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 | |
 | 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 | |
Gentamicin | rnt | This ribonuclease would have a logical role in degrading 30S bound by the antibiotic | Â |
 | 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] |