EnteroMark is a complete, automated genomic analysis pipeline for Enterococcus faecium, featuring parallel execution for rapid processing of bacterial genomes. The pipeline integrates multiple analysis modules into a unified workflow:

• Quality Control (FASTA QC) – Comprehensive sequence validation • Multi‑Locus Sequence Typing (MLST) – E. faecium scheme • Antimicrobial Resistance (AMR) – AMRfinderPlus and ABRicate databases • Virulence & Plasmid Profiling (ABRicate) – Multi‑database screening • Critical Genes Flagging – Priority markers for infection control • Interactive HTML Reports – Gene‑centric integrated analysis • Cross‑genome pattern discovery

Critical Genes Tracked: 🔴 Vancomycin (vanA, vanB, vanD, vanM) 🟠 Linezolid (optrA, cfr, poxtA) 🟡 High‑level Aminoglycosides (aac, ant, aph) 🟢 Efflux Pumps & Biocides (msrC, emeA, efmA, qac, sil, mer) 🔵 Adhesins & Biofilm (esp, ace, acm, scm, gelE) 🟣 Cytolysin & Hemolysin (cylA, cylL, cylM, cylR) ⚪ Enterococcal Surface Protein (esp) 🔶 Gelatinase (gelE) 💧 Quorum Sensing (fsrABC) 🧪 Plasmid Replicons (rep, repA_N)

Key Features: 🚀 Parallel Execution – Independent modules run concurrently for maximum speed 📊 Interactive Reports – HTML summaries with visualisation 🧬 Multi‑Database Integration – CARD, ResFinder, VFDB, NCBI, MEGARes, BacMet, PlasmidFinder ⚡ Easy Deployment – Single command analysis with automatic dependency handling 🎯 Comprehensive Gene Tracking – Resistance, virulence, plasmid, and environmental markers

Designed for clinical microbiology, outbreak investigation, and genomic surveillance of vancomycin-resistant enterococci (VRE), EnteroMark provides a complete solution for E. faecium genomic characterisation from raw sequencing data to publication‑ready reports.

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