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Background. Over the last three decades, coagulase-negative staphylococci (CoNS) have been recognised as opportunistic pathogens, especially in immunocompromised patients. CoNS serve as a reservoir of accessory genes, including virulence and antimicrobial resistance factors for the genus Staphylococcus. Recent diagnostic techniques allow recognising of novel CoNS species in human clinical specimens. Methods. Here, we characterised coagulase-negative staphylococcal strains from the Staphylococcus haemolyticus phylogenetic clade obtained from human ear swabs, wounds and bile. A polyphasic taxonomic approach based on whole genomic sequencing with expert annotation, extensive biotyping, DNA fingerprinting by rep-PCR, MALDI-TOF MS, and chemotaxonomy analyses was applied to establish their phylogenetic position and characterize virulence and drug-resistance genes. Results. Five isolates of Staphylococcus sp. were obtained from various human-related clinical specimens both from mixed culture and monoculture. Based on the polyphasic taxonomic approach, the novel species named Staphylococcus brunensis sp. nov. is proposed, with the closest relative Staphylococcus petrasii. The whole genome sequence analysis revealed the presence of several variable genomic elements including staphylococcal chromosomal cassette (SCC), prophages, genomic islands, various full and partial IS elements, and plasmids conferring beta-lactam and macrolide resistance. Three strains possess an 18.8 kb-long genomic island designated SbCIccr with a ccr gene complex designated ccrDE that had a conserved structure like a ccr gene complex from known SCC types. However, the SbCIccr was integrated into the serine acetyltransferase gene rimL, not into the canonical integration site for SCCs, methyltransferase gene rlmH (orfX). The genomic island harbours genes for the restriction-modification system commonly found on SCC elements, a putative transposon with IS6 family element similar to IS431mec, a putative transcriptional regulator and accessory genes, which have been found frequently on plasmids. By a PCR assay we showed that the SbCIccr could be mobilized from the bacterial chromosome. Conclusions. Study of SbCIccr has a crucial role in the understanding of the origin, evolution and transfer of SCC-like elements. It may also represent a primordial element able to accumulate virulence and drug resistance factors, whose spread into established pathogens such as S. aureus would be a threat to the healthcare system.