AMRFinderPlus
The AMRFinderPlus tool from the National Center for
Biotechnology Information (NCBI) is a bioinformatic tool that
NCBI Antimicrobial
allows users to identify antimicrobial resistance determinants, stress Resistance Gene Finder
response, and virulence genes in bacterial genomes.[2] This tool's (AMRFinderPlus)
development began in 2018 (as AMRFinder) and is still underway. Developer(s) National
The National Institutes of Health funds the development of the Center for
software and the databases it uses. Biotechnology
Information
Usage Written in C++[1]
Operating system UNIX, Linux,
AMRFinderPlus is used by NCBI's Pathogen Detection Project (ht
Mac, MS-
tps://www.ncbi.nlm.nih.gov/pathogens/), which clusters and finds
similar pathogen genomic sequences from food, environmental Windows
sources, and patients. AMRFinderPlus is run for each bacterial Type Bioinformatics
isolate in the Pathogen Detection Project, and the findings are tool
provided for public use. Since its scientific publication in 2021, it
License Public domain
has also gathered citations (https://citations.springernature.com/ite
m?doi=10.1038/s41598-021-91456-0) from other users. Website www.ncbi.nlm
.nih.gov
Database design and curation /pathogens
/antimicrobial-
AMRFinderPlus can detect acquired antibiotic resistance, stress resistance
response, and virulence genes, and genetic mutations that are /AMRFinder/ (h
known to confer antibiotic resistance.[2] When AMRFinderPlus ttps://www.ncb
was initially developed and distributed, there were already multiple i.nlm.nih.gov/p
databases containing antibiotic resistance determinants. The team athogens/anti
collaborated with database developers, expert panels, and others to microbial-resist
consolidate these sources and create a high-quality resource that ance/AMRFind
addressed limitations in these different data sources that the er/)
community had highlighted at the time. The NCBI team also
collaborates with expert groups to develop the database and its annotation on a regular basis. Continuous
evaluation of review papers and new reports of resistance proteins augment these sources.[2]
While some AMR gene identification tools rely on BLAST-based methodologies, others employ hidden
Markov model (HMM) approaches. BLAST-based methods can identify particular alleles and genes that
are closely related, but they often apply arbitrary cutoffs that can misidentify AMR genes or assign
resistance to non-AMR genes. In AMRFinderPlus, custom BLAST cutoffs are created for each gene to
optimize sensitivity and specificity of detection. Unlike BLAST-based approaches, which apply the same
penalty for sequence mismatches across any sequence, HMMs allow for the weighing of sequence
mismatches based on how prevalent they are in nature, resulting in higher accuracy in detecting true
homologs than BLAST-based approaches,[3] but these models require curation and validation to ensure
accuracy.[2]
The tool’s Bacterial Antimicrobial Resistance Reference Gene Database consists of up-to-date gene
nomenclature, a set of hidden Markov models (HMMs), and a curated protein family hierarchy. The
database contains over 627 AMR HMMs, 6,428 genes, and 682 mutations, placing this data in a
hierarchical framework of gene families, symbols, and names in collaboration with multiple groups. The
genes in the database consist of 5588 AMR genes, 210 stress response genes, and 630 virulence genes. The
AMR genes cover resistance to 31 different classes of antibiotic and 58 specific drugs.[2]
Sequence records include, where possible, an additional 100 bp on either side of the coding region to assist
in the design of primers. Cutoffs were set individually for each HMM through a manual process that
involved confirmation of the supporting literature, benchmarking against other AMR proteins from related
families, and the background of millions of additional proteins included in NCBI’s non redundant protein
sequence database.[2]
Usage rights
Under the rules of the United States Copyright Act, NCBI AMRFinderPlus is classed as "United States
Government Work." It is considered to be work performed as part of the developers' "official obligations
for the US government", and is therefore not protected by copyright. The software is therefore freely
accessible to the public for use and there are no limitations on its current or future use.[1]
See also
Antimicrobial resistance
Genomics
Bioinformatics
References
1. "NCBI Antimicrobial Resistance Gene Finder (AMRFinderPlus)" (https://github.com/ncbi/am
r). NCBI - National Center for Biotechnology Information/NLM/NIH. 23 November 2021.
Retrieved 14 December 2021.
2. Feldgarden, Michael; Brover, Vyacheslav; Gonzalez-Escalona, Narjol; Frye, Jonathan G.;
Haendiges, Julie; Haft, Daniel H.; Hoffmann, Maria; Pettengill, James B.; Prasad, Arjun B.;
Tillman, Glenn E.; Tyson, Gregory H.; Klimke, William (16 June 2021). "AMRFinderPlus and
the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial
resistance, stress response, and virulence" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8
208984). Scientific Reports. 11 (1): 12728. Bibcode:2021NatSR..1112728F (https://ui.adsab
s.harvard.edu/abs/2021NatSR..1112728F). doi:10.1038/s41598-021-91456-0 (https://doi.or
g/10.1038%2Fs41598-021-91456-0). PMC 8208984 (https://www.ncbi.nlm.nih.gov/pmc/articl
es/PMC8208984). PMID 34135355 (https://pubmed.ncbi.nlm.nih.gov/34135355).
3. Eddy, Sean R. (20 October 2011). "Accelerated Profile HMM Searches" (https://www.ncbi.nl
m.nih.gov/pmc/articles/PMC3197634). PLOS Computational Biology. 7 (10): e1002195.
Bibcode:2011PLSCB...7E2195E (https://ui.adsabs.harvard.edu/abs/2011PLSCB...7E2195
E). doi:10.1371/journal.pcbi.1002195 (https://doi.org/10.1371%2Fjournal.pcbi.1002195).
PMC 3197634 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3197634). PMID 22039361
(https://pubmed.ncbi.nlm.nih.gov/22039361).
External links
Github page (https://github.com/ncbi/amr)
Documentation (https://github.com/ncbi/amr/wiki)
Retrieved from "https://en.wikipedia.org/w/index.php?title=AMRFinderPlus&oldid=1093040637"
