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AMR (antimicrobial resistance)

Official registry Other

Antimicrobial resistance genes, sequences and literature from NCBI and UniProt

Source code Documentation

Install

Add this to your client's MCP configuration (Claude Desktop: claude_desktop_config.json; Cursor: .cursor/mcp.json; VS Code and others use the same "mcpServers" shape).

PYPI package amr-mcp
Claude Code 
claude mcp add amr-antimicrobial-resistance -e 'NCBI_API_KEY=<your ncbi_api_key>' -e 'NCBI_EMAIL=<NCBI_EMAIL>' -- uvx amr-mcp==0.1.2
JSON configuration (Claude Desktop, Cursor, VS Code) 
{
    "mcpServers": {
        "amr-antimicrobial-resistance": {
            "command": "uvx",
            "args": [
                "amr-mcp==0.1.2"
            ],
            "env": {
                "NCBI_API_KEY": "<your ncbi_api_key>",
                "NCBI_EMAIL": "<NCBI_EMAIL>"
            }
        }
    }
}

Environment variables

  • NCBI_API_KEY secret Optional free NCBI API key; raises the rate limit from 3 to 10 requests/s
  • NCBI_EMAIL Optional contact e-mail sent to NCBI with each request

Documentation

From the project's README on GitHub, refreshed weekly. Links open on GitHub.

Contents
  1. amr-mcp
  2. Example questions
  3. Tools
  4. Installation
  5. Configuration
  6. Development
  7. Data licensing
  8. License

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

ToolWhat it does
search_amr_genesSearch by text, drug class, subclass, organism or element type
get_amr_geneExact record for an allele (blaKPC-2) or summary of a family (blaKPC)
list_drug_classesDrug classes and how many catalog entries each has
catalog_infoCatalog version and size
fetch_sequenceProtein or nucleotide FASTA from NCBI by accession
get_pubmed_referencesTitle, journal, authors and DOI for PubMed IDs
search_uniprot / get_uniprot_entryUniProtKB search and entry details
run_amrfinderRun a local AMRFinderPlus install on a FASTA file

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"] }
  }
}
Without uv: pipx
pipx install amr-mcp
which amr-mcp   # e.g. /Users/you/.local/bin/amr-mcp

Then use that absolute path as the command, for example in claude_desktop_config.json:

{
  "mcpServers": {
    "amr": { "command": "/Users/you/.local/bin/amr-mcp" }
  }
}

Desktop apps don't inherit your shell's PATH, so if Claude Desktop can't start the server, use the absolute path for the command (this applies to uvx too: run which uvx to get it).

Configuration

VariablePurpose
NCBI_API_KEYOptional, free. Raises the NCBI rate limit from 3 to 10 requests/s
NCBI_EMAILOptional. Contact e-mail NCBI asks tools to send
AMR_MCP_CACHE_DIRWhere the catalog is cached (default ~/.cache/amr-mcp, refreshed every 30 days)

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.

Frequently asked questions

What is AMR (antimicrobial resistance)?

Antimicrobial resistance genes, sequences and literature from NCBI and UniProt

How do I install AMR (antimicrobial resistance)?

It runs on your machine. In Claude Code: claude mcp add amr-antimicrobial-resistance -e 'NCBI_API_KEY=<your ncbi_api_key>' -e 'NCBI_EMAIL=<NCBI_EMAIL>' -- uvx amr-mcp==0.1.2. For other clients, paste the JSON configuration from this page into their MCP settings.

Does AMR (antimicrobial resistance) need an API key?

Yes. It expects NCBI_API_KEY, which you set in its configuration.

Is AMR (antimicrobial resistance) open source?

Yes. Its code is on GitHub under the MIT license.

Who maintains AMR (antimicrobial resistance)?

It is published by pabloestepaa. AI.tn lists it but does not maintain or endorse it.

From the official MCP Registry. Listing is not an endorsement: review a server's code and permissions before giving it access to your data.