ℹ️ About this resource
This site presents the genomic epidemiology analysis of a fictional CRAB outbreak exercise run as part of the EURGen-RefLabCap EQA programme. The data, hospitals, patients, and country names are entirely fictitious and designed for training purposes. This analysis was reproduced independently using open bioinformatics tools.
Interactive Dashboard
Explore the complete genomic dataset interactively — phylogenetic tree, AMR resistance heatmap, SNP distance matrix, and sample timeline. Click any isolate to view full details.
Open Dashboard →Outbreak Investigation Report
Step-by-step walk-through of how the outbreak was solved: from epidemiological curve construction to WGS-based cluster confirmation across all six hospitals.
Read Report →Exercise Overview
Inject 1 — Epidemiological Data
The NRL receives records for 71 A. baumannii cases from 6 hospitals (Jan–Dec 2023). Participants construct epicurves and select 36 priority isolates for WGS based on dates, hospitals, travel history, and antibiograms.
Inject 2 — Hospital A Sequencing (18 isolates)
WGS data (FASTQ + FASTA) for Hospital A isolates AB_23–AB_40 are released. Participants perform MLST, AMR annotation, and SNP-based phylogenetics to identify within-hospital clusters.
Inject 3.1 — Hospital B & C Sequencing (10 isolates)
Sequences for AB_41–AB_50 (Hospital B and C) are provided. The outbreak investigation expands to determine links between hospitals and patients with travel history to Country Z.
Inject 3.2 — Hospital D, E & F Sequencing (8 isolates)
Final sequences (AB_51–AB_58) complete the dataset. A full phylogenomic view reveals the scope of the multi-hospital outbreak, inter-hospital transmission routes, and sporadic non-outbreak cases.
Bioinformatics Pipeline
Assemblies → AMR Profiling (Abricate 1.0.1, CARD database)
Assemblies → Core-genome alignment (Parsnp 2.1.1, 75,985 SNP sites)
SNP alignment → ML Phylogeny (IQ-TREE2, GTR+G, 1000 ultrafast bootstrap)
ML distances → Pairwise SNP matrix (IQ-TREE mldist × 4 Mb genome)