| name | pointfinder |
| description | PointFinder — CGE detection of antimicrobial resistance associated with chromosomal point mutations in selected bacterial pathogens. Use when acquired-gene screens miss mutation-driven resistance (e.g. gyrA, rpoB). DB: pointfinder_db; often run via ResFinder (-c) or staramr. Route via cge-finders / microbial-mining.
|
| license | MIT |
| category | analysis-tools |
| tags | ["PointFinder","CGE","AMR","chromosomal","mutation","SNP","resistome"] |
| upstream | https://bitbucket.org/genomicepidemiology/pointfinder_db |
| stage | mining |
PointFinder
Database: pointfinder_db ·
Typically invoked through ResFinder
(-c / --db_path_point) or staramr.
Citation
Zankari, E. et al. PointFinder: a novel web tool for WGS-based detection of
antimicrobial resistance associated with chromosomal point mutations in bacterial
pathogens. J. Antimicrob. Chemother. 72, 2764–2768 (2017).
https://doi.org/10.1093/jac/dkx217
See also docs/references.md, resfinder, and
cge-finders.
Analytical thinking
PointFinder is species-panel limited (e.g. E. coli, Salmonella,
Campylobacter, enterococci, … — check current DB). It finds known
resistance-associated chromosomal SNPs/indels, not novel mutations outside the
panel. Always state organism used for the PointFinder scheme.
Prefer running via current ResFinder / staramr so software and DB stay aligned.
Do not treat as a substitute for acquired-gene ResFinder/rgi hits.
How to run
python -m resfinder -ifa assembly.fasta -o point_out \
-db_res /path/to/resfinder_db \
-db_point /path/to/pointfinder_db -c
staramr search --pointfinder-organism escherichia_coli \
-o staramr_out assembly.fasta
Decision tree
Mutation-driven AMR?
├─ Species in PointFinder panel → pointfinder via resfinder/staramr
├─ Acquired genes → resfinder / rgi
├─ Unknown environmental MAG → prefer rgi; PointFinder often N/A
└─ Phenotype confirmation → AST / MIC (out of scope)
Related skills
cge-finders · resfinder · staramr · plasmidfinder · rgi ·
microbial-mining · tool-selection
