title: Searching Biomarkers in the Sequenced Genomes of Staphylococcus for their Rapid Identification.
abstract: 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.
authors: Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India.
authors: Ravi
authors: R
authors: Kumar
authors: Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India ; Academy for Scientific and Innovative Research (AcSIR), 2 Rafi Marg, New Delhi, 110001 India.
authors: Shikha
authors: S
authors: Koul
authors: Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India.
authors: Prasun
authors: P
authors: Kumar
authors: Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India ; Academy for Scientific and Innovative Research (AcSIR), 2 Rafi Marg, New Delhi, 110001 India.
authors: Vipin Chandra
authors: VC
authors: Kalia
keywords: Biomarkers; Diagnosis; Genome; In silico; Restriction endonuclease; Staphylococcus