# AMR (antimicrobial resistance) (pypi · amr-mcp)

Antimicrobial resistance genes, sequences and literature from NCBI and UniProt

- Trust score: 79/100 (medium)
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-11-05

## Components

- pypi · `amr-mcp`: 79/100 (this document), [markdown](https://verifymcp.io/servers/pabloestepaa-amr-mcp/amr-mcp.md), [page](https://verifymcp.io/servers/pabloestepaa-amr-mcp/amr-mcp)

## Channel facts

- Registry: `pypi`
- Package: `amr-mcp`
- Version: `0.1.3`
- Transport: `stdio`

## Trust breakdown

How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. Scores are 0–100 per category. Scoring method: https://verifymcp.io/docs/scoring (what has changed: https://verifymcp.io/docs/scoring/changelog)

Scored 2026-11-05.

- **Supply Chain Security**: 100/100
  - No malware found by supply-chain analysis.
  - No known CVEs affecting this package version or its production dependencies.
  - Runs hatchling.build at install time, a recognised build step with no custom scripting around it.
  - 1 of 31 dependencies flagged as unhealthy.
- **Provenance & Transparency**: 97/100
  - Source repository is publicly reachable at the declared URL.
  - Cryptographically verified build provenance (signed, bound to pabloestepaa/amr-mcp).
  - Clear OSI-approved license (MIT).
  - Actively maintained (last published 1 days ago).
  - Disclosure check failed: no security disclosure policy was found in the source repository.
- **Schema Quality & AI Usability**: 69/100
  - AI-judged instruction clarity (good).
  - Tool/resource definitions use about 850 tokens (~85/item across 10 items; 10 tools + 0 resources), lean.
  - Usage-examples check failed: none of the tools include examples.
- **Stability & Change Management**: 0/100
  - Stability not yet verified: not enough scan history yet (needs a 30-day window).
- **Tool Coverage**: 94/100
  - 100% of tools have a non-trivial description (not blank, and not just the tool's name).
  - 80% of tool parameters carry a description.
  - Structured output schemas are declared (100% of tools); any adoption earns full credit.
- **Tool Safety**: 100/100
  - No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.
  - We read all 10 captured tool definition(s), and no name or description among them implies an irreversible operation.
  - An AI judge read all 11 captured unit(s) of tool text and found none that tries to manipulate the model reading it.
- **Capabilities**: 100/100
  - Implements a current MCP spec version (2026-07-28).

**Unverified: 1 category.** A category scored 0 because we could not verify it: a data source with nothing on this package, evidence we could not reach, or a check we could not run. We only credit what we can confirm.

## Install

### How do I install the AMR (antimicrobial resistance) MCP server?

AMR (antimicrobial resistance) runs locally as a PyPI package, launched with uvx amr-mcp. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.

### Claude

```bash
claude mcp add pabloestepaa-amr-mcp -- uvx amr-mcp
```

### Cursor

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

### VS Code

```json
{
  "servers": {
    "pabloestepaa-amr-mcp": {
      "command": "uvx",
      "args": [
        "amr-mcp"
      ]
    }
  }
}
```

### Codex

```bash
codex mcp add pabloestepaa-amr-mcp -- uvx amr-mcp
```

### opencode

```json
{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "pabloestepaa-amr-mcp": {
      "type": "local",
      "command": [
        "uvx",
        "amr-mcp"
      ],
      "enabled": true
    }
  }
}
```

### OpenClaw

```bash
openclaw mcp add pabloestepaa-amr-mcp --command uvx --arg amr-mcp
```

### Hermes

```yaml
mcp_servers:
  pabloestepaa-amr-mcp:
    command: "uvx"
    args: ["amr-mcp"]
```

### Netclaw

```json
{
  "McpServers": {
    "pabloestepaa-amr-mcp": {
      "Transport": "stdio",
      "Command": "uvx",
      "Arguments": [
        "amr-mcp"
      ]
    }
  }
}
```

### Vellum

```bash
assistant mcp add pabloestepaa-amr-mcp -t stdio -c uvx -a amr-mcp
```

### Other

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

## Changelog

Every change recorded for this component, newest first. Days that predate change tracking, or that we cannot explain, say so: "we were watching and nothing happened" and "we were not watching" are different claims.

### 2026-11-03 (score 79)

First indexed and scored.

## MCP tools (10)

### `catalog_info` (~22 tokens)

Version and size of the NCBI Reference Gene Catalog in use.

### `list_drug_classes` (~24 tokens)

All drug classes in the catalog with the number of entries for each.

### `search_amr_genes` (~209 tokens)

Search the NCBI Reference Gene Catalog of AMR, stress and virulence genes and point mutations.

Input parameters:

- `drug_class`: e.g. BETA-LACTAM, COLISTIN, AMINOGLYCOSIDE
- `element_type`: Element type
- `group_by_family` (boolean): Return one row per gene family with its entry count; use for broad searches
- `limit` (integer): Max entries, or max families when grouping
- `organism`: Drop entries the catalog restricts to other taxa, e.g. 'Klebsiella pneumoniae'. Most acquired genes have no restriction, so this does not show where a gene has been found: use get_protein_hosts for t…
- `query`: Text in allele, gene family, product name or synonyms, e.g. 'KPC', 'mcr', 'carbapenemase'
- `subclass`: e.g. CARBAPENEM, CEPHALOSPORIN

### `get_amr_gene` (~60 tokens)

Full catalog record for an allele, or a summary of all alleles in a gene family.

Input parameters:

- `name` (string, required): Exact allele (e.g. 'blaKPC-2') or gene family (e.g. 'blaKPC')

### `fetch_sequence` (~59 tokens)

Fetch a protein or nucleotide sequence from NCBI in FASTA form.

Input parameters:

- `accession` (string, required): NCBI accession, e.g. WP_004199234.1 or NG_049253.1
- `kind` (string)

### `get_protein_hosts` (~69 tokens)

Species in which NCBI has sequenced this exact protein (Identical Protein Groups), with record counts.

Input parameters:

- `accession` (string, required): Protein accession, ideally the catalog's RefSeq WP_ one, e.g. WP_004199234.1
- `top` (integer)

### `get_pubmed_references` (~48 tokens)

Title, journal, date, authors and DOI for PubMed articles.

Input parameters:

- `pmids` (array, required): PubMed IDs, e.g. from a catalog entry's pubmed_reference

### `search_uniprot` (~76 tokens)

Search UniProtKB proteins.

Input parameters:

- `limit` (integer)
- `query` (string, required): UniProt query syntax, e.g. 'gene:KPC-2' or 'carbapenemase AND organism_id:573'
- `reviewed_only` (boolean): Only Swiss-Prot (manually reviewed) entries

### `get_uniprot_entry` (~45 tokens)

Function, keywords, cross-references and sequence of a UniProtKB entry.

Input parameters:

- `accession` (string, required): UniProt accession, e.g. Q9F663

### `run_amrfinder` (~86 tokens)

Screen a local genome or proteome for AMR genes with AMRFinderPlus (must be installed locally).

Input parameters:

- `fasta_path` (string, required): Absolute path to a local FASTA file
- `organism`: Enables point-mutation screening, e.g. 'Escherichia', 'Klebsiella_pneumoniae'
- `sequence_type` (string)

## Diagnostics

Captured diagnostic sections: Provenance, Install scripts, Dependencies. The full working is on the page: https://verifymcp.io/servers/pabloestepaa-amr-mcp/amr-mcp#diagnostics

## Score history

- 2026-11-05: 79
- 2026-11-04: 79
- 2026-11-03: 79

## Common questions

### What is the AMR (antimicrobial resistance) MCP server?

AMR (antimicrobial resistance) is an MCP server listed in the public MCP registry as io.github.pabloestepaa/amr-mcp. Antimicrobial resistance genes, sequences and literature from NCBI and UniProt. This page covers its PyPI package (amr-mcp).

### Is the AMR (antimicrobial resistance) MCP server safe to use?

AMR (antimicrobial resistance) scores 79 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 5 November 2026. Its build provenance is signed and verified. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.

### What tools does the AMR (antimicrobial resistance) MCP server expose?

AMR (antimicrobial resistance) exposes 10 tools: catalog_info, list_drug_classes, search_amr_genes, get_amr_gene, fetch_sequence, and 5 more. Their descriptions and schemas cost roughly 698 tokens of context every time the server is loaded.

### Is the AMR (antimicrobial resistance) MCP server still maintained?

AMR (antimicrobial resistance) is still listed as active in the MCP registry. We last reached this channel on 5 November 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.

### What licence is the AMR (antimicrobial resistance) MCP server under?

AMR (antimicrobial resistance) declares the MIT licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.

## Links

- PyPI project: https://pypi.org/project/amr-mcp/
- Socket report: https://socket.dev/pypi/package/amr-mcp
- Repository: https://github.com/pabloestepaa/amr-mcp
- Changelog RSS feed: https://verifymcp.io/servers/pabloestepaa-amr-mcp/amr-mcp.xml
- Changelog JSON feed: https://verifymcp.io/servers/pabloestepaa-amr-mcp/amr-mcp.json
- HTML version of this page: https://verifymcp.io/servers/pabloestepaa-amr-mcp/amr-mcp