AUTHOR=Lin Shudan , Sun Bianjin , Shi Xinrui , Xu Yi , Gu Yunfeng , Gu Xiaobin , Ma Xueli , Wan Tian , Xu Jie , Su Jianzhong , Lou Yongliang , Zheng Meiqin 

TITLE=Comparative Genomic and Pan-Genomic Characterization of Staphylococcus epidermidis From Different Sources Unveils the Molecular Basis and Potential Biomarkers of Pathogenic Strains

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.770191

DOI=10.3389/fmicb.2021.770191

ISSN=1664-302X

ABSTRACT=<p>Coagulase-negative <italic>Staphylococcus</italic> (CoNS) is the most common pathogen causing traumatic endophthalmitis. Among which, <italic>Staphylococcus epidermidis</italic> 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 <italic>S. epidermidis</italic>, the genome of ocular trauma-sourced <italic>S. epidermidis</italic> 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 <italic>S. epidermidis</italic> that caused traumatic endophthalmitis. By integrating publicly available genomes, we obtained a total of 187 <italic>S. epidermidis</italic> samples from healthy and diseased eyes, skin, respiratory tract, and blood. Combined with pan-genome, phylogenetic, and comparative genomic analyses, our study showed that <italic>S. epidermidis</italic>, regardless of niche source, exhibits two founder lineages with different pathogenicity. Moreover, we identified several potential biomarkers associated with the virulence of <italic>S. epidermidis</italic>, including <italic>essD</italic>, <italic>uhpt</italic>, <italic>sdrF</italic>, <italic>sdrG</italic>, <italic>fbe</italic>, and <italic>icaABCDR</italic>. <italic>EssD</italic> and <italic>uhpt</italic> have high homology with <italic>esaD</italic> and <italic>hpt</italic> in <italic>Staphylococcus aureus</italic>, showing that the genomes of <italic>S. epidermidis</italic> and <italic>S. aureus</italic> may have communicated during evolution. <italic>SdrF</italic>, <italic>sdrG</italic>, <italic>fbe</italic>, and <italic>icaABCDR</italic> are related to biofilm formation. Compared to <italic>S. epidermidis</italic> 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 <italic>S. epidermidis</italic> and improved our understanding of the evolution and pathogenicity among strains of different sources.</p>