Table 3 Putative antibiotic resistance-associated factors (ARF) encoded by the P. vermicola DSM_17385 genome
ARF Acronym | ARF Familya | Best hitb CARD | Best hitb Genbank | Antibiotic class |
|---|---|---|---|---|
Antibiotic uptake reduction | ||||
OmpK37 | porin | 56% (98%) | 91% (100%) | cephamycin, penem, monobactam, penam, cephalosporin, carbapenem |
Antibiotic efflux | ||||
AbeS | SMR | 48% (100%) | 89% (100%) | macrolides, aminocoumarin |
CRP | transcriptional regulator | 98% (78%) | 100% (100%) | penam, macrolide, fluoroquinolone |
CsrA (RsmA) | RND | 88% (100%) | 100% (100%) | phenicol, diaminopyrimidine, fluoroquinolone |
Bcr1 (Bcr1) | MFS | 44% (100%) | 93% (100%) | bicyclomycinsulfonamid |
Bcr1 (Bcr2/3) | MFS | 34% (98%) | 98% (100%) | bicyclomycin |
EmrE2 | SMR | 54% (100%) | 90% (100%) | macrolides, small polyaromatic cations, potentially ethidium bromide, erythromycinE. coli, tetraphenylphosphonium, methyl viologen, gentamicin, kanamycin, neomycin |
MdtG (YceE) | MFS | 70% (100%) | 99% (98%) | phosphomycin, deoxycholate |
MdtH | MFS | 75% (100%) | 98% (100%) | fluoroquinolone |
Tet(59) | MFS | 81% (100%) | 79% (97%) | tetracycline |
TolC | outer membrane efflux protein | 65% (97%) | 95% (99%) | macrolide, fluoroquinolone, aminoglycosides, carbapenem, cephalosporin, glycylcycline, cephamycin, penam, tetracycline, peptide antibiotics, aminocoumarin, rifamycin, phenicol, triclosan, penem |
AcrA | RND | 67% (98%) | 95% (95%) | fluoroquinolone, cephalosporin, glycylcycline, penam, tetracycline, rifamycin, phenicols, triclosan |
AcrB | RND | 75% (98%) | 98% (100%) | fluoroquinolone, cephalosporin, glycylcycline, penam, tetracycline, rifamycin, phenicols, triclosan |
AcrR | transcriptional regulator | 52% (100%) | 94% (99%) | fluoroquinolone, cephalosporin, glycylcycline, penam, tetracycline, rifamycin, phenicols, triclosan |
EmrA | MFS | 56% (100%) | 94% (100%) | fluoroquinolone, nalidixic acid, thiolactomycin |
EmrB | MFS | 66% (99%) | 99% (99%) | fluoroquinolone, nalidixic acid, thiolactomycin |
MacA (PvdR) | ABC | 37% (94%) | 90% (97%) | macrolideserythromycin |
MacB (PvdT) | ABC | 51% (100%) | 89% (100%) | macrolideserythromycin |
MdtA (YegM) | RND | 57% (100%) | 91% (100%) | aminocoumarin, novobiocin |
MdtB (YegN) | RND | 77% (99%) | 94% (100%) | aminocoumarin, novobiocin |
MdtC (YegO) | RND | 73% (100%) | 95% (100%) | aminocoumarin, novobiocin |
MexG | RND | 63% (96%) | 92% (100%) | fluoroquinolone, tetracycline, acridine, vanadium, norfloxacin, acriflavin |
MexH | RND | 58% (96%) | 93% (100%) | fluoroquinolone, tetracycline, acridine, vanadium, norfloxacin, acriflavin |
MexI | RND | 78% (100%) | 96% (100%) | fluoroquinolone, tetracycline, acridine, vanadium, norfloxacin, acriflavin |
KpnE (MdtJ) | SMR | 64% (100%) | 95% (100%) | macrolides, aminoglycosides, cephalosporin, tetracycline, peptide antibiotics, rifamycin |
KpnF (MdtI) | SMR | 71% (100%) | 99% (82%) | macrolides, aminoglycosides, cephalosporin, tetracycline, peptide antibiotics, rifamycin |
KpnG (EmrA) | MFS | 65% (100%) | 92% (100%) | peptide antibiotics, carbapenem, macrolides, cephalosporin, aminoglycosides, penam, fluoroquinolones, penem, nalidixic acid, thiolactomycin |
KpnH (EmrB) | MFS | 78% (99%) | 98% (99%) | peptide antibiotics, carbapenem, macrolides, cephalosporin, aminoglycosides, penam, fluoroquinolones, penem, nalidixic acid, thiolactomycin |
RosA | MFS | 75% (99%) | 96% (100%) | peptide antibioticspolymyxin B, fosmidomycin |
RosB | MFS | 69% (100%) | 99% (100%) | peptide antibioticspolymyxin B, fosmidomycin |
Antibiotic inactivation | ||||
AAC(2′)-Ia | aminoglycoside acetyltransferase | 70% (87%) | 72% (100%) | aminoglycosides |
CatIII | chloramphenicol acetyltransferase | 56% (100%) | 71% (100%) | phenicols |
FosA7.5 | phosphomycin thiol transferase | 62% (98%) | 74% (100%) | phosphomycin |
NmcR | transcriptional regulator | 56% (99%) | 89% (100%) | penam, cephalosporin, cephamycin, carbapenem |
SRT-2 | beta-lactamase | 56% (100%) | 86% (99%) | cephalosporins |
Antibiotic target alteration | ||||
EF-Tuc | translation elongation factor Tu | 95% (74%) | 99% (100%) | pulvomycin-class of elfamycins |
ErmX, (Erm34) | RNA methyltransferase | 29% (95%) | 98% (100%) | aminoglycosides |
GyrAc | DNA gyrase subunit alpha | 51% (100%) | 97% (100%) | fluoroquinolone |
GyrBc | DNA gyrase subunit beta | 55% (96%) | 99% (100%) | fluoroquinolone, aminocoumarin |
MurAc | UDP-N-acetylglucosamine enolpyruvyl transferase | 50% (99%) | 97% (100%) | phosphomycin |
RpoBc | RNA polymerase subunit beta | 55% (100%) | 99% (100%) | rifamycinrifampicin |
Ugd (PmrE) | UDP-glucose 6-dehydrogenase, phosphorethanolamine transferase | 73% (96%) | 98% (100%) | peptide antibiotics, polymyxin |
VanW | glycopeptide resistance protein | 29% (97%) | 92% (99%) | glycopeptidesvancomycin |