KlebNET-GSP — A genomic surveillance dashboard for Klebsiella pneumoniae.

KlebNET-GSP is a single-organism dashboard derived from the AMRnet platform. It surfaces genome-derived antimicrobial resistance (AMR) and virulence data for Klebsiella pneumoniae in a focused, dedicated UI.

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Architecture

This is a fork of AMRnet (commit baseline: see CHANGELOG.md) reduced to a single organism. The codebase intentionally keeps AMRnet's multi-organism scaffolding inert (in models/, client/src/util/drugs.js, etc.) so we can rebase against future AMRnet releases. The user-facing surface area has been trimmed:

• client/src/util/organismsCards.js — only the kpneumo card is exported
• routes/api/api.js — only /getDataForKpneumo, /getUNR, and /getCollectionCounts are mounted

Stack

• Backend: Node.js 22 + Express 5 + MongoDB 7
• Frontend: React 19 + Material-UI + Redux Toolkit + Recharts
• Deploy: PM2 + nginx on EC2 (mirrors AMRnet topology)

Local development

# 1. Configure environment
cp .env.example .env
# Edit .env to point at your local mongod

# 2. Install
npm install
cd client && npm install --legacy-peer-deps && cd ..

# 3. Start
npm run start:dev   # backend on :8080, client dev server on :3000

The backend expects a kpneumo database with collection amrnetdb_kpneumo to be reachable via MONGODB_URI.

Database

KlebNET-GSP reads a single MongoDB database:

Database	Collection	Source
kpneumo	amrnetdb_kpneumo	Extracted from AMRnet upstream

To bootstrap data, dump just the kpneumo database from AMRnet:

mongodump --uri "$AMRNET_SOURCE_URI" --db kpneumo --out /tmp/dump
mongorestore --uri "$KLEBNET_TARGET_URI" /tmp/dump

Deploy

See deploy/setup-ec2.sh and deploy/deploy-production.sh (adapted from AMRnet, paths rebased to /opt/klebnet).

TODOs after fork

A handful of cosmetic strings still reference AMRnet (deep PDF report templates in client/src/locales/*.json, the user-guide / contact links in client/src/util/menuItems.js). These don't break functionality — update at leisure as the KlebNET-GSP product matures.

License

GPL-3.0 — same as upstream AMRnet.

Credits

Built on the AMRnet platform by Cerdeira LT, Dyson ZA, Sharma V, et al. AMRnet: a data visualization platform to interactively explore pathogen variants and antimicrobial resistance. Nucleic Acids Res (2025), doi:10.1093/nar/gkaf1101.