bio-epidemiological-genomics-amr-surveillance SKILL.md skillA
bio-epidemiological-genomics-amr-surveillance from fridrichmethod/awesome-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add fridrichmethod/awesome-skills/bio-epidemiological-genomics-amr-surveillance@git:20260531.6e617c4Pins git:20260531.6e617c4 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- fridrichmethod/awesome-skills
- Path
skills/amr-surveillance/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260531.6e617c4, committed May 31, 2026
- First version recorded
- May 17, 2026
- Size
- 30,431 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
Detects acquired antimicrobial-resistance determinants and chromosomal point-mutation resistance in bacterial assemblies using AMRFinderPlus, ResFinder 4.0 (acquired + PointFinder), CARD-RGI, abritAMR, staramr, and species-specific callers (TB-Profiler, Mykrobe). Harmonises cross-tool output via hAMRonization, contextualises determinants with mobile-genetic-element annotation (MOB-suite, PlasmidFinder, MobileElementFinder, ICEberg), predicts phenotype against EUCAST or CLSI breakpoints, and…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## Version Compatibility Reference examples tested with: ncbi-amrfinderplus 4.0+, resfinder 4.5+, rgi 6.0+ (CARD 3.3+), abritamr 1.0.14+, staramr 0.10+, hamronization 1.1+, tb-profiler 6.2+, mykrobe 0.13+, mob_suite 3.1+, plasmidfinder 2.1+, MobileElementFinder 1.0+, pandas 2.2+, BioPython 1.84+. Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags - AMRFinderPlus: `amrfinder --list_organisms` for the current `--organism` catalogue - WHO Mtb catalogue: `tb-profiler list_db` and verify the bundled WHO edition - AMR database freshness: `amrfinder -u` (NCBI ReferenceGeneCatalog) and `tb-profiler update_tbdb` If a flag or column name does not match (`--species` vs `--organism`, `barcode_build` vs `barcode-build`), introspect the installed package rather than retrying. AMRFinderPlus, RGI, and ResFinder all renamed columns between major releases. # AMR Surveillance …
Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-epidemiological-genomics-amr-surveillance@sha256:f28e4ed9571e5786The line at the top of this page pins the label git:20260531.6e617c4, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_q3prxwo6meatvqrs)
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Versions
The registry has recorded 3 versions of this file, between May 17, 2026 and May 31, 2026, about one every 7 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260531.6e617c4 latest | 2026-05-31 | 6e617c4 | 30,431 B | A | view · diff |
| git:20260528.89ddef6 | 2026-05-28 | 89ddef6 | 30,431 B | A | view · diff |
| git:20260517.81511a7 | 2026-05-17 | 81511a7 | 7,581 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (30431 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
fridrichmethod/awesome-skills · 15 stars · license a license file GitHub does not identify · pushed 2026-10-18 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_q3prxwo6meatvqrs GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-epidemiological-genomics-amr-surveillance GET https://markdownregistry.com/api/v1/blob/f28e4ed9571e5786f2f342f6fc13990b571be9f1f6b1c6b9eadd2bcefbc7f500
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.