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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.

Yersinia spp. Identification Using Copy Diversity in the Chromosomal 16S rRNA Gene Sequence