disinfinder

name	disinfinder
description	DisinFinder — CGE disinfectant / biocide resistance gene screen via the DisinFinder database, typically run through ResFinder. Use for isolate biocide-resistance markers alongside acquired AMR. DB: https://bitbucket.org/genomicepidemiology/disinfinder_db. Route via cge-finders / resfinder / microbial-mining.
license	MIT
category	analysis-tools
tags	["DisinFinder","CGE","biocide","disinfectant","resistance","ResFinder"]
upstream	https://bitbucket.org/genomicepidemiology/disinfinder_db
stage	mining

DisinFinder

Database: disinfinder_db · Invoked through ResFinder (--db_path_disinf / disinfectant mode).

Citation

Cite ResFinder 4 / resource papers (DisinFinder ships as a CGE DB used by ResFinder):

Bortolaia, V. et al. ResFinder 4.0 for predictions of phenotypes from genotypes. J. Antimicrob. Chemother. 75, 3491–3500 (2020). https://doi.org/10.1093/jac/dkaa345

See also docs/references.md, resfinder, and cge-finders.

Analytical thinking

DisinFinder targets disinfectant / biocide-associated determinants (separate from ResFinder antibiotic genes and PointFinder chromosomal SNPs). Hit ≠ measured biocide MIC or clinical antiseptic failure. Keep tables separate from CARD/rgi antibiotic claims.

Prefer ResFinder CLI with the DisinFinder DB installed and pinned. Batch isolate AMR+plasmid workflows may still use staramr for antibiotics/plasmids, then add DisinFinder via ResFinder when biocide genes are in scope.

How to run

git clone https://bitbucket.org/genomicepidemiology/disinfinder_db.git
# ResFinder disinfectant search (flag names follow installed --help)
python -m resfinder -ifa assembly.fasta -o disinf_out \
  -db_res /path/to/resfinder_db \
  -db_disinf /path/to/disinfinder_db
# some builds use an explicit disinfectant / --disinf switch — check --help

Pin ResFinder software + disinfinder_db commit/tag.

Decision tree

Biocide / disinfectant genes?
├─ CGE DisinFinder DB → disinfinder via resfinder
├─ Antibiotic acquired genes → resfinder
├─ Chromosomal AMR SNPs → pointfinder
├─ CARD antibiotics → rgi
└─ Multi-DB mass screen → abricate (if DB includes relevant sets)

Related skills

cge-finders · resfinder · pointfinder · staramr · abricate · rgi · plasmidfinder · microbial-mining · tool-selection