Genetic Classification and Distinguishing of Staphylococcus Species Based on Different Partial gap, 16S rRNA, hsp60, rpoB, sodA, and tuf Gene Sequences

Otto-von-Guericke University, Clinical Microbiology, Leipziger Str. 44, Magdeburg, Germany.
Journal of clinical microbiology (Impact Factor: 3.99). 04/2008; 46(3):1019-25. DOI: 10.1128/JCM.02058-07
Source: PubMed


The analysis of 16S rRNA gene sequences has been the technique generally used to study the evolution and taxonomy of staphylococci.
However, the results of this method do not correspond to the results of polyphasic taxonomy, and the related species cannot
always be distinguished from each other. Thus, new phylogenetic markers for Staphylococcus spp. are needed. We partially sequenced the gap gene (∼931 bp), which encodes the glyceraldehyde-3-phosphate dehydrogenase, for 27 Staphylococcus species. The partial sequences had 24.3 to 96% interspecies homology and were useful in the identification of staphylococcal
species (F. Layer, B. Ghebremedhin, W. König, and B. König, J. Microbiol. Methods 70:542-549, 2007). The DNA sequence similarities
of the partial staphylococcal gap sequences were found to be lower than those of 16S rRNA (∼97%), rpoB (∼86%), hsp60 (∼82%), and sodA (∼78%). Phylogenetically derived trees revealed four statistically supported groups: S. hyicus/S. intermedius, S. sciuri, S. haemolyticus/S. simulans, and S. aureus/epidermidis. The branching of S. auricularis, S. cohnii subsp. cohnii, and the heterogeneous S. saprophyticus group, comprising S. saprophyticus subsp. saprophyticus and S. equorum subsp. equorum, was not reliable. Thus, the phylogenetic analysis based on the gap gene sequences revealed similarities between the dendrograms based on other gene sequences (e.g., the S. hyicus/S. intermedius and S. sciuri groups) as well as differences, e.g., the grouping of S. arlettae and S. kloosii in the gap-based tree. From our results, we propose the partial sequencing of the gap gene as an alternative molecular tool for the taxonomical analysis of Staphylococcus species and for decreasing the possibility of misidentification.

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    • "The study of genes other than 16S rRNA, has been considered for species discrimination. Thus, the 23S rRNA, the DNA gyrase b subunit (gyrB) (Chen and Tsen, 2002; La Duc et al., 2004), the RNA polymerase b subunit (rpoB) (Drancourt and Raoult, 2002; Qi et al., 2001) and the TU elongation factor (tuf) (Ghebremedhin et al., 2008) genes have been considered for the identification of certain bacterial taxons. Such genes may provide well conserved regions with potential usefulness for the design of primers and molecular probes for identification purposes in Bacillus spp. "
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    • "However, in three cases, S. capitis 35661, S. warneri 49454 and S. xylosus 29971 T , the fragment sequenced showed 99% or 100% similarity with the sequences of other species. Ghebremedhin et al. (2008) reported that some Staphylococcus taxa have the same 16S rRNA gene sequences in variable regions, including S. capitis subsp. urealyticus and S. caprae. "
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