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

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 b...

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Autores principales:	Shudan Lin, Bianjin Sun, Xinrui Shi, Yi Xu, Yunfeng Gu, Xiaobin Gu, Xueli Ma, Tian Wan, Jie Xu, Jianzhong Su, Yongliang Lou, Meiqin Zheng
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	Staphylococcus epidermidis ocular whole genome pan-genomic evolution comparative genomic Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/fd3497c212b1479298a3d7cdee93ec3c
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spelling	oai:doaj.org-article:fd3497c212b1479298a3d7cdee93ec3c2021-11-15T06:25:08ZComparative Genomic and Pan-Genomic Characterization of Staphylococcus epidermidis From Different Sources Unveils the Molecular Basis and Potential Biomarkers of Pathogenic Strains1664-302X10.3389/fmicb.2021.770191https://doaj.org/article/fd3497c212b1479298a3d7cdee93ec3c2021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fmicb.2021.770191/fullhttps://doaj.org/toc/1664-302XCoagulase-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.Shudan LinBianjin SunXinrui ShiYi XuYunfeng GuXiaobin GuXueli MaTian WanJie XuJianzhong SuYongliang LouMeiqin ZhengMeiqin ZhengFrontiers Media S.A.articleStaphylococcus epidermidisocularwhole genomepan-genomicevolutioncomparative genomicMicrobiologyQR1-502ENFrontiers in Microbiology, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Staphylococcus epidermidis ocular whole genome pan-genomic evolution comparative genomic Microbiology QR1-502
spellingShingle	Staphylococcus epidermidis ocular whole genome pan-genomic evolution comparative genomic Microbiology QR1-502 Shudan Lin Bianjin Sun Xinrui Shi Yi Xu Yunfeng Gu Xiaobin Gu Xueli Ma Tian Wan Jie Xu Jianzhong Su Yongliang Lou Meiqin Zheng Meiqin Zheng Comparative Genomic and Pan-Genomic Characterization of Staphylococcus epidermidis From Different Sources Unveils the Molecular Basis and Potential Biomarkers of Pathogenic Strains
description	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.
format	article
author	Shudan Lin Bianjin Sun Xinrui Shi Yi Xu Yunfeng Gu Xiaobin Gu Xueli Ma Tian Wan Jie Xu Jianzhong Su Yongliang Lou Meiqin Zheng Meiqin Zheng
author_facet	Shudan Lin Bianjin Sun Xinrui Shi Yi Xu Yunfeng Gu Xiaobin Gu Xueli Ma Tian Wan Jie Xu Jianzhong Su Yongliang Lou Meiqin Zheng Meiqin Zheng
author_sort	Shudan Lin
title	Comparative Genomic and Pan-Genomic Characterization of Staphylococcus epidermidis From Different Sources Unveils the Molecular Basis and Potential Biomarkers of Pathogenic Strains
title_short	Comparative Genomic and Pan-Genomic Characterization of Staphylococcus epidermidis From Different Sources Unveils the Molecular Basis and Potential Biomarkers of Pathogenic Strains
title_full	Comparative Genomic and Pan-Genomic Characterization of Staphylococcus epidermidis From Different Sources Unveils the Molecular Basis and Potential Biomarkers of Pathogenic Strains
title_fullStr	Comparative Genomic and Pan-Genomic Characterization of Staphylococcus epidermidis From Different Sources Unveils the Molecular Basis and Potential Biomarkers of Pathogenic Strains
title_full_unstemmed	Comparative Genomic and Pan-Genomic Characterization of Staphylococcus epidermidis From Different Sources Unveils the Molecular Basis and Potential Biomarkers of Pathogenic Strains
title_sort	comparative genomic and pan-genomic characterization of staphylococcus epidermidis from different sources unveils the molecular basis and potential biomarkers of pathogenic strains
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/fd3497c212b1479298a3d7cdee93ec3c
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Comparative Genomic and Pan-Genomic Characterization of Staphylococcus epidermidis From Different Sources Unveils the Molecular Basis and Potential Biomarkers of Pathogenic Strains

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