Recognition of two genetic groups in the Klebsiella oxytoca taxon on the basis of chromosomal β-lactamase and housekeeping gene sequences as well as ERIC-1R PCR typing

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Abstract
Whilst searching for a molecular method to identify the different species of Raoultella and Klebsiella oxytoca, it was observed that the OXY-1 and OXY-2 β-lactamase-producing K. oxytoca isolates displayed two distinguishable enterobacterial repetitive intergenic consensus (ERIC)-1R profiles. It was hypothesized that the two groups of chromosomal β-lactamases might correspond to two groups of strains in the K. oxytoca taxon. To confirm this hypothesis, clinical isolates and reference strains of K. oxytoca were studied by determination of the sequence of their blaOXY genes, and of a partial fragment of their 16S rRNA (387 bp) and rpoB (512 bp) genes. The sequence data were phylogenetically analysed by using the parsimony method. Four clinical isolates possessed a blaOXY-1 gene and nine possessed a blaOXY-2 gene. The mean percentage of rpoB and 16S rRNA gene identity was >99 % within each group of strains, whereas it was 96·56±0·24 % for rpoB genes and 97·80±0·22 % for 16S rRNA genes between the group of strains harbouring the blaOXY-1 gene and the group harbouring the blaOXY-2 gene. The phylogenetic tree resulting from combined analysis of the 16S rRNA and rpoB datasets showed that the K. oxytoca isolates were monophyletic and separated into two clades; these clades included strains with either the blaOXY-1 gene or the blaOXY-2 gene. This result was supported with high bootstrap values of 97 and 99 %, respectively. Moreover, the two groups of strains displayed distinct ERIC-1R profiles, with bands characteristic of each profile. Thus, the chromosomal blaOXY gene sequence is able to delineate not only two groups of β-lactamases in K. oxytoca, but also two clades in the K. oxytoca taxon, in a manner similar to the sequence of housekeeping genes. These results suggest that K. oxytoca should be divided into two genetic groups, group OXY-1 represented by K. oxytoca strain SL781 (=CIP 104963) and group OXY-2 by K. oxytoca strain SL911 (=CIP 106098).

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