AMRIT

Antimicrobial Resistance Monitoring, Intelligence and Tracking

AMRIT is a local-first antimicrobial-resistance (AMR) surveillance platform spanning laboratory desktop workflows, aggregate-safe national coordination, One Health programme operations, and standards-based interoperability. This repository is a reference implementation for development and controlled pilots; it is not a claim of production deployment or autonomous clinical decision support.

What is included

• An offline-capable React and Electron desktop application for laboratory configuration, isolate and AST workflows, imports, analysis, governed One Health capture, and standards exports.
• A Django central server for site enrolment, aggregate query dispatch, dashboards, outbreak-signal review, action plans, audit, and public-health programme coordination.
• Shared, versioned contracts for country profiles, geography, terminology, FHIR resources, and aggregate data products.
• Reproducible validation, benchmark, and operator documentation assets.

Architecture and privacy boundary

Laboratory edge (Electron + SQLite)
  identifiable operational records stay local
                 |
                 | authenticated aggregate queries/results
                 v
National control plane (Django + PostgreSQL + Redis)
  aggregate products, quality, lineage, alerts, actions, and governance
                 |
                 v
Restricted dashboards and disclosure-limited public views

Federation is aggregate-first: patient rows are not uploaded by the normal synchronization path. The server rejects direct identifiers at its ingest boundary and applies a configurable minimum-cell-size rule. Any separately authorized line-list exchange would require its own legal basis, endpoint, controls, and audit; it is not implemented by the aggregate ingest contract.

See ADR-001 and the privacy and safety documentation.

Repository map

Path	Purpose
app/	React, Electron, and SQLite desktop application
server/amrit_central_server/	Django central aggregation and control-plane server
shared/	Canonical cross-product contracts, country profiles, terminology, and test fixtures
fhir-ig/	FHIR implementation-guide source
docs/	Operator, deployment, outbreak-detection, and globalization documentation
architecture/	Architecture decision records
tools/	Data-generation, validation, documentation, and consistency tooling
.github/workflows/ci.yml	Cross-platform desktop, server, packaging, and repository gates

Core capabilities

• Multi-laboratory, local-first isolate and AST workflows.
• CSV, XLSX, XLSB, WHONET, and BacLink-style import with preview and validation.
• Explicitly activated, provenance-aware breakpoint sets; EUCAST support and licensed CLSI import boundaries.
• Resistance summaries, antibiograms, data-quality analysis, and outbreak-signal workflows.
• WHONET, FHIR R4, HL7 v2.5.1, JSON, and CSV interoperability.
• Country-neutral geography, configurable administrative hierarchies, and deployment branding.
• Governed One Health workflows across human, animal, food, environment, antimicrobial-use, and infection-prevention domains.
• Aggregate-only long-poll and WebSocket federation with enrolment, token rotation, audit, and privacy guards.
• Role-aware dashboards, reviewable alerts, action plans, and disclosure-limited public reporting.

Desktop development

Requirements: Node.js 22 or newer and pnpm 11.

cd app
pnpm install --frozen-lockfile
pnpm run check
pnpm test
pnpm run build
pnpm dev

Build an unpacked desktop application with pnpm run dist:dir, or platform installers with pnpm run dist.

The desktop creates its working database in the operating system's application-data directory. Set AMRIT_DATABASE_PATH only when an explicit writable database path is required for development or testing.

Central server development

Requirements: Docker with the Compose plugin.

cd server/amrit_central_server
cp .env.example .env
# Set the required values in .env, including a strong POSTGRES_PASSWORD.
docker compose up --build

The server listens on 127.0.0.1:8000 by default. It creates no default administrator credential. Follow the central-server setup guide to bootstrap an administrator and register a site. Put a TLS-terminating reverse proxy in front before exposing a deployment beyond localhost.

Repository verification

python3 tools/sync_shared.py --check
python3 tools/check_data_licences.py
python3 tools/check_country_neutral.py

cd app
pnpm install --frozen-lockfile
pnpm run check
pnpm test
pnpm run build

cd ../server/amrit_central_server
python3 -m pip install -r requirements.txt
python3 manage.py check
python3 manage.py makemigrations --check --dry-run
python3 manage.py test

Continuous integration also exercises supported desktop platforms, country profiles, reduced outbreak benchmarks, Electron packaging, the server smoke flow, dependency audit, OpenAPI generation, and the Docker build.

Clinical and operational boundaries

• AMRIT supports surveillance and laboratory workflows; it does not make autonomous treatment decisions.
• Breakpoint interpretation depends on the selected standard, edition, method, organism, specimen context, and local authorization.
• A qualified laboratory authority must review provenance and explicitly activate a staged breakpoint set.
• Production operation still requires institutional controls such as PKI and key management, SSO/MFA, signed releases, backups, monitoring, vulnerability assessment, accessibility/localization review, and approved data-sharing agreements.
• Do not commit runtime databases, environment files, credentials, patient data, or site tokens. Demonstration data must be clearly labelled and non-identifiable.

Reference data and licensing

Bundled datasets have different redistribution and use conditions. Review the data licence register before redistribution or deployment. In particular, CLSI content is not bundled, SNOMED CT use depends on the deployment's licence position, and some geographic datasets require attribution or a separate licence.

The application package is currently marked UNLICENSED. No open-source licence is granted by this repository; all rights are reserved unless the repository owner provides separate terms.

Documentation

• Operator and methods manual
• Desktop application guide
• Central server guide
• Outbreak detection
• International deployment plan
• National reference implementation overview

Status

Research and reference implementation for controlled evaluation. Production readiness, clinical effectiveness, national-scale performance, and regulatory suitability must be established independently in the intended deployment environment.