| Sample name | ST | Gene | Scaffold | Gene name | Product | Best hit ARO | Drug class | Resistance mechanism | AMRF gene symbol | Amr gene family | AMRF element type | AMRF class | Core classification | RoaryGroup |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 83T | 392 | AH0325v1g0038 | AH0325_v1_c1 | uhpT | Hexose-6-phosphate:phosphate antiporter | Escherichia coli UhpT with mutation conferring resistance to fosfomycin | fosfomycin | antibiotic target alteration | — | UhpT | — | — | core | K_pneu_uhpT |
| 83T | 392 | AH0325v1g0057 | AH0325_v1_c1 | bla_1 | Beta-lactamase CTX-M-1 | CTX-M-15 | cephalosporin | antibiotic inactivation | blaCTX-M-15 | CTX-M beta-lactamase | AMR | BETA-LACTAM | shell | K_pneu_group_18244 |
| 83T | 392 | AH0325v1g0272 | AH0325_v1_c1 | arnC | Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase | PmrF | peptide antibiotic | antibiotic target alteration | — | pmr phosphoethanolamine transferase | — | — | core | K_pneu_arnC |
| 83T | 392 | AH0325v1g0376 | AH0325_v1_c1 | crp | cAMP-activated global transcriptional regulator CRP | CRP | macrolide antibiotic; fluoroquinolone antibiotic; penam | antibiotic efflux | — | resistance-nodulation-cell division (RND) antibiotic efflux pump | — | — | core | K_pneu_crp |
| 83T | 392 | AH0325v1g0395 | AH0325_v1_c1 | tufA_1 | Elongation factor Tu 1 | Escherichia coli EF-Tu mutants conferring resistance to Pulvomycin | elfamycin antibiotic | antibiotic target alteration | — | elfamycin resistant EF-Tu | — | — | core | K_pneu_tufA_1 |
| 83T | 392 | AH0325v1g0709 | AH0325_v1_c1 | parC | DNA topoisomerase 4 subunit A | Escherichia coli parC conferring resistance to fluoroquinolone | fluoroquinolone antibiotic | antibiotic target alteration | — | fluoroquinolone resistant parC; fluoroquinolone self resistant parC | — | — | core | K_pneu_parC |
| 83T | 392 | AH0325v1g1110 | AH0325_v1_c1 | emrB_1 | Multidrug export protein EmrB | emrB | fluoroquinolone antibiotic | antibiotic efflux | — | major facilitator superfamily (MFS) antibiotic efflux pump | — | — | core | K_pneu_emrB_1 |
| 83T | 392 | AH0325v1g1112 | AH0325_v1_c1 | mprA | Transcriptional repressor MprA | emrR | fluoroquinolone antibiotic | antibiotic efflux | — | major facilitator superfamily (MFS) antibiotic efflux pump | — | — | core | K_pneu_mprA |
| 83T | 392 | AH0325v1g1154 | AH0325_v1_c1 | bepE_1 | Efflux pump membrane transporter BepE | oqxB | fluoroquinolone antibiotic; glycylcycline; tetracycline antibiotic; diaminopyrimidine antibiotic; nitrofuran antibiotic | antibiotic efflux | oqxB | resistance-nodulation-cell division (RND) antibiotic efflux pump | AMR | PHENICOL/QUINOLONE | shell | K_pneu_bepE |
| 83T | 392 | AH0325v1g1155 | AH0325_v1_c1 | bepF | Efflux pump periplasmic linker BepF | oqxA | fluoroquinolone antibiotic; glycylcycline; tetracycline antibiotic; diaminopyrimidine antibiotic; nitrofuran antibiotic | antibiotic efflux | oqxA | resistance-nodulation-cell division (RND) antibiotic efflux pump | AMR | PHENICOL/QUINOLONE | soft core | K_pneu_bepF |
| 83T | 392 | AH0325v1g1293 | AH0325_v1_c1 | acrB_1 | Multidrug efflux pump subunit AcrB | acrD | aminoglycoside antibiotic | antibiotic efflux | — | resistance-nodulation-cell division (RND) antibiotic efflux pump | — | — | core | K_pneu_acrB_1 |
| 83T | 392 | AH0325v1g1377 | AH0325_v1_c1 | vapB | Antitoxin VapB | vgaC | streptogramin antibiotic; pleuromutilin antibiotic | antibiotic target protection | — | ABC-F ATP-binding cassette ribosomal protection protein | — | — | shell | K_pneu_group_2174 |
| 83T | 392 | AH0325v1g1503 | AH0325_v1_c1 | gyrA | DNA gyrase subunit A | Escherichia coli gyrA conferring resistance to fluoroquinolones | fluoroquinolone antibiotic; nybomycin | antibiotic target alteration | gyrA_S83I | fluoroquinolone resistant gyrA | AMR | QUINOLONE | core | K_pneu_gyrA |
| 83T | 392 | AH0325v1g1604 | AH0325_v1_c1 | baeR | Transcriptional regulatory protein BaeR | baeR | aminoglycoside antibiotic; aminocoumarin antibiotic | antibiotic efflux | — | resistance-nodulation-cell division (RND) antibiotic efflux pump | — | — | core | K_pneu_baeR |
| 83T | 392 | AH0325v1g1607 | AH0325_v1_c1 | mdtC | Multidrug resistance protein MdtC | mdtC | aminocoumarin antibiotic | antibiotic efflux | — | resistance-nodulation-cell division (RND) antibiotic efflux pump | — | — | core | K_pneu_mdtC |
| 83T | 392 | AH0325v1g1608 | AH0325_v1_c1 | mdtB | Multidrug resistance protein MdtB | mdtB | aminocoumarin antibiotic | antibiotic efflux | — | resistance-nodulation-cell division (RND) antibiotic efflux pump | — | — | core | K_pneu_mdtB |
| 83T | 392 | AH0325v1g2569 | AH0325_v1_c1 | marR_2 | Multiple antibiotic resistance protein MarR | Escherichia coli marR mutant conferring antibiotic resistance | fluoroquinolone antibiotic; cephalosporin; glycylcycline; penam; tetracycline antibiotic; rifamycin antibiotic; phenicol antibiotic; triclosan | antibiotic target alteration; antibiotic efflux | — | resistance-nodulation-cell division (RND) antibiotic efflux pump | — | — | core | K_pneu_marR_2 |
| 83T | 392 | AH0325v1g2570 | AH0325_v1_c1 | marA | Multiple antibiotic resistance protein MarA | marA | fluoroquinolone antibiotic; monobactam; carbapenem; cephalosporin; glycylcycline; cephamycin; penam; tetracycline antibiotic; rifamycin antibiotic; phenicol antibiotic; triclosan; penem | antibiotic efflux; reduced permeability to antibiotic | — | resistance-nodulation-cell division (RND) antibiotic efflux pump; General Bacterial Porin with reduced permeability to beta-lactams | — | — | core | K_pneu_marA |
| 83T | 392 | AH0325v1g2590 | AH0325_v1_c1 | bla_2 | Beta-lactamase SHV-1 | SHV-11 | carbapenem; cephalosporin; penam | antibiotic inactivation | blaSHV-11 | SHV beta-lactamase | AMR | BETA-LACTAM | soft core | K_pneu_bla_1 |
| 83T | 392 | AH0325v1g2758 | AH0325_v1_c1 | ompN_2 | Outer membrane protein N | Klebsiella pneumoniae OmpK37 | monobactam; carbapenem; cephalosporin; cephamycin; penam; penem | reduced permeability to antibiotic | — | General Bacterial Porin with reduced permeability to beta-lactams | — | — | soft core | K_pneu_ompN_2 |
| 83T | 392 | AH0325v1g3242 | AH0325_v1_c1 | msbA_1 | Lipid A export ATP-binding/permease protein MsbA | msbA | nitroimidazole antibiotic | antibiotic efflux | — | ATP-binding cassette (ABC) antibiotic efflux pump | — | — | core | K_pneu_msbA_1 |
| 83T | 392 | AH0325v1g3310 | AH0325_v1_c1 | mdfA | Multidrug transporter MdfA | Escherichia coli mdfA | tetracycline antibiotic; benzalkonium chloride; rhodamine | antibiotic efflux | — | major facilitator superfamily (MFS) antibiotic efflux pump | — | — | core | K_pneu_mdfA |
| 83T | 392 | AH0325v1g3738 | AH0325_v1_c1 | acrA | Multidrug efflux pump subunit AcrA | Klebsiella pneumoniae acrA | fluoroquinolone antibiotic; cephalosporin; glycylcycline; penam; tetracycline antibiotic; rifamycin antibiotic; phenicol antibiotic; triclosan | antibiotic efflux | — | resistance-nodulation-cell division (RND) antibiotic efflux pump | — | — | core | K_pneu_acrA |
| 83T | 392 | AH0325v1g3739 | AH0325_v1_c1 | acrB_3 | Multidrug efflux pump subunit AcrB | acrB | fluoroquinolone antibiotic; cephalosporin; glycylcycline; penam; tetracycline antibiotic; rifamycin antibiotic; phenicol antibiotic; triclosan | antibiotic efflux | — | resistance-nodulation-cell division (RND) antibiotic efflux pump | — | — | soft core | K_pneu_acrB_3 |
| 83T | 392 | AH0325v1g4117 | AH0325_v1_c1 | ftsI_2 | Peptidoglycan D%2CD-transpeptidase FtsI | Haemophilus influenzae PBP3 conferring resistance to beta-lactam antibiotics | monobactam; carbapenem; cephalosporin; cephamycin; penam | antibiotic target alteration | — | Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics | — | — | core | K_pneu_ftsI_2 |
| 83T | 392 | AH0325v1g4318 | AH0325_v1_c1 | fosA | Glutathione transferase FosA | FosA6 | fosfomycin | antibiotic inactivation | fosA | fosfomycin thiol transferase | AMR | FOSFOMYCIN | soft core | K_pneu_fosA |
| 83T | 392 | AH0325v1g4706 | AH0325_v1_c1 | tufA_2 | Elongation factor Tu 1 | Escherichia coli EF-Tu mutants conferring resistance to Pulvomycin | elfamycin antibiotic | antibiotic target alteration | — | elfamycin resistant EF-Tu | — | — | core | K_pneu_tufA_2 |
| 83T | 392 | AH0325v1g5006 | AH0325_v1_c2 | folP_2 | Dihydropteroate synthase | sul2 | sulfonamide antibiotic; sulfone antibiotic | antibiotic target replacement | sul2 | sulfonamide resistant sul | AMR | SULFONAMIDE | shell | K_pneu_folP_2 |
| 83T | 392 | AH0325v1g5007 | AH0325_v1_c2 | neo | Aminoglycoside 3'-phosphotransferase | APH(3'')-Ib | aminoglycoside antibiotic | antibiotic inactivation | aph(3'')-Ib | APH(3'') | AMR | AMINOGLYCOSIDE | shell | K_pneu_neo |
| 83T | 392 | AH0325v1g5008 | AH0325_v1_c2 | — | hypothetical protein | APH(6)-Id | aminoglycoside antibiotic | antibiotic inactivation | aph(6)-Id | APH(6) | AMR | AMINOGLYCOSIDE | shell | K_pneu_group_5032 |
| 83T | 392 | AH0325v1g5010 | AH0325_v1_c2 | bla_3 | Beta-lactamase TEM | TEM-1 | monobactam; cephalosporin; penam; penem | antibiotic inactivation | blaTEM-1 | TEM beta-lactamase | AMR | BETA-LACTAM | shell | K_pneu_bla_2 |
| 83T | 392 | AH0325v1g5015 | AH0325_v1_c2 | bla_4 | Beta-lactamase CTX-M-1 | CTX-M-15 | cephalosporin | antibiotic inactivation | blaCTX-M-15 | CTX-M beta-lactamase | AMR | BETA-LACTAM | shell | K_pneu_bla_3 |
| 83T | 392 | AH0325v1g5386 | AH0325_v1_c3 | bla_5 | Beta-lactamase OXA-10 | OXA-48 | cephalosporin; penam | antibiotic inactivation | blaOXA-48 | OXA beta-lactamase | AMR | BETA-LACTAM | shell | K_pneu_bla_5 |
| 83T | 392 | AH0325v1g5464 | AH0325_v1_c4 | aacA4 | Aminoglycoside N(6')-acetyltransferase type 1 | AAC(6')-Ib-cr | fluoroquinolone antibiotic; aminoglycoside antibiotic | antibiotic inactivation | — | AAC(6') | — | — | shell | K_pneu_group_1873 |
| 83T | 392 | AH0325v1g5465 | AH0325_v1_c4 | bla_6 | Beta-lactamase OXA-1 | OXA-1 | cephalosporin; penam | antibiotic inactivation | blaOXA-1 | OXA beta-lactamase | AMR | BETA-LACTAM | cloud | K_pneu_group_7482 |
| 83T | 392 | AH0325v1g5466 | AH0325_v1_c4 | cat | Chloramphenicol acetyltransferase | catB3 | phenicol antibiotic | antibiotic inactivation | catB3 | chloramphenicol acetyltransferase (CAT) | AMR | PHENICOL | shell | K_pneu_cat_2 |
| 83T | 392 | AH0325v1g5467 | AH0325_v1_c4 | — | hypothetical protein | arr-3 | rifamycin antibiotic | antibiotic inactivation | arr-3 | rifampin ADP-ribosyltransferase (Arr) | AMR | RIFAMYCIN | cloud | K_pneu_aadB |
| 83T | 392 | AH0325v1g5469 | AH0325_v1_c4 | folP_3 | Dihydropteroate synthase | sul1 | sulfonamide antibiotic; sulfone antibiotic | antibiotic target replacement | sul1 | sulfonamide resistant sul | AMR | SULFONAMIDE | cloud | K_pneu_folP_3 |
| 83T | 392 | AH0325v1g5473 | AH0325_v1_c4 | — | Pentapeptide repeat protein | QnrB20 | fluoroquinolone antibiotic | antibiotic target protection | qnrB2 | quinolone resistance protein (qnr) | AMR | QUINOLONE | cloud | K_pneu_group_2484 |
| 83T | 392 | AH0325v1g5475 | AH0325_v1_c4 | folP_4 | Dihydropteroate synthase | sul1 | sulfonamide antibiotic; sulfone antibiotic | antibiotic target replacement | sul1 | sulfonamide resistant sul | AMR | SULFONAMIDE | cloud | K_pneu_group_12011 |
| 83T | 392 | AH0325v1g5538 | AH0325_v1_c2 | — | — | AAC(3)-Ib/AAC(6')-Ib'' | aminoglycoside antibiotic | antibiotic inactivation | — | AAC(3); AAC(6') | — | — | — | None |
| 91T | 392 | AH0326v1g0038 | AH0326_v1_c1 | uhpT | Hexose-6-phosphate:phosphate antiporter | Escherichia coli UhpT with mutation conferring resistance to fosfomycin | fosfomycin | antibiotic target alteration | — | UhpT | — | — | core | K_pneu_uhpT |
| 91T | 392 | AH0326v1g0057 | AH0326_v1_c1 | bla_1 | Beta-lactamase CTX-M-1 | CTX-M-15 | cephalosporin | antibiotic inactivation | blaCTX-M-15 | CTX-M beta-lactamase | AMR | BETA-LACTAM | shell | K_pneu_group_18244 |
| 91T | 392 | AH0326v1g0275 | AH0326_v1_c1 | arnC | Undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase | PmrF | peptide antibiotic | antibiotic target alteration | — | pmr phosphoethanolamine transferase | — | — | core | K_pneu_arnC |
| 91T | 392 | AH0326v1g0379 | AH0326_v1_c1 | crp | cAMP-activated global transcriptional regulator CRP | CRP | macrolide antibiotic; fluoroquinolone antibiotic; penam | antibiotic efflux | — | resistance-nodulation-cell division (RND) antibiotic efflux pump | — | — | core | K_pneu_crp |
| 91T | 392 | AH0326v1g0398 | AH0326_v1_c1 | tufA_1 | Elongation factor Tu 1 | Escherichia coli EF-Tu mutants conferring resistance to Pulvomycin | elfamycin antibiotic | antibiotic target alteration | — | elfamycin resistant EF-Tu | — | — | core | K_pneu_tufA_1 |
| 91T | 392 | AH0326v1g0712 | AH0326_v1_c1 | parC | DNA topoisomerase 4 subunit A | Escherichia coli parC conferring resistance to fluoroquinolone | fluoroquinolone antibiotic | antibiotic target alteration | — | fluoroquinolone resistant parC; fluoroquinolone self resistant parC | — | — | core | K_pneu_parC |
| 91T | 392 | AH0326v1g1113 | AH0326_v1_c1 | emrB_1 | Multidrug export protein EmrB | emrB | fluoroquinolone antibiotic | antibiotic efflux | — | major facilitator superfamily (MFS) antibiotic efflux pump | — | — | core | K_pneu_emrB_1 |
| 91T | 392 | AH0326v1g1115 | AH0326_v1_c1 | mprA | Transcriptional repressor MprA | emrR | fluoroquinolone antibiotic | antibiotic efflux | — | major facilitator superfamily (MFS) antibiotic efflux pump | — | — | core | K_pneu_mprA |
| 91T | 392 | AH0326v1g1157 | AH0326_v1_c1 | bepE_1 | Efflux pump membrane transporter BepE | oqxB | fluoroquinolone antibiotic; glycylcycline; tetracycline antibiotic; diaminopyrimidine antibiotic; nitrofuran antibiotic | antibiotic efflux | oqxB | resistance-nodulation-cell division (RND) antibiotic efflux pump | AMR | PHENICOL/QUINOLONE | shell | K_pneu_bepE |
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