title: Yersinia spp. Identification Using Copy Diversity in the Chromosomal 16S rRNA Gene Sequence.
abstract: API 20E strip test, the standard for Enterobacteriaceae identification, is not sufficient to discriminate some Yersinia species for some unstable biochemical reactions and the same biochemical profile presented in some species, e.g. Yersinia ferderiksenii and Yersinia intermedia, which need a variety of molecular biology methods as auxiliaries for identification. The 16S rRNA gene is considered a valuable tool for assigning bacterial strains to species. However, the resolution of the 16S rRNA gene may be insufficient for discrimination because of the high similarity of sequences between some species and heterogeneity within copies at the intra-genomic level. In this study, for each strain we randomly selected five 16S rRNA gene clones from 768 Yersinia strains, and collected 3,840 sequences of the 16S rRNA gene from 10 species, which were divided into 439 patterns. The similarity among the five clones of 16S rRNA gene is over 99% for most strains. Identical sequences were found in strains of different species. A phylogenetic tree was constructed using the five 16S rRNA gene sequences for each strain where the phylogenetic classifications are consistent with biochemical tests; and species that are difficult to identify by biochemical phenotype can be differentiated. Most Yersinia strains form distinct groups within each species. However Yersinia kristensenii, a heterogeneous species, clusters with some Yersinia enterocolitica and Yersinia ferderiksenii/intermedia strains, while not affecting the overall efficiency of this species classification. In conclusion, through analysis derived from integrated information from multiple 16S rRNA gene sequences, the discrimination ability of Yersinia species is improved using our method.
authors.affiliation: National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China.
authors.forename: Huijing
authors.initials: H
authors.lastname: Hao
authors.affiliation: National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China.
authors.forename: Junrong
authors.initials: J
authors.lastname: Liang
authors.affiliation: National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China.
authors.forename: Ran
authors.initials: R
authors.lastname: Duan
authors.affiliation: National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China.
authors.forename: Yuhuang
authors.initials: Y
authors.lastname: Chen
authors.affiliation: National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China.|Department of Pathogenic Biology, School of Medical Science, Jiangsu University, Zhenjiang, Jiangsu Province, China.
authors.forename: Chang
authors.initials: C
authors.lastname: Liu
authors.affiliation: National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China.
authors.forename: Yuchun
authors.initials: Y
authors.lastname: Xiao
authors.affiliation: National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China.
authors.forename: Xu
authors.initials: X
authors.lastname: Li
authors.affiliation: Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Mingming
authors.initials: M
authors.lastname: Su
authors.affiliation: National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China.
authors.forename: Huaiqi
authors.initials: H
authors.lastname: Jing
authors.affiliation: National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Wang
mesh_terms: D002876:Chromosomes, Bacterial; D003001:Cloning, Molecular; D056915:DNA Copy Number Variations; D005798:Genes, Bacterial; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D015007:Yersinia / Q000235:genetics*
chemical_list: D012336:RNA, Ribosomal, 16S