Main tool : NCBI AMRFinderPlus
Full documentation: https://github.com/ncbi/amr/wiki
# list out the available organisms for the -O/--organism flag
$ amrfinder -l
Running: amrfinder -l
Software directory: '/amrfinder/'
Software version: 3.10.24
Database directory: '/amrfinder/data/2021-12-21.1'
Database version: 2021-12-21.1
Available --organism options: Acinetobacter_baumannii, Campylobacter, Clostridioides_difficile, Enterococcus_faecalis,
Enterococcus_faecium, Escherichia, Klebsiella, Neisseria, Pseudomonas_aeruginosa, Salmonella, Staphylococcus_aureus,
Staphylococcus_pseudintermedius, Streptococcus_agalactiae, Streptococcus_pneumoniae, Streptococcus_pyogenes, Vibrio_cholerae
# run amrfinder with an genome assembly (FASTA/FNA) as input (nucleotide mode)
$ amrfinder --plus --name GCA_011245895.1 -n GCA_011245895.1_PDT000672941.1_genomic.fna -O Salmonella -o GCA_011245895.1-amrfinder.tsv
# part of output 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_011245895.1 NA AAPPHT010000001.1 373875 376130 - parC_S80I Salmonella quinolone resistant ParC core AMR POINT QUINOLONE QUINOLONE POINTX 752 752 100.00 99.60 752 WP_001281910.1 DNA topoisomerase IV subunit A ParC NA NA
GCA_011245895.1 NA AAPPHT010000003.1 338394 338855 - golS Au(I) sensor transcriptional regulator GolS plus STRESS METAL GOLD GOLD BLASTX 154 154 100.00 99.35 154 AAL19308.1 Au(I) sensor transcriptional regulator GolS NA NA
GCA_011245895.1 NA AAPPHT010000003.1 338870 341155 - golT gold/copper-translocating P-type ATPase GolT plus STRESS METAL COPPER/GOLD COPPER/GOLD BLASTX 762 762 100.00 99.48 762 AAL19307.1 gold/copper-translocating P-type ATPase GolT NA NA
GCA_011245895.1 NA AAPPHT010000003.1 341432 342655 + mdsA multidrug efflux RND transporter periplasmic adaptor subunit MdsA plus AMR AMR EFFLUX EFFLUX BLASTX 408 408 100.00 98.28 408 AAL19306.1 multidrug efflux RND transporter periplasmic adaptor subunit MdsA NA NA
GCA_011245895.1 NA AAPPHT010000003.1 342655 345819 + mdsB multidrug efflux RND transporter permease subunit MdsB plus AMR AMR EFFLUX EFFLUX BLASTX 1055 1055 100.00 99.53 1055 AAL19305.1 multidrug efflux RND transporter permease subunit MdsB NA NA
GCA_011245895.1 NA AAPPHT010000009.1 96940 99129 + sinH intimin-like inverse autotransporter SinH plus VIRULENCE VIRULENCE NA NA BLASTX 730 730 100.00 98.77 730 AAL21411.1 intimin-like inverse autotransporter SinH NA NA
GCA_011245895.1 NA AAPPHT010000010.1 173540 176173 + gyrA_D87G Salmonella quinolone/triclosan resistant GyrA core AMR POINT QUINOLONE/TRICLOSAN QUINOLONE/TRICLOSAN POINTX 878 878 100.00 99.77 878 WP_001281271.1 DNA gyrase subunit A GyrA NA NA
GCA_011245895.1 NA AAPPHT010000010.1 173540 176173 + gyrA_S83F Salmonella quinolone/triclosan resistant GyrA core AMR POINT QUINOLONE/TRICLOSAN QUINOLONE/TRICLOSAN POINTX 878 878 100.00 99.77 878 WP_001281271.1 DNA gyrase subunit A GyrA NA NA
GCA_011245895.1 NA AAPPHT010000014.1 51361 52473 + iroB salmochelin biosynthesis C-glycosyltransferase IroB plus VIRULENCE VIRULENCE NA NA BLASTX 371 371 100.00 86.52 371 EOW04219.1 salmochelin biosynthesis C-glycosyltransferase IroB NA NA
GCA_011245895.1 NA AAPPHT010000014.1 52557 56183 + iroC salmochelin/enterobactin export ABC transporter IroC plus VIRULENCE VIRULENCE NA NA BLASTX 1209 1219 98.85 80.18 1211 AUH19662.1 salmochelin/enterobactin export ABC transporter IroC NA NA