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.

Highlights

  • The genus Yersinia is widely distributed in nature and currently has 17 species [1,2,3], three of which are pathogenic (Y. enterocolitica, Y. pestis, and Y. pseudotuberculosis) and have been exhaustively researched

  • Speaking, for Yersinia, the limitation of commercial tests for identification systems such as API 20E strip test has shown a deficiency in distinguishing some species[18, 19], which can be made up through the method based on 16S rRNA gene

  • The similarity of 16S rRNA gene sequence between species is as high as 96.9%-99.8%; it is easy to misclassify species of high homology[20]

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Summary

Introduction

The genus Yersinia is widely distributed in nature and currently has 17 species [1,2,3], three of which are pathogenic (Y. enterocolitica, Y. pestis, and Y. pseudotuberculosis) and have been exhaustively researched. The remaining species are referred to as Y. enterocolitica-like bacteria where their etiology in disease is not understood [4, 5]. Bacteria were classified according to similarities and differences in phenotypes, such as morphology and biochemical reactions. The API 20E strip test is the standard for identifying Enterobacteriaceae; this test has limitations in identifying Yersinia species. Several Yersinia species can be identified using API 20E strip test where the accuracy is influenced by passage number, culture conditions, and instability of some biochemical reactions [6]. Sensitive molecular biology methods are needed to assist the traditional approach to identify the Yersinia

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