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

• Published in: Frontiers in microbiology Vol. 12; p. 770191
• Main Authors: Lin, Shudan, Sun, Bianjin, Shi, Xinrui, Xu, Yi, Gu, Yunfeng, Gu, Xiaobin, Ma, Xueli, Wan, Tian, Xu, Jie, Su, Jianzhong, Lou, Yongliang, Zheng, Meiqin
• Format: Journal Article
• Language: English
• Published: Frontiers Media S.A 15-11-2021
• Subjects: comparative genomic; evolution; Microbiology; ocular; pan-genomic; Staphylococcus epidermidis; whole genome
• ISSN: 1664-302X; 1664-302X
• DOI: 10.3389/fmicb.2021.770191

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.