Molecular Identification and Phylogenetic Analysis of Streptococcus Pyogenes Clinical Isolates from Human Throat Swab

Abstract

Streptococcus pyogenes is gram-positive, versatile human pathogen produced many virulence factors and toxins that target various component of immune response and caused multitude of local and systemic infection. The aim of the study was to use conventional PCR to identify Streptococcus pyogenes based on 16S rRNA, speB, and smeZ genes. During the period from January to May 2022, fifty throat swabs were collected from humans suffering respiratory signs. They detected the infection with standard biochemical tests such as gram stain and sensitivity to bacitracin disc, then confirmed by PCR. The synthesized DNA was further‎ amplified through conventional PCR targeting the 16S rRNA, speB, and smeZ genes. These ‎amplified products were ‎ submitted to Macrogen, South Korea, for sequencing. The result of the sequences analysis revealed multiple points of mutation within 16S rRNA gene G/A, showing transition mutation at 433 and 911 locations, while T/A and G/C had trans version mutation at 554 and 693 respectively. The phylogenetic analysis indicated 99% similarity of the 16sRNAgene of the isolated bacteria with a known strain of Egypt and India strains. Overall, the result concluded that standard molecular technique shows 16S rRNA, speB, and smeZ genes found with long lengths 1250bp, 978bp and 246bp, respectively when detection by conventional PCR as essential virulence genes which have crucial role in the confirmation of S. pyogenes  infection with establishes that the circulating strain exhibits high genetic resemblance to  Egypt and India strains.