ANIHWA call2: Prevalence and optimised detection of resistance to antibiotics vital for animal and human health

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The arsenal of antibiotics for use in medicine is ever decreasing, while the rates of resistance are ever increasing. There is a great need to identify and control all sources of antibiotic resistance, and minimise the transfer of resistance genes and/or bacteria within animals and between animals and humans. The aims of this collaborative project are to address resistance to three critically important classes ofantibiotic classes; polymyxins (colistin), aminoglycosides and carbapenems among gut microflora from pigs and cattle. Colistin is an important antibiotic in the treatment of animals with intestinal infections i.e. Escherichia coli and Salmonella species. Carbapenemases were thought to be restricted to human pathogens, since carbapenems are not used in veterinary medicine. However, they have recently been identified in food animals.This project will evaluate the rates of resistance (or reduced susceptibility) to colistin, aminoglycosides and carbapenems and among Gram negative enteric bacteria from pigs and cattle, and compare these with the levels of prescribing in the different countries. We will identify the mechanisms leading to the resistance or reduced susceptibility to those antibiotics, and decipher their genetic environment. In cases where no known resistance mechanism can be identified we will utilise whole genome sequencing and functional metagenomics to decipher the novel resistance mechanism. Using this data we can then evaluate the relationship between mobile resistance elements within and between countries. Recently-developed rapid diagnostic techniques for cheap identification of carbapenemase-producing isolates will be applied to investigate carbapenem resistance. We will also develop further diagnostic tools for the identification of colistin and aminoglycoside resistances. The use of antibiotics in veterinary medicine, the emergence of antibiotic resistance and the potential transfer of resistance through the food chain to humans are topics of high priority at both the national and EU policy levels. Comprehensive EU-wide scientific data is required to guide future policy in this area and to ensure the maintenance of both animal and human health and welfare. Traceability and transparency within the food industry are vital to build on the reputation that Europe has built up over many years as an area of safe food production, with high standards in animal health and welfare.