Summary auto-generated
This study developed a dnaJ gene sequence-based assay for identifying and classifying Staphylococcus species. Researchers analyzed approximately 883 base pairs of the dnaJ gene from 45 staphylococcal type strains and compared it with 16S rRNA and other conserved genes (hsp60, sodA, rpoB). The dnaJ gene proved significantly more discriminatory between species, showing 77.6% mean sequence similarity compared to 97.4% for 16S rRNA, allowing better differentiation of closely related species. Analysis of 20 clinical isolates of S. aureus and S. epidermidis showed minimal intraspecies variation (0.7% and 0.4% divergence, respectively). Phylogenetic analysis identified eight distinct Staphylococcus species groups with high bootstrap support values, with results generally concordant with 16S rRNA gene and DNA-DNA reassociation studies. The dnaJ sequence could discriminate most species and some subspecies pairs (such as S. cohnii subspecies with 7% divergence and S. aureus subspecies with 3.7% divergence), though most subspecies showed >97.3% similarity. The authors concluded that dnaJ gene sequencing offers a reliable alternative to 16S rRNA sequencing for species-level identification and phylogenetic analysis of Staphylococcus.
Key findings
- The dnaJ gene sequence showed higher discriminatory power (77.6% mean similarity between species) than 16S rRNA (97.4%) and other conserved genes, making it superior for species differentiation
- Phylogenetic analysis of dnaJ sequences identified eight major Staphylococcus species groups with results largely concordant with 16S rRNA gene and DNA-DNA reassociation studies
- Clinical isolates of S. aureus subsp. aureus and S. epidermidis demonstrated low intraspecies sequence variation (0.7% and 0.4%, respectively), supporting utility of dnaJ-based identification
- The dnaJ assay successfully discriminated closely related species pairs that cannot be resolved by 16S rRNA analysis, such as S. condimenti and S. carnosus
- dnaJ gene sequencing provides an effective alternative to 16S rRNA sequencing for species-level identification and subspecies classification of clinically important Staphylococcus strains
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Abstract
In the last few years, many attempts have been made to use conserved gene sequences for identification and for phylogenetic studies of Staphylococcus species. In an effort to identify a more reliable approach, a dnaJ gene sequence-based database was created. In this study, an approximately 883 bp portion of the dnaJ gene sequence from 45 staphylococcal type strains was compared with 16S rRNA and other conserved gene (hsp60, sodA and rpoB) sequences available in public databases. Nucleotide sequence comparisons revealed that the staphylococcal dnaJ gene showed higher discrimination (mean similarity 77.6 %) than the 16S rRNA (mean similarity 97.4 %), rpoB (mean similarity 86 %), hsp60 (mean similarity 82 %) and sodA (mean similarity 81.5 %) genes. Analysis of the dnaJ gene sequence from 20 Staphylococcus isolates representing two clinically important species showed <1 % sequence divergence. Phylogenetic data obtained from the dnaJ gene sequence were in general agreement with those of 16S rRNA gene sequence analysis and DNADNA reassociation studies. In conclusion, the dnaJ gene sequence-based assay is an effective alternative to currently used methods, including 16S rRNA gene sequencing, for identification and taxonomical analysis of Staphylococcus species.