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

Abstract

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.

Beyond the Wild MRSA: Genetic Features and Phylogenomic Review of mecC-Mediated Methicillin Resistance in Non-aureus Staphylococci and Mammaliicocci

“…Moreover, M. lentus and M. sciuri are considered etiological agents of exudative epidermitis with zoonotic potentials [ 70 ]. Much more recently, whole-genome data of non- aureus staphylococci species have led to the identification and characterization of numerous putative virulence factors [ 71 , 72 , 73 ].…”

“…Moreover, M. lentus and M. sciuri are considered etiological agents of exudative epidermitis with zoonotic potentials [70]. Much more recently, whole-genome data of non-aureus staphylococci species have led to the identification and characterization of numerous putative virulence factors [71][72][73]. The finding of a beta-lactam-resistant S. edaphicus strain from an antarctic environment sample showed that the mecC gene located between a pseudo-staphylococcus cassette chromosome mec (ψSCCmecP5085) and other SCCs implies the integration and exchange of foreign DNA [54].…”

Difficult-to-Treat Pathogens: A Review on the Management of Multidrug-Resistant Staphylococcus epidermidis

“…A similar study was conducted in 2021 in China, in which 187 samples from the eyes, skin, respiratory tract, and blood of eleven endophthalmitis patients were examined [ 47 ]. These samples were analyzed using pan-genome, phylogenetic, and comparative genomic analysis, confirming the presence of lineage ST2 and ST5 as strains related to diseases opposed to ST169 and associated with healthy skin.…”

In vitro antimicrobial mechanism of diacerein and potential to reverse MRSE resistance to β-lactams

“…Then, roary performs pan-genomic analyses based on core genes and RAxML constructs evolutionary tree using maximum likelihood methods. Finally, iTol that is an online tool was used to visualize and beautify evolutionary trees [35] . Meanwhile, the remaining DNA was used to detect whether the mecA gene was missing after 20 successive generations by PCR, as what mentioned before.…”