Main tool : NCBI AMRFinderPlus
Additional tools:
- hmmer v3.3.2
- ncbi-blast+ v2.16.0
- stxtyper v1.0.27 (Shiga toxin subtyping tool, added in AMRFinderPlus v4.0.3)
The database included at time of docker image build is 2024-10-22.1. More information can be found in the changelog.txt on NCBI's FTP.
Full documentation: https://github.com/ncbi/amr/wiki
Beginning with AMRFinderPlus v3.11.2, we will include the version of AMRFinderPlus followed by the database version in the docker image tag so that it is more informative to users. The format is as follows:
# general format
staphb/ncbi-amrfinderplus:<amrfinderplus-version>-<database-version>
# example
staphb/ncbi-amrfinderplus:3.11.14-2023-04-17.1You can view all available docker images on dockerhub and quay.io
# list out the available organisms for the -O/--organism flag
$ amrfinder -l
Running: amrfinder -l
Software directory: '/amrfinder/'
Software version: 3.12.8
Database directory: '/amrfinder/data/2024-01-31.1'
Database version: 2024-01-31.1
Available --organism options: Acinetobacter_baumannii, Burkholderia_cepacia, Burkholderia_pseudomallei, Campylobacter,
Citrobacter_freundii, Clostridioides_difficile, Enterobacter_asburiae, Enterobacter_cloacae, Enterococcus_faecalis,
Enterococcus_faecium, Escherichia, Klebsiella_oxytoca, Klebsiella_pneumoniae, Neisseria_gonorrhoeae,
Neisseria_meningitidis, Pseudomonas_aeruginosa, Salmonella, Serratia_marcescens, Staphylococcus_aureus,
Staphylococcus_pseudintermedius, Streptococcus_agalactiae, Streptococcus_pneumoniae, Streptococcus_pyogenes,
Vibrio_cholerae, Vibrio_parahaemolyticus, Vibrio_vulnificus
# download Klebsiella oxytoca genome FASTA/FNA to use as a test
$ wget "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/003/812/925/GCA_003812925.1_ASM381292v1/GCA_003812925.1_ASM381292v1_genomic.fna.gz"
# uncompress the FNA file
$ gzip -d GCA_003812925.1_ASM381292v1_genomic.fna.gz
# run amrfinder (nucleotide mode) on the uncompressed FNA file
$ amrfinder --plus --name GCA_003812925.1 -n GCA_003812925.1_ASM381292v1_genomic.fna -O Klebsiella_oxytoca -o GCA_003812925.1-amrfinder.tsv
# view output TSV
$ column -t -s $'\t' -n GCA_003812925.1-amrfinder.tsv
Name Protein identifier Contig id Start Stop Strand Gene symbol Sequence name Scope Element type Element subtype Class Subclass Method Target length Reference sequence length % Coverage of reference sequence % Identity to reference sequence Alignment length Accession of closest sequence Name of closest sequence HMM id HMM description
GCA_003812925.1 NA CP033844.1 369234 370406 + oqxA multidrug efflux RND transporter periplasmic adaptor subunit OqxA core AMR AMR PHENICOL/QUINOLONE PHENICOL/QUINOLONE BLASTX 391 391 100.00 90.79 391 WP_002914189.1 multidrug efflux RND transporter periplasmic adaptor subunit OqxA NA NA
GCA_003812925.1 NA CP033844.1 370433 373582 + oqxB multidrug efflux RND transporter permease subunit OqxB core AMR AMR PHENICOL/QUINOLONE PHENICOL/QUINOLONE BLASTX 1050 1050 100.00 96.86 1050 WP_023323140.1 multidrug efflux RND transporter permease subunit OqxB15 NA NA
GCA_003812925.1 NA CP033844.1 636118 637917 - ybtQ yersiniabactin ABC transporter ATP-binding/permease protein YbtQ plus VIRULENCE VIRULENCE NA NA BLASTX 600 600 100.00 89.17 600 AAC69584.1 yersiniabactin ABC transporter ATP-binding/permease protein YbtQ NA NA
GCA_003812925.1 NA CP033844.1 637913 639706 - ybtP yersiniabactin ABC transporter ATP-binding/permease protein YbtP plus VIRULENCE VIRULENCE NA NA BLASTX 598 600 99.67 89.30 598 CAA21388.1 yersiniabactin ABC transporter ATP-binding/permease protein YbtP NA NA
GCA_003812925.1 NA CP033844.1 3473617 3474798 + emrD multidrug efflux MFS transporter EmrD plus AMR AMR EFFLUX EFFLUX BLASTX 394 394 100.00 94.16 394 ACN65732.1 multidrug efflux MFS transporter EmrD NA NA
GCA_003812925.1 NA CP033844.1 5085488 5086357 - blaOXY-2-1 extended-spectrum class A beta-lactamase OXY-2-1 core AMR AMR BETA-LACTAM CEPHALOSPORIN ALLELEX 290 290 100.00 100.00 290 WP_032727905.1 extended-spectrum class A beta-lactamase OXY-2-1 NA NA
GCA_003812925.1 NA CP033845.1 5102 5632 - ant(2'')-Ia aminoglycoside nucleotidyltransferase ANT(2'')-Ia core AMR AMR AMINOGLYCOSIDE GENTAMICIN/KANAMYCIN/TOBRAMYCIN BLASTX 177 177 100.00 98.31 177 WP_000381803.1 aminoglycoside nucleotidyltransferase ANT(2'')-Ia NA NA
GCA_003812925.1 NA CP033846.1 748 1932 - tet(39) tetracycline efflux MFS transporter Tet(39) core AMR AMR TETRACYCLINE TETRACYCLINE EXACTX 395 395 100.00 100.00 395 WP_004856455.1 tetracycline efflux MFS transporter Tet(39)