Table 1 DNA sequence variation among the top 18 mutants
StrainFitness rank in LBgyrAa,bSecond-site mutationscFold increase in minimum inhibitory concentration (MIC) to nalidixic acidDifference in log(MIC) following addition of efflux inhibitor d,eMinimum number of mutationsGenotype classf
SBW251910.798 ± 0.1770Wild type
3-1-B14NANANA1A
1-5-D87mexCD regulator:  Leu134Phe  (C514G)47.41.457 ± 0.129**1B
2-10-G1015NANANA1A
1-7-F52Asp87Ala (GAC260GCC)NA47.41.545 ± 0.116**1C
1-4-B91Asp87Gly (GAC260GGC)mexAB regulator:  GC ins stop codon  at AA 4447.40.088 ± 0.173**2D
1-8-G411Asp87Gly (GAC260GGC)NA25.21.007 ± 0.1281E
1-6-F812Asp87Gly (GAC260GGC)NA25.20.968 ± 0.1731E
2-9-H43Asp87Tyr (GAC259TAC)25.20.304 ± 0.128*1F
1-1-H106Asp87Tyr (GAC259TAC)mexEF regulator:  Ser88Asn (G863A)101.00.389 ± 0.112*2G
2-4-A128Asp87Tyr (GAC259TAC)101.00 ± 0**2H
2-8-F710Asp87Tyr (GAC259TAC)NA21.00.576 ± 0.1281I
1-10-H1013Asp87Tyr (GAC259TAC)NA101.00 ± 0**2H
1-1-G117Asp87Tyr (GAC259TAC)NA25.20.176 ± 0.245*1J
2-8-F85Gly81Cys (GGC241TGC)56.81.537 ± 0.208*1K
3-1-A69Thr83Ile (ACT248ATT)NA31.60 ± 0.164**1L
1-6-A914Thr83Ile (ACT248ATT)NA19.90.401 ± 0.208*1M
1-8-A116Thr83Ile (ACT248ATT)NA101.00.908 ± 0.2101N
2-7-C318Thr83Ile (ACT248ATT)mexAB regulator:  Arg90His (G269A)56.80 ± 0**2O
  • a —, identical to wild type (SBW25).

  • b NA, not sequenced or data not available.

  • c Sequences assayed were the QRDR of gyrB, parC, and parE, as well as the DNA-binding sites of the putative efflux pump regulators mexAB, mexCD, mexEF, and a generic mex-family regulator; see Materials and Methods for details.

  • d Values shown are mean difference in log(MIC) without and with the efflux inhibitor, PAbN ± 95% confidence intervals; see Materials and Methods for details.

  • e Significant from SBW25 at *P < 0.05. Significant from SBW25 following Bonferroni correction for 16 tests such that **P < 0.003.

  • f Genotypes sharing the same letter are putatively identical on the basis of direct sequencing and the efflux inhibitor assay. Wild type is the genome of the ancestral, nalidixic acid-sensitive SBW25 strain from which all strains are derived.