TABLE 1.

Gene loci included in the Klebsiella pneumoniae MLST scheme, PCR and sequencing primers, and variation indices for 67 strainsa

LocusPutative function of genePrimer sequenceb,cSize (bp)LocationdTemp (°C)No. of allelesNucleotide diversityPolymorphic sites (nonsynonymous substitutions)
rpoBBeta-subunit of RNA polymerase BVIC3: GGC GAA ATG GCW GAG AAC CA5014,771,502-4,772,0025080.001667 (1)
VIC2: GAG TCT TCG AAG TTG TAA CC
gapAGlyceraldehyde 3-phosphate dehydrogenasegapA173: TGA AAT ATG ACT CCA CTC ACG G4501,347,540-1,347,0916060.001365 (0)
gapA181: CTT CAG AAG CGG CTT TGA TGG CTT
mdhMalate dehydrogenasemdh130: CCC AAC TCG CTT CAG GTT CAG4774,004,045-4,003,56950100.0016110 (3)
mdh867: CCG TTT TTC CCC AGC AGC AG
pgiPhosphoglucose isomerasepgi1F: GAG AAA AAC CTG CCT GTA CTG CTG GC4324,831,091-4,831,5225060.000925 (0)
pgi1R: CGC GCC ACG CTT TAT AGC GGT TAA T
pgi2F(seq): CTG CTG GCG CTG ATC GGC AT
pgi2R(seq): TTA TAG CGG TTA ATC AGG CCG T
phoEPhosphoporine EphoE604.1: ACC TAC CGC AAC ACC GAC TTC TTC GG420320,309-320,72850140.0072718 (2)
phoE604.2: TGA TCA GAA CTG GTA GGT GAT
infBTranslation initiation factor 2infB1F: CTC GCT GCT GGA CTA TAT TCG3183,937,568-3,937,88550100.003811 (0)
infB1R: CGC TTT CAG CTC AAG AAC TTC
infB2F(seq): ACT AAG GTT GCC TCC GGC GAA GC
tonBPeriplasmic energy transducertonB1F: CTT TAT ACC TCG GTA CAT CAG GTT4142,394,251-2,394,66445210.0101914 (5)
tonB2R: ATT CGC CGG CTG RGC RGA GAG
  • a Genes aroA, tyrB, and ureD were also amplified and sequenced successfully but were not included due to lower sequence quality in general. Genes gyrA and parC used previously (7) were excluded as amino acid changes may be selected by the clinical use of quinolones.

  • b Sequencing primers were the same as the PCR primers, except when indicated.

  • c Primer sources were as follows: for mdh, reference 25; for phoE, reference 9; for pgi1F and pgi1R, reference 29; gapA173, reference 8; for rpoB, E. Ageron and P. Grimont, unpublished. All other primers were designed in this study.

  • d Based on the complete sequence of strain MGH78578 available at http://genome.wustl.edu/projects/bacterial/kpneumoniae/.