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Table 4 Characterization of RRF drug resistance candidates in the pseudomonas data from the literature

From: Identifying genetic determinants of complex phenotypes from whole genome sequence data

Drug Gene Evidence References
Ciprofloxacin pchE Siderophore family, extracellular iron-acquisition system, upregulation associated with exposure to natural quinolones [58]
   Iron is required for virulence and is deficient in the human lung environment of these clinical strains [59]
  cupB3 Part of an outer membrane porin family, mutation that reduce membrane permeability are linked to Gram-negative bacterial mechanisms for antibiotic resistance [60]
  permease Reduces accumulation of drug inside cell by decreased cell wall permeability or by pumping drug out [61]
  ABC transporter See permease [61]
  SH3 Controls numerous protein-protein interactions, some implicated in virulence of pathogenic bacteria [62]
  alkB DNA repair system (fluoroquinolones prevent proper winding and unwinding of DNA during replication), also affects outer membrane lipids - and thus permeability - it may affect antibiotic resistance [60]
  sbrR Anti-sigma factor, identified as necessary during the chronic infection of respiratory tracts [53]
  mnmC Part of tRNA modification, and thus protein synthesis, no obvious antibiotic or lung environment connection  
Ceftazidime MFS Membrane translocases, include many multidrug resistant proteins of Gram-positive bacteria [63]
  pscC Type III secretion outer membrane protein, probable general resistance candidate [60, 64]
  algW Mutations are known to confer susceptibility to the beta-lactam family of antibiotics [65]
  glyA2 Produces anti-oxidant coenzymes, involved in cell response to TiO2-based nanocomposite antimicrobials [66]
  lysR Associated with minimum inhibitory concentration of antibiotics and oxidative stress chemicals [67, 68]
Gentamicin rnt This ribonuclease would have a logical role in degrading 30S bound by the antibiotic  
  algW Correlated to Ceftazidime resistance?  
  quinone OR Antibiotic resistance in response to antibiotics that inhibit protein synthesis - including binding of the 50S ribosomal subunit [69]