title: Comparative analyses of phenotypic methods and 16S rRNA, khe, rpoB genes sequencing for identification of clinical isolates of Klebsiella pneumoniae.
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.
authors.affiliation: Department of Parasitology, West China School of Preclinical and Forensic Medicine, Sichuan University, 610041, Chengdu, China.|Department of Pathogen Biology and Immunology, Medical College, Hubei University for Nationalities, 445000, Enshi, China.
authors.forename: Yanxia
authors.initials: Y
authors.lastname: He
authors.affiliation: Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China.
authors.forename: Xianguang
authors.initials: X
authors.lastname: Guo
authors.affiliation: Affiliated Minda Hospital, Hubei University for Nationalities, 445000, Enshi, China.
authors.forename: Shifei
authors.initials: S
authors.lastname: Xiang
authors.affiliation: Department of Parasitology, West China School of Preclinical and Forensic Medicine, Sichuan University, 610041, Chengdu, China.
authors.forename: Jiao
authors.initials: J
authors.lastname: Li
authors.affiliation: Central Hospital of Enshi Autonomous Prefecture, 445000, Enshi, China.
authors.forename: Xiaoqin
authors.initials: X
authors.lastname: Li
authors.affiliation: Affiliated Minda Hospital, Hubei University for Nationalities, 445000, Enshi, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Xiang
authors.affiliation: Department of Parasitology, West China School of Preclinical and Forensic Medicine, Sichuan University, 610041, Chengdu, China.
authors.forename: Jinlei
authors.initials: J
authors.lastname: He
authors.affiliation: Department of Parasitology, West China School of Preclinical and Forensic Medicine, Sichuan University, 610041, Chengdu, China. cdl1978119@sina.com.
authors.forename: Dali
authors.initials: D
authors.lastname: Chen
authors.affiliation: Department of Parasitology, West China School of Preclinical and Forensic Medicine, Sichuan University, 610041, Chengdu, China. jpchen007@163.com.|Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Sichuan University, 610041, Chengdu, China. jpchen007@163.com.
authors.forename: Jianping
authors.initials: J
authors.lastname: Chen
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000235:genetics*; D005798:Genes, Bacterial; D006239:Haplotypes; D006801:Humans; D007710:Klebsiella Infections / Q000382:microbiology*; D007711:Klebsiella pneumoniae / Q000235:genetics* / Q000302:isolation & purification*; D010641:Phenotype; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012321:DNA-Directed RNA Polymerases
keywords: 16S rRNA; Bayesian phylogenetic analysis; Klebsiella pneumoniae; Species identification; khe; rpoB