TABLE 2.
Nucleotide polymorphisms among K. oxytoca isolates and MLST target and PCR primer information
| Gene | Putative gene function | Oligonucleotide | Oligonucleotide sequence (5′ to 3′)a | Size of analyzed fragment (bp) | No. of allelesb | No. of polymorphic sitesb | Mean % G+C content | Variation indicesb |
|
|---|---|---|---|---|---|---|---|---|---|
| πc | dN/dSd | ||||||||
| gapA | Glyceraldehyde-3-phosphate dehydrogenase | gapA_fwd | GTTTTCCCAGTCACGACGTTGTATGAAGTATGACTCCACTCACGG | 450 | 8 (9) | 15 (16) | 53.7 | 0.01340 (0.01335) | 0.000 (0.000) |
| gapA_rev | TTGTGAGCGGATAACAATTTCAACGCCTTTCATTGCGCCTTCGGAA | ||||||||
| infB | Translation initiation factor 2 | infB_fwd | GTTTTCCCAGTCACGACGTTGTACTCTCTGCTGGACTACATTCG | 318 | 15 (17) | 48 (50) | 59.2 | 0.05615 (0.05625) | 0.139 (0.137) |
| infB_rev | TTGTGAGCGGATAACAATTTCCGCTTTCAGCTCCAGAACTTC | ||||||||
| mdh | Malate dehydrogenase | mdh_fwd | GTTTTCCCAGTCACGACGTTGTACCCAACTGCCTTCAGGTTCAG | 477 | 25 (25) | 86 (86) | 52.1 | 0.05222 (0.05233) | 0.032 (0.031) |
| mdh_rev | TTGTGAGCGGATAACAATTTCCCTTCCACGTAGGCGCATTCC | ||||||||
| pgi | Phosphoglucose isomerase | pgi_fwd | GTTTTCCCAGTCACGACGTTGTAGAGAAAAACCTGCCGGTGCTGCTG | 432 | 27 (29) | 45 (45) | 56.2 | 0.03008 (0.03023) | 0.008(0.008) |
| pgi_rev | TTGTGAGCGGATAACAATTTCCGGTTAATCAGGCCGTTAGTGGAGC | ||||||||
| phoE | Phosphoporine E | phoE_fwd | GTTTTCCCAGTCACGACGTTGTAACCTGGCGCAACACCGATTTCTTC | 420 | 26 (28) | 52 (54) | 53.7 | 0.03315 (0.03337) | 0.020 (0.019) |
| phoE_rev | TTGTGAGCGGATAACAATTTCTTCAGCTGGTTGATTTTGTAATCCAC | ||||||||
| rpoB | RNA polymerase subunit β | rpoB_fwd | GTTTTCCCAGTCACGACGTTGTAGGCGAAATGGCGGAAAACCA | 501 | 19 (21) | 40 (42) | 54.3 | 0.01777 (0.01812) | 0.001 (0.001) |
| rpoB_rev | TTGTGAGCGGATAACAATTTCGAGTCTTCGAAGTTGTAACC | ||||||||
| tonB | Periplasmic energy transducer | tonB_fwd | GTTTTCCCAGTCACGACGTTGTACTCTATACTTCGGTACATCAGGTT | 405 | 25 (27) | 78 (79) | 61.9 | 0.05920 (0.06001) | 0.092 (0.095) |
| tonB_rev | TTGTGAGCGGATAACAATTTCCCTGTTTGGCGGCCAGCACCTGGT | ||||||||
| Concatenated sequence | 3,003 | 55.6 | 0.03607 (0.03631) | ||||||
a
Specific oligonucleotides: bold-type sequence binds target gene, underlined sequence (overhang) serves as annealing site for sequencing primer (phoE was sequenced with distinct nested primers).
b
Publicly available K. oxytoca NCBI sequence data were combined with the Sanger sequences from clinical isolates to generate a separate alignment which yielded the values given in brackets.
c
Diversity index (π) is equal to the average number of nucleotide differences per site.
d
dN/dS, ratio of nonsynonymous to synonymous substitutions.