dapb1 gene used for taxonomic classification and species identification of Nocardia

  Objective  To evaluate the ability of the dapb1 gene in taxonomic classification and species identification of Nocardia.

  Methods  The genome sequences of 230 strains (198 Nocardia strains and 32 non-Nocardia strains) were downloaded from public database, and the dapb1 genes were extracted from the genomes of 198 Nocardia strains (90 type strains, 31 reference strains and 77 clinical strains). Multi sequence alignment was conducted with clustalo, and the phylogenetic trees were constructed by using iqtree. The average nucleotide identity (ANI) was calculated, and the 16S rRNA sequence was amplified by PCR, and the amplified fragment was purified and sequenced and compared with the identification result of the dapb1 gene.

  Results  Based on the dapb1 gene, a phylogenetic tree of type strains of Nocardia was constructed, 90 type strains were divided into five clades. The sequence similarity of the dapb1 gene among species was 73.80%–97.74%, and the average similarity was 82.40%. This method was applied for 31 reference strains and 77 clinical strains of Nocardia. The result showed that the concordance rate between 16S rRNA gene and ANI was 77.7%, while the concordance rate between the dapb1 gene and ANI was 100%. Using dapb1 gene has higher resolution ratio and accuracy than using 16S rRNA gene to accurately identify Nocardia species. The sequence similarity of 98.08% can be used as a cut-off value for the species identification of Nocardia.

  Conclusion  Using dapb1 gene has a good interspecies resolution ratio to quickly and accurately identify Nocardia species and truly reflect the phylogenetic relationship among Nocardia species, which can be widely applied in the analysis on genetic structure of Nocardia, outbreak tracing, and surveillance for circulating strains.