Genome sequence of a methicillin-resistant Staphylococcus epidermidis (MRSE) resistant to dalbavancin and teicoplanin isolated in Italy, 2023

OBJECTIVE: Methicillin-resistant Staphylococcus epidermidis (MRSE) is a commensal bacterium that colonizes the skin surface of humans and animals and represents an important opportunistic pathogen related to nosocomial and community-acquired infections. Here, we characterized the whole genome of an MRSE isolate, named SEPI150, resistant to dalbavancin and teicoplanin, collected from the blood of a patient with recurrent bacteraemic episodes. METHODS: DNA sequencing was performed using a hybrid approach with Illumina MiSeq and Minion Oxford Nanopore platforms. Hybrid de novo assembly was performed using Unicycler, and analysis of mutations or insertions was performed by mapping Illumina reads of an MRSE strain susceptible to dalbavancin and teicoplanin collected from the same patient against the assembled genome of the SEPI150 strain. RESULTS: The SEPI150 strain exhibited resistance to β-lactams, rifampicin, gentamicin, dalbavancin and teicoplanin, while remaining susceptible to vancomycin. The strain belonged to sequence type ST23 and carried different antimicrobial resistance determinants (aant(9)-Ia, aadD, aac(6')-aph(2''), mecA, blaZ, erm(A) and bleO). Genome analysis in comparison with the dalbavancin-susceptible MRSE strain isolated from the same patient demonstrated that the SEPI150 strain carried wild-type walK/R, pbps and varR/S genes, and specific mutations were observed within rpoB (F597L) and vraG (D470G) genes. CONCLUSIONS: Herein, we hypothesized that accumulation of different mutations within genes targeting different pathways (i.e., RNA transcription and cell-wall biosynthesis) may be involved in resistance to dalbavancin and cross-resistance with other glycopeptides.