TABLE 1.
Gene loci included in the Klebsiella pneumoniae MLST scheme, PCR and sequencing primers, and variation indices for 67 strainsa
| Locus | Putative function of gene | Primer sequenceb,c | Size (bp) | Locationd | Temp (°C) | No. of alleles | Nucleotide diversity | Polymorphic sites (nonsynonymous substitutions) |
|---|---|---|---|---|---|---|---|---|
| rpoB | Beta-subunit of RNA polymerase B | VIC3: GGC GAA ATG GCW GAG AAC CA | 501 | 4,771,502-4,772,002 | 50 | 8 | 0.00166 | 7 (1) |
| VIC2: GAG TCT TCG AAG TTG TAA CC | ||||||||
| gapA | Glyceraldehyde 3-phosphate dehydrogenase | gapA173: TGA AAT ATG ACT CCA CTC ACG G | 450 | 1,347,540-1,347,091 | 60 | 6 | 0.00136 | 5 (0) |
| gapA181: CTT CAG AAG CGG CTT TGA TGG CTT | ||||||||
| mdh | Malate dehydrogenase | mdh130: CCC AAC TCG CTT CAG GTT CAG | 477 | 4,004,045-4,003,569 | 50 | 10 | 0.00161 | 10 (3) |
| mdh867: CCG TTT TTC CCC AGC AGC AG | ||||||||
| pgi | Phosphoglucose isomerase | pgi1F: GAG AAA AAC CTG CCT GTA CTG CTG GC | 432 | 4,831,091-4,831,522 | 50 | 6 | 0.00092 | 5 (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 | ||||||||
| phoE | Phosphoporine E | phoE604.1: ACC TAC CGC AAC ACC GAC TTC TTC GG | 420 | 320,309-320,728 | 50 | 14 | 0.00727 | 18 (2) |
| phoE604.2: TGA TCA GAA CTG GTA GGT GAT | ||||||||
| infB | Translation initiation factor 2 | infB1F: CTC GCT GCT GGA CTA TAT TCG | 318 | 3,937,568-3,937,885 | 50 | 10 | 0.0038 | 11 (0) |
| infB1R: CGC TTT CAG CTC AAG AAC TTC | ||||||||
| infB2F(seq): ACT AAG GTT GCC TCC GGC GAA GC | ||||||||
| tonB | Periplasmic energy transducer | tonB1F: CTT TAT ACC TCG GTA CAT CAG GTT | 414 | 2,394,251-2,394,664 | 45 | 21 | 0.01019 | 14 (5) |
| tonB2R: ATT CGC CGG CTG RGC RGA GAG |
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.
Sequencing primers were the same as the PCR primers, except when indicated.
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25; for phoE, reference 9; for pgi1F and pgi1R, reference 29; gapA173, reference 8; for rpoB, E. Ageron and P. Grimont, unpublished.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.
Based on the complete sequence of strain MGH78578 available at http://genome.wustl.edu/projects/bacterial/kpneumoniae/.