COMPARE - Diagnostic metagenomics on clinical samples: Prediction of antibiotic resistance genes and pathogen discovery in shot-gun metagenomic data from swine feces. COMPARE: Antibiotic resistance marker in swine feces

Shot-gun metagenomic NGS data sets generated from swine holdings with acute diarrhoea. The causative agent, Porcine epidemic diarrhea virus (PEDV), was identified. Metadiagnostic analysis via FLI RIEMS pipeline revealed co-infection with bacteria. The use of antibiotics in these holdings cannot be excluded. Prediction of antibiotic resistance markers will be done as a pilot to test pipelines and algorithms with clincal metagenomics data.