resfinder

name	resfinder
description	ResFinder — CGE identification of acquired antimicrobial resistance genes (and optional PointFinder chromosomal mutations / DisinFinder biocide genes) from assemblies or reads. Use for isolate resistome typing with ResFinder DB phenotype mapping. Upstream: https://github.com/genomicepidemiology/resfinder. Route via cge-finders / microbial-mining; biocide-only → disinfinder; complement with rgi (CARD) and deeparg — keep tables separate.
license	MIT
category	analysis-tools
tags	["ResFinder","CGE","AMR","resistome","PointFinder","DisinFinder"]
upstream	https://github.com/genomicepidemiology/resfinder
stage	mining

ResFinder

Upstream: genomicepidemiology/resfinder · DB: resfinder_db

Citation

Zankari, E. et al. Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 67, 2640–2644 (2012). https://doi.org/10.1093/jac/dks261

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

Bortolaia, V. et al. ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes. J. Antimicrob. Chemother. 77, e1–e10 (2022). https://doi.org/10.1093/jac/dkac018

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

Analytical thinking

ResFinder detects acquired AMR genes against the CGE ResFinder DB and can emit genotype→phenotype summaries for supported taxa. Optional PointFinder (-c / point DB) adds chromosomal resistance mutations; DisinFinder covers selected disinfectant resistance markers when databases are installed.

Not interchangeable with CARD/rgi ontology. Genotype prediction ≠ MIC / treatment guidance. For metagenomes, prefer gene catalogues + rgi/deeparg and treat ResFinder as isolate/HQ-MAG screening.

How to run

# install resfinder + clone resfinder_db (± pointfinder_db, disinfinder_db)
python -m resfinder -ifa assembly.fasta -o resfinder_out \
  -db_res /path/to/resfinder_db \
  -l 0.6 -t 0.9
# chromosomal mutations (species-aware):
python -m resfinder -ifa assembly.fasta -o resfinder_out \
  -db_res /path/to/resfinder_db -db_point /path/to/pointfinder_db -c
# convenience wrapper for Res+Point+Plasmid DBs → staramr

Pin ResFinder software and all DB versions used.

Decision tree

Resistome claim?
├─ CGE acquired AMR (+ optional phenotype map) → resfinder
├─ Chromosomal AMR SNPs → pointfinder / resfinder -c
├─ Biocide / disinfectant genes → disinfinder
├─ Combined Res+Point+Plasmid → staramr
├─ Multi-DB screen → abricate
├─ CARD catalogue / meta gene catalogue → rgi
├─ ML complement → deeparg (separate table)
└─ Plasmid context → plasmidfinder / pmlst / genomad / mob-suite ∩ hits

Related skills

cge-finders · pointfinder · disinfinder · plasmidfinder · pmlst · staramr · abricate · rgi · deeparg · virulencefinder · mobileelementfinder · genomad · microbial-mining · tool-selection