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.

Keywords: Staphylococcus epidermidis; antimicrobial resistance; comparative genomic; evolution; ocular; pan-genomic; virulence gene; whole genome.

Figure 1

Circular genome maps of representative ocular strain. From the outer to the inner circle: (1) scale marks of genomes; (2) assigned clusters of orthologous group (COG) classes of protein-coding genes (CDSs) on the forward strand; (3) reverse strand CDSs; (4) tRNA (blue) and rRNA (red) genes on the forward strand; (5) tRNA (blue) and rRNA (red) genes on the reversed strand; (6) GC content (swell fire red/sky blue indicates higher/lower G+C compared with the average G+C content); (7) GC skew (black/orange indicate positive/negative values).

Figure 2

Pan-genome and phylogenetic feature of Staphylococcus epidermidis from different host niches and health state. (A) Gene accumulation curves for pan-genome (red) and core-genome (blue) of collected all strains. (B) Gene accumulation curves for pan-genome (red) and core-genome (blue) of ocular sources strains. (C) COG functional categories from the pan-genomes within strains from different niches. Involved COG categories are as follows: [B]Chromatin structure & dynamics; [C]Energy production & conversion; [D]Cell cycle control, cell division, chromosome partitioning; [E]Amino acid transport & metabolism; [F]Nucleotide transport & metabolism; [G]Carbohydrate transport & metabolism; [H]Coenzyme transport & metabolism; [I]Lipid transport & metabolism; [J]Translation, ribosomal structure & biogenesis; [K]Transcription; [L]Replication, recombination & repair; [M]Cell wall/membrane/envelope biogenesis; [N]Cell motility; [O]Post−translational modification, protein turnover & chaperones; [P]Inorganic ion transport & metabolism; [Q]Secondary metabolites biosynthesis, transport & catabolism and; [T]Signal transduction mechanisms; [U]Intracellular trafficking, secretion & vesicular transport; [V]Defense mechanisms; [W]Extracellular structures. Poorly characterized COG categories contains [R]General function prediction only and [S]Function unknown. (D) Phylogenetic core SNP maximum likelihood tree was constructed for 187 genomes. The blue branch represents strains from diseased hosts, while heathy source strains put color on red. Different color of strains ID stand for different host niches: blood (blue), ocular (green), skins (yellow), and respiratory tract (brick-red). Legends on the left stand for colors of sequence type (ST) from multilocus sequence typing. Ocular strains marked in green circle.

Figure 3

Heatmap of virulence genes in all 187 S. epidermidis strains. The red square indicates the presence of the gene, while the white square indicates absence. Legends on the right stand for colors of different host healthy state, isolates source, and virulence factor categories.

Figure 4

Gene function difference between healthy and disease source genomes. (A) Heatmap of enriched genes (Fisher’s exact test, adjust p<0.05) between disease and healthy sources strains. Only the accessory genes were shown. Gene clusters present in all genomes (core gene) or present in only a single genome (unique genes) are omitted. The red color stands for genes that existed and the blue color for missing ones. (B) Pie graph of KEGG function related with enriched genes from different health sources (Left are healthy source and Right are disease source). Bigger pie represented KEGG function proportion of the enriched genes showed in (A), while three smaller pie were account for function categories of metabolism, genetic information process, signaling and cellular processes, human diseases, respectively.

Figure 5

Key genes associated with diseased source pathogens. (A) Frequency of key genes among bacteria isolated from different health state. OR, odds ratio for association between the presence of the genes and disease vs. health source; values of p were calculated using Fisher’s exact test. (B) Frequency of key genes among bacteria isolated from different human source. OR, odds ratio for association between the presence of the genes and disease vs. health source; values of p were calculated using Fisher’s exact test. (C) Multiple alignment of virulence gene sdrG and non-virulence gene sdrG protein sequences across the collected blood source S. epidermidis (blue), intraocular isolates (green), Staphylococcus aureus and sdrG positive skin source strains.

Figure 6

The presence of antibiotic resistant genes across S. epidermidis strains. Heatmap indicates of 41 antibiotic resistant genes involved. The red color stands for genes that existed and the dark blue color for missing ones.