AMR (antimicrobial resistance)

Name: AMR (antimicrobial resistance)
Author: pabloestepaa

by pabloestepaaversion 0.1.4i★ –iRuns on your computer

Registry nameio.github.pabloestepaa/amr-mcp

Install

Overview

Description from the maker (original English)

Antimicrobial resistance genes, sequences and literature from NCBI and UniProt

PopNx MCP’s three pillars

These three are never merged into one score: opinions, measurements and popularity are different things.

User voiceiNo reviews yetReviews open together with accounts in a later step
Our basic checksi1 of 1 passedChecked from public information; code not scanned yet
UsageiEarly↓ 785/wk · ★ –

What you can do with it

We have not written a plain-language summary for this one yet. Below are the facts we read from the registry.

Connection: Runs on your computer
Transport: stdio
Category: Other
You need to fill in: NCBI_API_KEY

Install

Pick the AI app you use, then copy the settings.

Before you install

Basic checks: 1 of 1 passed
Runs on your computer with your user’s permissions (files, network, apps).
You fill in yourself: NCBI_API_KEY, NCBI_EMAIL

Values marked secret are keys to your account. Never share them or paste them into a chat.

You need

PyPIPython’s uv installed (for the uvx command)

Which app do you use?

ClaudeClaude CodeCursorVS CodeChatGPT

Pick your app above. We remember it, so next time the button says “Install in …”.

Open Claude Desktop → Settings → Developer → Edit Config, and paste this into claude_desktop_config.json

{
  "mcpServers": {
    "amr": {
      "command": "uvx",
      "args": [
        "amr-mcp"
      ],
      "env": {
        "NCBI_API_KEY": "your-value",
        "NCBI_EMAIL": "your-value"
      }
    }
  }
}

Run this in your terminal

claude mcp add amr --env NCBI_API_KEY=your-value --env NCBI_EMAIL=your-value -- uvx amr-mcp

Fill in the empty values before running it.

Open in Cursor

Or copy the settings yourself

Paste into .cursor/mcp.json in your project, or ~/.cursor/mcp.json

{
  "mcpServers": {
    "amr": {
      "command": "uvx",
      "args": [
        "amr-mcp"
      ],
      "env": {
        "NCBI_API_KEY": "your-value",
        "NCBI_EMAIL": "your-value"
      }
    }
  }
}

Your browser asks to open the app, then the app shows the settings and asks you to confirm. Key values are left empty for you to fill in.

Open in VS Code

Or copy the settings yourself

Paste into .vscode/mcp.json in your project

{
  "servers": {
    "amr": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "amr-mcp"
      ],
      "env": {
        "NCBI_API_KEY": "your-value",
        "NCBI_EMAIL": "your-value"
      }
    }
  }
}

Your browser asks to open the app, then the app shows the settings and asks you to confirm. Key values are left empty for you to fill in.

This one runs on your computer, and ChatGPT can only connect to servers on the internet. Pick another app.

Your choice stays on this device in a cookie; no account needed.

Values you fill in

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

These settings are generated from the maker’s registry entry. If the README says otherwise, follow the README.

What it can do

Runs on your computer; the tool list appears in your AI app after you install it.

Basic checksi

We check information anyone can see; we have not read the code. Checks that do not apply are left out of the count. · Checked Nov 8, 2026

✓ Pass
Maker matches the repo
The registry name was verified with the GitHub account pabloestepaa, which owns the repo
… Not checked yet
Still maintained
We have not read this repo from GitHub yet
… Not checked yet
Has a licence
We have not read this repo from GitHub yet
– Not applicable
Endpoint responds
This one runs on your computer; there is no internet endpoint
– Not applicable
Sign-in with OAuth
Runs on your computer and uses local settings instead
… Not checked yet
No hidden instructions in tool descriptions
Runs on your computer; we can only read tool lists from internet endpoints

Compared with others in Otheri

More stars than 0% of the other 18513 servers in this category
Published to the registry more recently than 95% of the other 18513 servers in this category
Basic checks equal to or better than 100% of the other 18513 servers in this category

Compared with every active server in this category in the registry. Stars count only when the publisher owns the repo.

Common questions

Is AMR (antimicrobial resistance) safe?

It passed 1 of 1 applicable basic checks. We have not read the code. Before adding a key or token, see what access the server asks for and use a key with only the permissions you need.

What keys or codes does it need?

You need to fill in: NCBI_API_KEY

Does it run on my computer or in the cloud?

It runs on your computer. Your AI app starts it when needed, and data does not pass through the maker’s servers (unless it calls an online service itself).

Is it still maintained?

The GitHub repo last changed –, and the latest version (0.1.4) reached the registry 2 days ago.

Which apps can use it?

Apps that support MCP, such as Claude Desktop, Claude Code, Cursor and VS Code. You also need Python (uv) on your computer.

What can I use instead?

In the same category: Spec Driven Development, Remote Desktop Commander, Cape Winelands Visit Planner

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README from the maker

Open the README

Copied from the maker’s repo as written. PopNx MCP has not reviewed or endorsed it. HTML, images and scripts are removed. Links lead off this site.

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.

Demo

Claude Code answering the first example question below: the server looks up blaKPC-2 in the catalog, counts the species NCBI has found it in, pulls the protein sequence and resolves the original paper.

Example questions

Which species carry the KPC-2 carbapenemase, what is the original paper describing it, and what does its protein sequence look like?

Summarise the carbapenemase gene families in the catalog and how many variants each has.

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

Tool	What it does
`search_amr_genes`	Search by text, drug class, subclass, organism or element type; `group_by_family` for broad searches
`get_amr_gene`	Exact record for an allele (`blaKPC-2`) or summary of a family (`blaKPC`)
`list_drug_classes`	Drug classes and how many catalog entries each has
`catalog_info`	Catalog version and size
`fetch_sequence`	Protein or nucleotide FASTA from NCBI by accession
`get_protein_hosts`	Species in which NCBI has sequenced an exact protein (Identical Protein Groups)
`get_pubmed_references`	Title, journal, authors and DOI for PubMed IDs
`search_uniprot` / `get_uniprot_entry`	UniProtKB search and entry details
`run_amrfinder`	Run 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).

Agent skill (optional)

skills/amr-research/SKILL.md tells the agent when to reach for these tools and how to chain them (gene → hosts → sequence → paper, family overviews, genome screening), plus the pitfalls to avoid. It works with any agent that reads SKILL.md files (Claude Code, Cursor, Codex, Copilot…):

npx skills add pabloestepaa/amr-mcp

Or copy the folder by hand, e.g. to ~/.claude/skills/amr-research/ for Claude Code. The skill uses the MCP server above, so install that too.

Configuration

Variable	Purpose
`NCBI_API_KEY`	Optional, free. Raises the NCBI rate limit from 3 to 10 requests/s
`NCBI_EMAIL`	Optional. Contact e-mail NCBI asks tools to send
`AMR_MCP_CACHE_DIR`	Where 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.

AMR (antimicrobial resistance)

Overview

PopNx MCP’s three pillars

What you can do with it

Install

Before you install

Values you fill in

What it can do

Basic checksi

Maker matches the repo

Still maintained

Has a licence

Endpoint responds

Sign-in with OAuth

No hidden instructions in tool descriptions

Compared with others in Otheri

Common questions

Alternatives

Spec Driven Development

Remote Desktop Commander

Cape Winelands Visit Planner

README from the maker

amr-mcp

Demo

Example questions

Tools

Installation

Claude Code

Claude Desktop

Without uv: pipx

Agent skill (optional)

Configuration

Development

Data licensing

License