FED-AMR D2.2: Preliminary data collection on ARG prevalence and ARG background load in the compartments analysed so far (T2.4)
- 1. Austrian Agency for Health and Food Safety, Vienna, Austria
- 2. Infectious Diseases Department, National Institute of Health DrRicardo Jorge, Lisboa, Portugal
- 3. National Institute of Public Health, University of Chemistry and Technology, Prague, Czech Republic
- 4. lnstitute of Technology, University of Tartu, Estonia
- 5. Department of Natural Sciences, National University of Ireland Galway
- 6. Department of Animal Health and Food Safety, Section of Food Safety and Antimicrobial Resistance, Norwegian Veterinary Institute, Oslo, Norway
Deliverable 2.2 of Workpackage 2 - Implementation of a pilot experiment to confirm that the target enrichment approach worked better than conventional shotgun metagenomics for the detection of ARGs. The results showed that the conventional shotgun sequencing followed by ametagenomics analysis enabled pathogen identification and AMR marker detection. In further consequence, targeted sequencing with a panel that includes all AMR markers within ARESdb seemed the best alternative to shotgun metagenomics.