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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]