicrobial resistance, plasmids and virulence genes as well as phylogenetic analysis (http://cge.cbs.dtu.dk/services/all.php), that so far have handled more than 250,000 whole genome data submissions and currently are handling +30,000 submissions monthly.