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.
Highlights
Coagulase-negative staphylococci (CoNS) usually live on human skin (Piette and Verschraegen, 2009), nasal cavity (97%; Wos-Oxley et al, 2010), and ocular surface (60%; Graham et al, 2007; Willcox, 2013) and is the most common isolate recovered from nosocomial bloodstream infections (31%; Wisplinghoff et al, 2004)
With phylogenetic analysis and comparative genomics, we revealed the evolutionary relationships of different sources, exploring how different host niches may shape the genetic diversity of S. epidermidis
This study analyzed the whole genomes of 187 S. epidermidis isolates, including 11 ocular strain isolates from the Department of Laboratories, Eye Hospital of Wenzhou Medical University, Wenzhou, China, and 176 available genome sequences downloaded from the GenBank database (Sayers et al, 2020) of the National Center for Biotechnology Information (NCBI)1 and PATRIC v3.6.10,2 with detailed information showed in Supplementary Table 1
Summary
Coagulase-negative staphylococci (CoNS) usually live on human skin (Piette and Verschraegen, 2009), nasal cavity (97%; Wos-Oxley et al, 2010), and ocular surface (60%; Graham et al, 2007; Willcox, 2013) and is the most common isolate recovered from nosocomial bloodstream infections (31%; Wisplinghoff et al, 2004). Staphylococcus epidermidis is the most common CoNS species (Otto, 2004), and it plays a central role in the skin microbiota; for example, it can protect against colonization by skin pathogens (Cogen et al, 2010a,b), maintain the ecological balance of human skin flora (Schommer and Gallo, 2013), and modulate the immune system (Egert et al, 2017; Linehan et al, 2018). Once it breaches the skin surface and enters the bloodstream, it is considered pathogenic. A high positive rate of S. epidermidis was detected in clinical specimens, whether they represent actual infection or only colonization/contamination remains to be discussed
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