Enteroflow: Automated Pipeline for In Silico Characterization of Enterococcus faecium/faecalis Isolates from Short Reads

Antimicrobial resistance (AMR) is a critical global health challenge that affects both human and animal populations. In accordance with the One Health paradigm, AMR has been monitored in Italy since 2014 in major zoonotic pathogens and opportunistic commensal bacteria from animal productions, in the frame of the EU Harmonized Monitoring Program for AMR (according to EU Decision 2013/652, repealed by EU Decision 2020/1729), conducted by the Italian National Reference Center (CRN-AR) and National Reference Laboratory (NRL-AR) for antimicrobial resistance at the "Istituto Zooprofilattico Sperimentale del Lazio e della Toscana (IZSLT)" (on behalf of the Italian Ministry of Health). Among all monitored bacterial species, the commensal <i>Enterococcus</i> (<i>E.</i>) <i>faecium</i> and <i>E. faecalis</i> have emerged as opportunistic human pathogens with increasing AMR profiles. To address this challenge, the CRN-AR and NRL-AR have developed a custom bioinformatic pipeline, named Enteroflow, which enables the efficient analysis of high-throughput sequencing (HTS) data for the genomic characterization of <i>E. faecium</i>/<i>faecalis</i> isolates. A pivotal feature in this tool is the integration of Nextflow's workflow manager and Domain Specific Language (DSL), ensuring the reproducibility and scalability of genomic analyses while allowing the monitoring of processes and computational performances. The list of tools included in the workflow spans from short read assemblers to genomic characterization tools for AMR and virulence gene detection and plasmid replicon typing, with results also being combined in structured and usable reports. These developments represent a major step forward in supporting the surveillance efforts and mitigation strategies for AMR in zoonotic and commensal bacteria.