Table 2 Antibiotic-resistant genes based on RGI analysis on CARD database
RGI Criteria | ARO Term | Detection Criteria | AMR Gene Family | Drug Class | Resistance Mechanism | % Identity of Matching Region | % Length of Reference Sequence |
|---|---|---|---|---|---|---|---|
Perfect | AcrE | protein homolog model | resistance-nodulation-cell division (RND) antibiotic efflux pump | fluoroquinolone antibiotic, cephalosporin, cephamycin, penam | antibiotic efflux | 100 | 100 |
Perfect | TolC | protein homolog model | ATP-binding cassette (ABC) antibiotic efflux pump, major facilitator superfamily (MFS) antibiotic efflux pump, resistance-nodulation-cell division (RND) antibiotic efflux pump | macrolide antibiotic, fluoroquinolone antibiotic, aminoglycoside antibiotic, carbapenem, cephalosporin, glycylcycline, cephamycin, penam, tetracycline antibiotic, peptide antibiotic, aminocoumarin antibiotic, rifamycin antibiotic, phenicol antibiotic, penem, disinfecting agents and antiseptics | antibiotic efflux | 100 | 99,6 |
Perfect | msbA | protein homolog model | ATP-binding cassette (ABC) antibiotic efflux pump | nitroimidazole antibiotic | antibiotic efflux | 100 | 100 |
Perfect | baeR | protein homolog model | resistance-nodulation-cell division (RND) antibiotic efflux pump | aminoglycoside antibiotic, aminocoumarin antibiotic | antibiotic efflux | 100 | 100 |
Perfect | baeS | protein homolog model | resistance-nodulation-cell division (RND) antibiotic efflux pump | aminoglycoside antibiotic, aminocoumarin antibiotic | antibiotic efflux | 100 | 100 |
Perfect | evgA | protein homolog model | major facilitator superfamily (MFS) antibiotic efflux pump, resistance-nodulation-cell division (RND) antibiotic efflux pump | macrolide antibiotic, fluoroquinolone antibiotic, penam, tetracycline antibiotic | antibiotic efflux | 100 | 100 |
Perfect | emrK | protein homolog model | major facilitator superfamily (MFS) antibiotic efflux pump | tetracycline antibiotic | antibiotic efflux | 100 | 110,26 |
Perfect | PmrF | protein homolog model | pmr phosphoethanolamine transferase | peptide antibiotic | antibiotic target alteration | 100 | 100 |
Perfect | H-NS | protein homolog model | major facilitator superfamily (MFS) antibiotic efflux pump, resistance-nodulation-cell division (RND) antibiotic efflux pump | macrolide antibiotic, fluoroquinolone antibiotic, cephalosporin, cephamycin, penam, tetracycline antibiotic | antibiotic efflux | 100 | 100 |
Perfect | mdtH | protein homolog model | major facilitator superfamily (MFS) antibiotic efflux pump | fluoroquinolone antibiotic | antibiotic efflux | 100 | 100 |
Perfect | mdtG | protein homolog model | major facilitator superfamily (MFS) antibiotic efflux pump | phosphonic acid antibiotic | antibiotic efflux | 100 | 100 |
Perfect | acrD | protein homolog model | resistance-nodulation-cell division (RND) antibiotic efflux pump | aminoglycoside antibiotic | antibiotic efflux | 100 | 100 |
Perfect | mdtE | protein homolog model | resistance-nodulation-cell division (RND) antibiotic efflux pump | macrolide antibiotic, fluoroquinolone antibiotic, penam | antibiotic efflux | 100 | 100 |
Perfect | mdtF | protein homolog model | resistance-nodulation-cell division (RND) antibiotic efflux pump | macrolide antibiotic, fluoroquinolone antibiotic, penam | antibiotic efflux | 100 | 100 |
Perfect | gadX | protein homolog model | resistance-nodulation-cell division (RND) antibiotic efflux pump | macrolide antibiotic, fluoroquinolone antibiotic, penam | antibiotic efflux | 100 | 100 |
Perfect | Escherichia coli acrA | protein homolog model | resistance-nodulation-cell division (RND) antibiotic efflux pump | fluoroquinolone antibiotic, cephalosporin, glycylcycline, penam, tetracycline antibiotic, rifamycin antibiotic, phenicol antibiotic, disinfecting agents and antiseptics | antibiotic efflux | 100 | 100 |
Perfect | cpxA | protein homolog model | resistance-nodulation-cell division (RND) antibiotic efflux pump | aminoglycoside antibiotic, aminocoumarin antibiotic | antibiotic efflux | 100 | 100 |
Perfect | kdpE | protein homolog model | kdpDE | aminoglycoside antibiotic | antibiotic efflux | 100 | 100 |
Perfect | emrA | protein homolog model | major facilitator superfamily (MFS) antibiotic efflux pump | fluoroquinolone antibiotic | antibiotic efflux | 100 | 100 |
Perfect | emrB | protein homolog model | major facilitator superfamily (MFS) antibiotic efflux pump | fluoroquinolone antibiotic | antibiotic efflux | 100 | 100 |
Perfect | marA | protein homolog model | resistance-nodulation-cell division (RND) antibiotic efflux pump, General Bacterial Porin with reduced permeability to beta-lactams | fluoroquinolone antibiotic, monobactam, carbapenem, cephalosporin, glycylcycline, cephamycin, penam, tetracycline antibiotic, rifamycin antibiotic, phenicol antibiotic, penem, disinfecting agents and antiseptics | antibiotic efflux, reduced permeability to antibiotic | 100 | 100 |
Strict | AcrF | protein homolog model | resistance-nodulation-cell division (RND) antibiotic efflux pump | fluoroquinolone antibiotic, cephalosporin, cephamycin, penam | antibiotic efflux | 99,71 | 100 |
Strict | AcrS | protein homolog model | resistance-nodulation-cell division (RND) antibiotic efflux pump | fluoroquinolone antibiotic, cephalosporin, glycylcycline, cephamycin, penam, tetracycline antibiotic, rifamycin antibiotic, phenicol antibiotic, disinfecting agents and antiseptics | antibiotic efflux | 99,55 | 100 |
Strict | bacA | protein homolog model | undecaprenyl pyrophosphate related proteins | peptide antibiotic | antibiotic target alteration | 99,63 | 100 |
Strict | Escherichia coli mdfA | protein homolog model | major facilitator superfamily (MFS) antibiotic efflux pump | tetracycline antibiotic, disinfecting agents and antiseptics | antibiotic efflux | 97,07 | 100 |
Strict | YojI | protein homolog model | ATP-binding cassette (ABC) antibiotic efflux pump | peptide antibiotic | antibiotic efflux | 99,63 | 100 |
Strict | mdtC | protein homolog model | resistance-nodulation-cell division (RND) antibiotic efflux pump | aminocoumarin antibiotic | antibiotic efflux | 99,51 | 201,56 |
Strict | mdtA | protein homolog model | resistance-nodulation-cell division (RND) antibiotic efflux pump | aminocoumarin antibiotic | antibiotic efflux | 99,04 | 100 |
Strict | evgS | protein homolog model | major facilitator superfamily (MFS) antibiotic efflux pump, resistance-nodulation-cell division (RND) antibiotic efflux pump | macrolide antibiotic, fluoroquinolone antibiotic, penam, tetracycline antibiotic | antibiotic efflux | 99,58 | 98,58 |
Strict | emrY | protein homolog model | major facilitator superfamily (MFS) antibiotic efflux pump | tetracycline antibiotic | antibiotic efflux | 99,41 | 100 |
Strict | mdtP | protein homolog model | major facilitator superfamily (MFS) antibiotic efflux pump | nucleoside antibiotic, disinfecting agents and antiseptics | antibiotic efflux | 97,95 | 100 |
Strict | mdtO | protein homolog model | major facilitator superfamily (MFS) antibiotic efflux pump | nucleoside antibiotic, disinfecting agents and antiseptics | antibiotic efflux | 99,41 | 100 |
Strict | mdtN | protein homolog model | major facilitator superfamily (MFS) antibiotic efflux pump | nucleoside antibiotic, disinfecting agents and antiseptics | antibiotic efflux | 99,71 | 100 |
Strict | eptA | protein homolog model | pmr phosphoethanolamine transferase | peptide antibiotic | antibiotic target alteration | 99,63 | 100 |
Strict | leuO | protein homolog model | major facilitator superfamily (MFS) antibiotic efflux pump | nucleoside antibiotic, disinfecting agents and antiseptics | antibiotic efflux | 99,04 | 100 |
Strict | EC-15 | protein homolog model | EC beta-lactamase | Cephalosporin | antibiotic inactivation | 98,41 | 100 |
Strict | Klebsiella pneumoniae KpnE | protein homolog model | small multidrug resistance (SMR) antibiotic efflux pump | macrolide antibiotic, aminoglycoside antibiotic, cephalosporin, tetracycline antibiotic, peptide antibiotic, rifamycin antibiotic, disinfecting agents and antiseptics | antibiotic efflux | 82,2 | 100,83 |
Strict | Klebsiella pneumoniae KpnF | protein homolog model | small multidrug resistance (SMR) antibiotic efflux pump | macrolide antibiotic, aminoglycoside antibiotic, cephalosporin, tetracycline antibiotic, peptide antibiotic, rifamycin antibiotic, disinfecting agents and antiseptics | antibiotic efflux | 84,4 | 100 |
Strict | acrB | protein homolog model | resistance-nodulation-cell division (RND) antibiotic efflux pump | fluoroquinolone antibiotic, cephalosporin, glycylcycline, penam, tetracycline antibiotic, rifamycin antibiotic, phenicol antibiotic, disinfecting agents and antiseptics | antibiotic efflux | 99,9 | 100 |
Strict | vanG | protein homolog model | glycopeptide resistance gene cluster, Van ligase | glycopeptide antibiotic | antibiotic target alteration | 38,23 | 104,3 |
Strict | mdtM | protein homolog model | major facilitator superfamily (MFS) antibiotic efflux pump | fluoroquinolone antibiotic, lincosamide antibiotic, nucleoside antibiotic, phenicol antibiotic, disinfecting agents and antiseptics | antibiotic efflux | 97,8 | 100 |
Strict | rsmA | protein homolog model | resistance-nodulation-cell division (RND) antibiotic efflux pump | fluoroquinolone antibiotic, diaminopyrimidine antibiotic, phenicol antibiotic | antibiotic efflux | 85,25 | 100 |
Strict | CRP | protein homolog model | resistance-nodulation-cell division (RND) antibiotic efflux pump | macrolide antibiotic, fluoroquinolone antibiotic, penam | antibiotic efflux | 99,52 | 100 |
Strict | Escherichia coli gyrA conferring resistance to fluoroquinolones | protein variant model | fluoroquinolone resistant gyrA | fluoroquinolone antibiotic | antibiotic target alteration | 99,77 | 100 |
Strict | Haemophilus influenzae PBP3 conferring resistance to beta-lactam antibiotics | protein variant model | Penicillin-binding protein mutations conferring resistance to beta-lactam antibiotics | cephalosporin, cephamycin, penam | antibiotic target alteration | 53,11 | 96,39 |
Strict | Escherichia coli soxS with mutation conferring antibiotic resistance | protein overexpression model | ATP-binding cassette (ABC) antibiotic efflux pump, major facilitator superfamily (MFS) antibiotic efflux pump, resistance-nodulation-cell division (RND) antibiotic efflux pump, General Bacterial Porin with reduced permeability to beta-lactams | fluoroquinolone antibiotic, monobactam, carbapenem, cephalosporin, glycylcycline, cephamycin, penam, tetracycline antibiotic, rifamycin antibiotic, phenicol antibiotic, penem, disinfecting agents and antiseptics | antibiotic target alteration, antibiotic efflux, reduced permeability to antibiotic | 100 | 100 |
Strict | Escherichia coli soxR with mutation conferring antibiotic resistance | protein overexpression model | ATP-binding cassette (ABC) antibiotic efflux pump, major facilitator superfamily (MFS) antibiotic efflux pump, resistance-nodulation-cell division (RND) antibiotic efflux pump | fluoroquinolone antibiotic, cephalosporin, glycylcycline, penam, tetracycline antibiotic, rifamycin antibiotic, phenicol antibiotic, disinfecting agents and antiseptics | antibiotic target alteration, antibiotic efflux | 100 | 100 |
Strict | Escherichia coli AcrAB-TolC with AcrR mutation conferring resistance to ciprofloxacin, tetracycline, and ceftazidime | protein overexpression model | resistance-nodulation-cell division (RND) antibiotic efflux pump | fluoroquinolone antibiotic, cephalosporin, glycylcycline, penam, tetracycline antibiotic, rifamycin antibiotic, phenicol antibiotic, disinfecting agents and antiseptics | antibiotic target alteration, antibiotic efflux | 100 | 100 |
Strict | Escherichia coli AcrAB-TolC with MarR mutations conferring resistance to ciprofloxacin and tetracycline | protein overexpression model | resistance-nodulation-cell division (RND) antibiotic efflux pump | fluoroquinolone antibiotic, cephalosporin, glycylcycline, penam, tetracycline antibiotic, rifamycin antibiotic, phenicol antibiotic, disinfecting agents and antiseptics | antibiotic target alteration, antibiotic efflux | 100 | 100 |