| 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
python -m resfinder -ifa assembly.fasta -o disinf_out \
-db_res /path/to/resfinder_db \
-db_disinf /path/to/disinfinder_db
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
