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Searching Biomarkers in the Sequenced Genomes of Staphylococcus for their Rapid Identification


Bacterial identification using rrs (16S rRNA) gene is widely reported. Bacteria possessing multiple copies of rrs lead to overestimation of its diversity. Staphylococcus genomes carries 5–6 copies of rrs showing high similarity in their nucleotide sequences, which lead to ambiguous results. The genomes of 31 strains of Staphylococcus representing 7 species were searched for the presence of common genes. In silico digestion of 34 common genes using 10 restriction endonucleases (REs) lead to select gene-RE combinations, which could be used as biomarkers. RE digestion of recA allowed unambiguous identification of 13 genomes representing all the 7 species. In addition, a few more genes (argH, argR, cysS, gyrB, purH, and pyrE) and RE combinations permitted further identification of 12 strains. By employing additional RE and genes unique to a particular strain, it was possible to identify the rest 6 Staphylococcus aureus strains. This approach has the potential to be utilized for rapid detection of Staphylococcus strains.

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We are thankful to the Director of CSIR-Institute of Genomics and Integrative Biology (IGIB), and CSIR projects—GENESIS (BSC0121) and INDEPTH (BSC0111) for providing the necessary funds, facilities and moral support. Authors are also thankful to the Academy of Scientific & Innovative Research (AcSIR), New Delhi.

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Correspondence to Vipin Chandra Kalia.

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Kumar, R., Koul, S., Kumar, P. et al. Searching Biomarkers in the Sequenced Genomes of Staphylococcus for their Rapid Identification. Indian J Microbiol 56, 64–71 (2016).

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  • Biomarkers
  • Diagnosis
  • Genome
  • In silico
  • Restriction endonuclease
  • Staphylococcus