Surveillance of pathogens of veterinary importance and their antimicrobial resistance profiles

For pathogens of veterinary importance and their antimicrobial resistance (AMR), from terrestrial and aquatic food-producing animals:
• Address antimicrobial susceptibility testing methodology not previously evaluated for bacteria from aquatic animals, and propose ECOFFs and clinical breakpoints for selected bacterial pathogens (continuation/supplementation of EARS-VET/EU-JAMRAI)
• Map the incidence and prevalence of selected pathogens and AMR genes identified by whole-genome sequencing (WGS) of isolates from animals and the surrounding environment, including wildlife
• Develop hubs for genomic data, and select/develop tools for analysis and visualisation for pathogen and AMR surveillance using WGS data, harmonised with National and European One Health genomic surveillance Systems
• Collate existing data from passive pathogen-surveillance from all partner countries and compare/describe resistance profiles occurring in different surveillance components; evaluate the potential of transfer of resistance between surveillance components
• Identify potential transfer of resistance between pathogenic bacteria and indicator Escherichia coli
• Assess the potential spread of AMR genes from farmed animals to the surrounding environment, and identify wildlife species for sentinel surveillance
• Collect new data in active pathogen-surveillance surveys on healthy and diseased animals in a selection of case countries; use the data for validation of pathogen and resistance surveillance with metagenomics, by comparing the results of culture, WGS and metagenomics-based approaches
• Use metagenomics to identify associations between the microbiome and the resistome/pathogens in healthy and diseased animals