Table_1_Comparative Genomic and Pan-Genomic Characterization of Staphylococcus epidermidis From Different Sources Unveils the Molecular Basis and Potential Biomarkers of Pathogenic Strains.DOCX

Coagulase-negative Staphylococcus (CoNS) is the most common pathogen causing traumatic endophthalmitis. Among which, Staphylococcus epidermidis is the most common species that colonizes human skin, eye surfaces, and nasal cavity. It is also the main cause of nosocomial infection, specially foreign body-related bloodstream infections (FBR-BSIs). Although some studies have reported the genome characteristics of S. epidermidis, the genome of ocular trauma-sourced S. epidermidis strain and a comprehensive understanding of its pathogenicity are still lacking. Our study sequenced, analyzed, and reported the whole genomes of 11 ocular trauma-sourced samples of S. epidermidis that caused traumatic endophthalmitis. By integrating publicly available genomes, we obtained a total of 187 S. epidermidis samples from healthy and diseased eyes, skin, respiratory tract, and blood. Combined with pan-genome, phylogenetic, and comparative genomic analyses, our study showed that S. epidermidis, regardless of niche source, exhibits two founder lineages with different pathogenicity. Moreover, we identified several potential biomarkers associated with the virulence of S. epidermidis, including essD, uhpt, sdrF, sdrG, fbe, and icaABCDR. EssD and uhpt have high homology with esaD and hpt in Staphylococcus aureus, showing that the genomes of S. epidermidis and S. aureus may have communicated during evolution. SdrF, sdrG, fbe, and icaABCDR are related to biofilm formation. Compared to S. epidermidis from blood sources, ocular-sourced strains causing intraocular infection had no direct relationship with biofilm formation. In conclusion, this study provided additional data resources for studies on S. epidermidis and improved our understanding of the evolution and pathogenicity among strains of different sources.

凝固酶阴性葡萄球菌（CoNS）是导致创伤性眼内炎最常见的病原体。其中，表皮葡萄球菌是最常见的物种，栖息于人类皮肤、眼表和鼻腔。它亦是医院感染的主要原因，尤其是异物相关血流感染（FBR-BSIs）。尽管一些研究报道了表皮葡萄球菌的基因组特征，但关于源自眼外伤的表皮葡萄球菌菌株的基因组及其致病性的全面理解仍显不足。本研究对11个导致创伤性眼内炎的表皮葡萄球菌眼外伤样本进行了测序、分析和报告。通过整合公开可用的基因组，我们共获得了来自健康和患病眼、皮肤、呼吸道和血液中的187个表皮葡萄球菌样本。结合全基因组、系统发育和比较基因组分析，本研究显示，无论栖息地来源如何，表皮葡萄球菌均展现出两个具有不同致病性的奠基谱系。此外，我们鉴定出与表皮葡萄球菌致病性相关的几个潜在生物标志物，包括essD、uhpt、sdrF、sdrG、fbe和icaABCDR。essD和uhpt与金黄色葡萄球菌中的esaD和hpt具有较高的同源性，表明表皮葡萄球菌和金黄色葡萄球菌的基因组可能在进化过程中进行了交流。sdrF、sdrG、fbe和icaABCDR与生物膜形成相关。与血液来源的表皮葡萄球菌相比，导致眼内感染的菌株与生物膜形成无直接关联。总之，本研究为表皮葡萄球菌的研究提供了额外的数据资源，并加深了我们对于不同来源菌株进化与致病性的理解。