Horizontal gene transfer plays an important role in changing the compositions of bacterial genomes over a short period of time. This process entails the transfer of genetic elements between different bacteria which is a key mechanism in bacterial diversity and evolution. In this study, I aimed to investigate the evolution of the S. epidermidis genome by focusing on three aspects: the prevalence of the SCC mobile element, the presence of the core-genes paralogs and the variability of sugar transporters. A core genome phylogenetic tree of 58 S. epidermidis clinical isolates was constructed. The MLST data showed that more than half the isolates belonged to the clinically predominant ST2 clone. Genomic analysis revealed the presence of the SCCmec in the majority of the isolates and identified ACME-positive isolates clustered in one lineage, with most of them belonging to ST48. COMER-like elements were identified in ST2 lineages. Interestingly, this is the first molecular characterization of the COMER-like element in S. epidermidis isolates. Several genomic analyses were carried out to identify core-gene paralogs using S. epidermidis ATCC12228 as a reference strain. Three out of four ST5 isolates were found to harbour five core-gene paralogs in two operons involved in the pentose phosphate pathway and formaldehyde assimilation. A different isolate was found to carry an oleate hydratase gene (ohyA) paralog, and this isolate showed lower susceptibility to the antimicrobial fatty acid in comparison to the control. Finally, the genomic analysis identified 19 putative carbohydrate transporter encoding genes, the majority of which (9/19) encoded PTS transporters. Additionally, a putative sorbitol PTS transporter was detected in STAPH 25. The analysis showed that this transporter was located in the SCCmec IV element, and the phenotypic assay revealed the ability of STAPH 25 to utilize sorbitol in comparison to the control.
