A New Specific DNA Target Sequence for Identification of Staphylococcus epidermidis  using Modified Comparative Genomic Analysis

Reza  Khoshbakht; Hosna  Zare; Reza Kamali  Kakhki; Alireza  Neshani; Maryam  Arfaatabar

doi:10.18502/ajmb.v14i3.9828

Reza Khoshbakht Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
Hosna Zare Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
Reza Kamali Kakhki Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
Alireza Neshani Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
Maryam Arfaatabar Department of Medical Laboratory Sciences, Kashan Branch, Islamic Azad University, Kashan, Iran

DOI: https://doi.org/10.18502/ajmb.v14i3.9828

Keywords: Comparative genomic analysis, Detection, Pathogen, Polymerase chain reaction, Se400, Staphylococcus epidermidis

Abstract

Background: Staphylococcus epidermidis (S. epidermidis) is the most frequently isolated pathogen from prostheses infections in the body. Therefore, improving its diagnostic methods, including rapid Nucleic Acid Amplification Tests (NAAT), seems necessary. Since the first step in designing a NAAT is to find a specific sequence and all DNA targets that have been introduced so far are not completely specific, we introduced a new 100% specific DNA target sequence to identify S. epidermidis in this study.

Methods: Modified comparative genomic analysis was used to find the best specific target sequence to detect S. epidermidis. A PCR method was designed for the evaluation of this target. To determine the detection limit and analytical specificity, pure genomic DNA of 18 bacteria include 12 standard strains (one S. epidermidis and 11 non-S. epidermidis) and six clinical isolates (five S. epidermidis and one non-S. epidermidis) were used.

Results: The 400 bp sequence of S. epidermidis ATCC 14990 was identified as the most specific sequence (Se400), having a 100% sequence similarity to S. epidermidis genomes but not with other bacteria. The detection limit of Se400-PCR was 10 fg, equal to about 4 copies of S. epidermidis genomic DNA/μl. All pure DNA templates from S. epidermidis generated a detectable amplicon by 264 bp length, but the PCR test was negative for the non-S. epidermidis group.

Conclusion: The Se400 sequence can be considered as a specific target for detecting S. epidermidis, based on our findings.