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Comparative analyses of phenotypic methods and 16S rRNA, khe, rpoB genes sequencing for identification of clinical isolates of Klebsiella pneumoniae

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Abstract

The present work aimed to evaluate 16S rRNA, khe and rpoB gene sequencing for the identification of Klebsiella pneumoniae in comparison with phenotypic methods. Fifteen clinical isolates were examined, which were initially identified as K. pneumoniae subsp. pneumoniae using the automated VITEK 32 system in two hospitals in Enshi City, China. Their identity was further supported by conventional phenotypic methods on the basis of morphological and biochemical characteristics. Using Bayesian phylogenetic analyses and haplotypes network reconstruction, 13 isolates were identified as K. pneumoniae, whereas the other two isolates (K19, K24) were classified as Shigella sp. and Enterobacter sp., respectively. Of the three genes, 16S rRNA and khe gene could discriminate the clinical isolates at the genus level, whereas rpoB could discriminate Klebsiella at the species and even subspecies level. Overall, the gene tree based on rpoB is more compatible with the currently accepted classification of Klebsiella than those based on 16S rRNA and khe genes, showing that rpoB can be a powerful tool for identification of K. pneumoniae isolates. Above all, our study challenges the utility of khe as a species-specific marker for identification of K. pneumoniae.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (31572240, 81171607, and J1103604), and the fund of collaboration between Sichuan University and Luzhou City (2013CDLZ-S16). Xianguang Guo was supported by the National Natural Science Foundation of China (31272281).

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Authors and Affiliations

  1. Department of Parasitology, West China School of Preclinical and Forensic Medicine, Sichuan University, 610041, Chengdu, China

    Yanxia He, Jiao Li, Jinlei He, Dali Chen & Jianping Chen

  2. Department of Pathogen Biology and Immunology, Medical College, Hubei University for Nationalities, 445000, Enshi, China

    Yanxia He

  3. Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Sichuan University, 610041, Chengdu, China

    Jianping Chen

  4. Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China

    Xianguang Guo

  5. Affiliated Minda Hospital, Hubei University for Nationalities, 445000, Enshi, China

    Shifei Xiang & Hui Xiang

  6. Central Hospital of Enshi Autonomous Prefecture, 445000, Enshi, China

    Xiaoqin Li

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  1. Yanxia He
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Correspondence to Dali Chen or Jianping Chen.

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He, Y., Guo, X., Xiang, S. et al. Comparative analyses of phenotypic methods and 16S rRNA, khe, rpoB genes sequencing for identification of clinical isolates of Klebsiella pneumoniae . Antonie van Leeuwenhoek 109, 1029–1040 (2016). https://doi.org/10.1007/s10482-016-0702-9

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