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Updated: May 7, 2026
A Duplex Digital PCR Assay for Simultaneous Quantification of the Enterococcus spp. and the Human Fecal-associated HF183 Marker in Waters
Published on: March 9, 2016
Enteroflow: Automated Pipeline for In Silico Characterization of Enterococcus faecium/faecalis Isolates from Short
Daniele Smedile1, Elena L Diaconu1, Matteo Grelloni1
1National Reference Laboratory for Antimicrobial Resistance, Department of General Diagnostics, Istituto Zooprofilattico Sperimentale del Lazio e Della Toscana "M. Aleandri", 00178 Rome, Italy.
Abstract:
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animal productions, in the frame of the EU Harmonized Monitoring Program for AMR (according to EU Decision 2013/652, repealed by EU Decision 2020/1729), conducted by the Italian National Reference Center (CRN-AR) and National Reference Laboratory (NRL-AR) for antimicrobial resistance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 Enterococcus (E.) faecium and E. faecalis 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 E. faecium/faecalis 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.
Insights
Antimicrobial resistance (AMR) is a global threat. A new bioinformatics pipeline, Enteroflow, aids in genomic characterization of Enterococcus species, supporting AMR surveillance in animal productions.
Area of Science:
- Microbiology and Bioinformatics
- Genomic Surveillance of Antimicrobial Resistance (AMR)
- One Health Paradigm
Background:
- Antimicrobial resistance (AMR) poses a significant global health risk to both humans and animals.
- Enterococcus faecium and Enterococcus faecalis are commensal bacteria that are increasingly recognized as opportunistic human pathogens with rising AMR.
- Monitoring AMR in zoonotic and commensal bacteria from animal production is crucial under the One Health approach.
Purpose of the Study:
- To develop a custom bioinformatics pipeline for the efficient genomic characterization of Enterococcus faecium and Enterococcus faecalis isolates.
- To support the surveillance efforts for antimicrobial resistance in zoonotic and commensal bacteria.
- To enhance the mitigation strategies against AMR in animal productions.
Main Methods:
- Development of a custom bioinformatics pipeline named Enteroflow.
- Integration of Nextflow's workflow manager and Domain Specific Language (DSL) for reproducibility and scalability.
- Inclusion of tools for short-read assembly, AMR and virulence gene detection, and plasmid replicon typing.
Main Results:
- Enteroflow enables efficient analysis of high-throughput sequencing (HTS) data for Enterococcus genomic characterization.
- The pipeline ensures reproducibility and scalability of genomic analyses, with monitoring of processes and computational performance.
- Structured and usable reports are generated, combining results from various genomic characterization tools.
Conclusions:
- The Enteroflow pipeline represents a significant advancement in the genomic characterization of Enterococcus species.
- This tool strengthens the capacity for AMR surveillance in animal productions, aligning with the One Health strategy.
- The developed pipeline supports informed decision-making for AMR mitigation strategies.
