Isolation and Characterization of a Clinically-Derived Staphylococcus epidermidis HE23: Revealing Its Antibiotic Resistome and Metabolic Potential

Neonatal incubators may serve as environmental reservoirs for antimicrobial-resistant bacteria in neonatal intensive care units. In this study, Staphylococcus epidermidis HE23 was isolated from a high-touch surface of a neonatal incubator and characterized using whole-genome sequencing, comparative genomics, antimicrobial susceptibility testing, and metabolomic analysis. Hybrid assembly of Illumina and Nanopore sequencing reads generated a complete genome consisting of a circular chromosome (2,542,743 bp) and two plasmids (50,114 bp and 9,031 bp). Genomic analysis identified nine antibiotic resistance genes, including the chromosomal β-lactam resistance determinants blaZ and mecA and the plasmid-borne mupirocin resistance gene mupA . Antimicrobial susceptibility testing further confirmed resistance to multiple antibiotics, including β-lactams and quinolones. Genes associated with resistance to cationic antimicrobial peptides were also identified, suggesting potential mechanisms that may facilitate persistence under antimicrobial pressure. Metabolomic profiling detected several secondary metabolites, including putatively annotated cinobufagin and harmaline. Comparative genomic analysis further revealed conserved and strain-specific genomic features of HE23. The coexistence of chromosomal resistance determinants and plasmid-associated mupA highlights the potential of incubator-associated S. epidermidis to act as a reservoir of antimicrobial resistance in neonatal intensive care environments. These findings support strengthened microbial surveillance and targeted infection-control strategies for neonatal incubators.