Phylogenetic and characteristic analysis of 16S rDNA and rpoB gene sequence of Klebsiella / 中华微生物学和免疫学杂志

ABSTRACT

Objective To compare and analyze the phylogenetic tree and sequence variant characteristics of Klebsiella species between 16S rDNA and rpoB. Methods Eighteen isolates identified as genus Klebsiella (with 15 of K. Pneumoniae and 3 of K. Oxytoca) by automated biochemical tests were selected. DNA were extracted, 16S rDNA and rpoB genes were amplified and sequenced with Klebsiella 16S rDNA and rpoB primers. Together with already published 8 species of Klebsiella and 9 species of Enterobacteriaceae 16S rDNA and rpoB sequences from GenBank, totally 35 sequences of 16S rDNA and rpoB respectively, phylogenetic trees were constructed with MEGA 4.0 to the analysis of groups. DNAStar/MegAlign was used for comparison of variable regions of 16S rDNA and rpoB, with analysis of degree of divergent at the same time. Results As for all 35 sequences, both 16S rDNA and rpoB phylogenetic trees divided Klebsiella species into three groups, 15 of K. Pneumoniae in this study and 6 of K. Pneumoniae from GenBank (except for K. Oxytoca and K. Mobilis) cluster to group Ⅰ, K. Oxytoca and K. Mobilis were cluster to group Ⅱ and Ⅲ, respectively. In rpoB phylogenetic tree, no matter group Ⅰ and group Ⅱ, or subgroup within group Ⅰ, the bootstrap values in each node of rpoB phylogenetic tree is obviously higher than that of 16S rDNA. Moreover, as for cluster to K. Oxytoca, rpoB is better than 16S rDNA. Analysis nucleic acid sequences of Klebsiella species, with 41 variable regions and 4 most significant regions were found within the Klebsiella 16S rDNA, while rpoB with 63 variable regions, and 1 most significant region. The similarity of 16S rDNA and rpoB within Klebsiella were 95.9%-100% and 90.2%-100% respectively. Further analysis divergent degree of 16S rDNA and rpoB within Klebsiella, the divergent value of rpoB (0-10.6) is higher than that of the 16S rDNA(0-4.0). Conclusion As for molecular classification and identification within KlebsieUa species, rpoB has more advantages than 16S rDNA.