amr-mcp

An MCP server that lets AI assistants (Claude, Codex, Cursor…) query antimicrobial resistance (AMR) data from public, free sources:

• NCBI Reference Gene Catalog, the curated database behind AMRFinderPlus: ~11,500 AMR genes, point mutations, stress and virulence genes
• NCBI E-utilities: protein and nucleotide sequences, PubMed references
• UniProtKB: protein function, keywords and cross-references
• AMRFinderPlus (optional, if installed locally): screen your own genomes

All data sources are public domain or freely accessible; no API keys are required.

Example questions

Which carbapenemases are reported in Klebsiella pneumoniae, and what is the original paper for KPC-2?

Give me the protein sequence of mcr-1.1 and its UniProt function annotation.

Run AMRFinderPlus on ~/data/isolate_17.fasta as Escherichia and explain the hits by drug class.

Tools

Installation

Run it with uv (no install step needed), or pip install amr-mcp.

Claude Code

claude mcp add amr -- uvx amr-mcp

Claude Desktop

Add to claude_desktop_config.json:

{
  "mcpServers": {
    "amr": { "command": "uvx", "args": ["amr-mcp"] }
  }
}

Configuration

To enable run_amrfinder: conda install -c bioconda ncbi-amrfinderplus && amrfinder -u.

Development

python -m venv .venv && .venv/bin/pip install -e ".[dev]"
.venv/bin/pytest -m "not network"   # offline tests
.venv/bin/pytest                    # also hits the live NCBI/UniProt APIs

Data licensing

The NCBI Reference Gene Catalog and NCBI sequence data are US government works in the public domain. UniProt data is available under CC BY 4.0. Please cite the original sources when you publish results:

• Feldgarden M, et al. AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep. 2021.
• The UniProt Consortium. UniProt: the Universal Protein Knowledgebase. Nucleic Acids Res.

License

MIT

Developed with AI assistance (Claude Code); all code reviewed and tested by the author.