Table 3.

Mutations that occurred in 34 genes during airway infections in 29 CF patients

Gene name Gene annotation no.Gene functionNo. of nonsynonymous mutations (nonsense)No. of synonymous mutationsNo. of insertions/deletions (frameshifts and transposon insertions)No. of intergenic mutationsTotal no. of independent mutations No. of patients with at least one mutated isolate
mexZ PA2020Transcriptional regulator of multidrug efflux13 (5)011 (9)02418
lasR PA1430Transcriptional regulator of quorum sensing18 (3)04 (4)02218
PA0313Probable permease of ABC transporter4 (1)010 (2)11513
mexA PA0425RND multidrug efflux membrane fusion protein MexA precursor13 (4)01 (1)01411
accC PA4848Biotin carboxylase603 (2)099
*vfr PA0652Transcriptional regulator403 (2)187
mexS PA2491Probable oxidoreductase701086
exsA PA1713Transcriptional regulator of type III secretion602 (1)086
PA0506Probable acyl-CoA dehydrogenase501 (1)177
*wspF PA3703Probable methylesterase involved in chemosensory signal transduction4 (2)02 (1)066
*rpoN PA4462RNA polymerase σ-54 factor2 (1)03 (2)055
*fleQ PA1097Transcriptional regulator of flagella synthesis5 (1)00055
mexT PA2492Transcriptional regulator of multidrug efflux400155
*nalD PA3574Probable transcriptional regulator111 (1)144
*ampD PA4522β-Lactamase expression regulator301044
PA0366Probable aldehyde dehydrogenase102 (2)144
*cyaB PA3217Adenylate cyclase210033
P1-001In 45-kb genomic island § Hypothetical protein102 (2)032
PA3817Probable methyltransferase210033
pilB PA4526 Type 4 fimbrial biogenesis protein110022
PA1333Hypothetical protein000111
PA3565Probable transcriptional regulator100011
PA2312Probable transcriptional regulator010011
*anr PA1544Transcriptional regulator of anaerobic metabolism000111
*rhlR PA3477Transcriptional regulator of quorum sensing000111
*phoP PA1179Two-component response regulator000000
rhlI PA3476Autoinducer synthesis protein000000
PA4796Hypothetical protein000000
pqsB PA0997Homologous to β-keto-acyl-acyl-carrier protein synthase000000
toxR PA0707Transcriptional regulator000000
PA2435Probable cation-transporting P-type ATPase000000
PA4420Hypothetical protein000000
None § Hypothetical protein ORF C/SG114000000
PA2121Hypothetical protein000000
Total103 (17)547 (30)9164143
  • The 10 gene names that are preceded by an asterisk were candidate genes based on other studies. The remaining 24 genes were mutated in the 96-month isolate of patient 1.

  • Each gene was amplified with PCR and completely sequenced in 91 isolates. Most patients had three representative isolates that had been collected longitudinally. A mutation was defined as any difference in sequence between clonally related isolates from the same patient. When the same mutation was present in multiple isolates from the same patient, we assumed that the mutation occurred once during the infection and was then propagated clonally. Some patients had two isolates with different mutations in the same gene; we considered these as two independent mutations.

  • §Two genes are not present in all strains: the gene P1-001 is present in isolates from five patients, and gene C/SG114 is present in isolates from 21 patients. pilA and pilB were only partially sequenced because the locus exhibits high strain-to-strain divergence.