Department of Botany and Microbiology, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.
Department of Botany and Microbiology, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.
J Infect Public Health. 2021 Dec;14(12):1740-1749. doi: 10.1016/j.jiph.2021.11.010. Epub 2021 Nov 16.
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.
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.
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.
酿脓链球菌是一种机会致病菌，定植于人体上呼吸道（URT）。酿脓链球菌与中间链球菌和星座链球菌一起，属于酿脓链球菌群，与多种人类感染有关。然而，我们对这种细菌的基因型水平的了解，包括确定与致病性和抗菌药物耐药性（AMR）相关的基因，还很有限。47S1 菌株从咽痛感染中分离出来，对其全基因组进行了特征描述，并研究了导致致病性的毒力和 AMR 基因。
使用 Illumina 测序技术对 47S1 的全基因组进行测序。使用不同的策略对 47S1 基因组进行从头组装，并通过 PGAP、PROKKA 和 RAST 管道进行注释。使用 CRISPRloci 和 PhiSpy 工具分别鉴定 CRISPR-Cas 系统和噬菌体序列。使用 VFDB 数据库预测毒力基因。使用 NCBI AMRFinderPlus 管道和 CARD 数据库在计算机上检测 AMR 基因，并与体外 AST 结果进行比较。
通过传统微生物学技术鉴定 47S1 为β-溶血菌株，并通过 16S rRNA 基因序列进行确认。47S1 基因组由 1981512bp 组成。在 47S1 基因组中检测到 I-C 型 CRISPR-Cas 系统和 4 个噬菌体。预测了一些毒力基因，其中大多数基因存在于其他致病性链球菌中，主要有 lmb、pavA、htra/degP、eno、sagA、psaA 和 cpsI，它们在定植、入侵宿主组织和逃避免疫系统方面发挥着重要作用。计算机 AMR 研究结果表明，47S1 基因组携带 tetA、tetB 和 tet32、aac(6')-I、aadK 和 aph(3')-IVa、fusC 和 PmrA 基因，分别介导对四环素、氨基糖苷类、夫西地酸和氟喹诺酮的耐药性，与体外 AST 获得的结果相对应。总之，WGS 是预测毒力和 AMR 基因的关键方法，本研究的结果可能有助于更好地了解机会性酿脓链球菌的致病性。
