Shotgun whole genome sequencing of drug-resistance Streptococcus anginosus strain 47S1 isolated from a patient with pharyngitis in Saudi Arabia

Galal Ali Esmail; Naif Abdullah Al-Dhabi; Badr AlDawood; Ali Mohammed Somily

doi:10.1016/j.jiph.2021.11.010

Shotgun whole genome sequencing of drug-resistance Streptococcus anginosus strain 47S1 isolated from a patient with pharyngitis in Saudi Arabia

J Infect Public Health. 2021 Dec;14(12):1740-1749. doi: 10.1016/j.jiph.2021.11.010. Epub 2021 Nov 16.

Authors

Galal Ali Esmail¹, Naif Abdullah Al-Dhabi², Badr AlDawood³, Ali Mohammed Somily⁴

Affiliations

¹ Department of Botany and Microbiology, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.
² Department of Botany and Microbiology, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia. Electronic address: naldhabi@ksu.edu.sa.
³ Department of Emergency Medicine, College of Medicine, King Saud University, King Saud University Medical City, Riyadh 11461, Saudi Arabia.
⁴ Department of Pathology and Laboratory Medicine/Microbiology, College of Medicine, King Saud University, King Saud University Medical City, Riyadh 11461, Saudi Arabia. Electronic address: ali.somily@gmail.com.

PMID: 34836797
DOI: 10.1016/j.jiph.2021.11.010

Abstract

Background: Streptococcus anginosus is an emergence opportunistic pathogen that colonize the human upper respiratory tract (URT), S. anginosus alongside with S. intermedius and S. constellatus, members of S. anginosus group, are implicated in several human infections. However, our understanding this bacterium to the genotype level with determining the genes associated with pathogenicity and antimicrobial resistance (AMR) is scarce. S. anginosus 47S1 strain was isolated from sore throat infection, the whole genome was characterized and the virulence & AMR genes contributing in pathogenicity were investigated.

Methodology: The whole genome of 47S1 was sequenced by Illumina sequencing technology. Strain 47S1 genome was de novo assembled with different strategies and annotated via PGAP, PROKKA and RAST pipelines. Identifying the CRISPR-Cass system and prophages sequences was performed using CRISPRloci and PhiSpy tools respectively. Prediction the virulence genes were performed with the VFDB database. AMR genes were detected in silico using NCBI AMRFinderPlus pipeline and CARD database and compared with in vitro AST findings.

Results: β-hemolytic strain 47S1 was identified with conventional microbiology techniques and confirmed by the sequences of 16S rRNA gene. Genome of 47S1 comprised of 1981512 bp. Type I-C CRISPR-Cas system and 4 prophages were detected among the genome of 47S1. Several virulence genes were predicted, most of these genes are found in other pathogenic streptococci, mainly lmb, pavA, htrA/degP, eno, sagA, psaA and cpsI which play a significant role in colonizing, invading host tissues and evade form immune system. In silico AMR findings showed that 47S1 gnome harbors (tetA, tetB &tet32), (aac(6')-I, aadK &aph(3')-IVa), fusC, and PmrA genes that mediated-resistance to tetracyclines, aminoglycosides, fusidic acid, and fluoroquinolone respectively which corresponds with in vitro AST obtained results. In conclusion, WGS is a key approach to predict the virulence and AMR genes, results obtained in this study may contribute for a better understanding of the opportunistic S. anginosus pathogenicity.

Keywords: AMR genes; De novo assembly; S. anginosus; Whole genome sequencing.

MeSH terms

Humans
Pharmaceutical Preparations*
Pharyngitis*
RNA, Ribosomal, 16S / genetics
Saudi Arabia
Streptococcus anginosus / genetics
Whole Genome Sequencing

Substances

Pharmaceutical Preparations
RNA, Ribosomal, 16S