Background and Objective: Staphylococcus aureus (S. aureus) is a gram-positive bacterium and one of the major nosocomial pathogen. It has the ability to acquire resistance against almost all available classes of antibiotics; Methicillin-Resistant S. aureus (MRSA) is a well-known antibiotic resistance. S. aureus is a globally distributed pathogen that need in-depth epidemiological and genomic level investigation for proper treatment and prevention. Methods: To explore the genomic epidemiology of S. aureus in-silico Multi Locus Sequence Typing (MLST) was carried out for 355 complete genomes. Diversity within the species was investigated through pan-genome analysis and subtractive genomic approach was employed for identification of core immunogenic targets. Results: Epidemiological study identified 62 different sequence types (STs) of S. aureus distributed worldwide, in which ST-8, ST-5, ST-398, ST-239, and ST-30 are the most dominant STs comprising more than 50% of the isolates. The pan-genome of S. aureus is still open with 7,199 genes and there is a major contribution (80%) of MRSA strains in the S. aureus species pangenome. The core genome (2,025 genes) of S. aureus is almost stable (comprises of 72% of S. aureus genome size) while accessory and unique genes (28% of S. aureus genome size) are gradually increasing. Screening of 2,025 core genes identified putative vaccine candidates. The best scoring and dominant B-cell and T-cell epitopes were predicted out of the selected potential vaccine candidate proteins with the help of a multi-step screening procedure. Conclusion: We believe that the current study will provide insight into the genetic epidemiology and diversity of S. aureus and the predicted epitopes against the pathogen can be tested further for its immunological responses within the host and may provide both humoral and cellular immunity against the disease.

中文翻译：

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金黄色葡萄球菌的流行病学和泛基因组景观以及保守的新型候选疫苗抗原的鉴定

背景与目的：金黄色葡萄球菌（S. aureus）是一种革兰氏阳性菌，是院内主要病原菌之一。它能够对几乎所有可用的抗生素类别产生抗药性；耐甲氧西林金黄色葡萄球菌 (MRSA) 是一种众所周知的抗生素耐药性。金黄色葡萄球菌是一种全球分布的病原体，需要深入的流行病学和基因组水平调查以进行适当的治疗和预防。方法：为了探索金黄色葡萄球菌的基因组流行病学，对355个完整基因组进行了计算机多位点序列分型（MLST）。通过泛基因组分析研究物种内的多样性，并采用减法基因组方法鉴定核心免疫原性靶标。结果：流行病学研究确定了 62 种不同的 S.S. 金黄色葡萄球菌分布于世界各地，其中 ST-8、ST-5、ST-398、ST-239 和 ST-30 是最主要的 ST，占分离株的 50% 以上。金黄色葡萄球菌的泛基因组仍然开放，有 7,199 个基因，并且在金黄色葡萄球菌物种泛基因组中 MRSA 菌株占主要贡献（80%）。金黄色葡萄球菌的核心基因组（2,025 个基因）几乎是稳定的（占金黄色葡萄球菌基因组大小的 72%），而附属基因和独特基因（占金黄色葡萄球菌基因组大小的 28%）正在逐渐增加。筛选 2,025 个核心基因确定了推定的候选疫苗。在多步筛选程序的帮助下，从选定的潜在疫苗候选蛋白中预测出最佳评分和优势 B 细胞和 T 细胞表位。结论：我们相信，目前的研究将为了解金黄色葡萄球菌的遗传流行病学和多样性提供见解。