Monitoring Antimicrobial Resistance (AMR) in clinical bacterial pathogens

The COVID-19 pandemic highlighted the need for robust genomic surveillance. Inspired by SARS-CoV-2 monitoring efforts, we established a central data hub and an automated Nextflow bioinformatics workflow to collect, store, and analyze bacterial sequencing data from clinical patients. This project aims to detect emerging pathogens, monitor antimicrobial resistance (AMR) in bacterial pathogens, and is part of the Genomic Pathogen Surveillance in Germany (GenSurv and GenSurv+) initiatives. Our Nextflow pipeline efficiently handles short- and long-read bacterial sequencing data, automating genome assembly, annotation, plasmid identification, and AMR gene identification. By leveraging Nextflow's capabilities, the hub supports customizable configurations, Docker-based deployment, and persistent storage, ensuring seamless data processing and analysis.