Staphylococcus brunensis sp. nov. isolated from human clinical specimens with a staphylococcal cassette chromosome-related genomic island outside of the rlmH gene bearing the ccrDE recombinase gene complex

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Authors

KOVAŘOVIC Vojtěch FINSTRLOVÁ Adéla SEDLÁČEK Ivo PETRÁŠ Petr ŠVEC Pavel MAŠLAŇOVÁ Ivana NEUMANN-SCHAAL Meina ŠEDO Ondrej BOTKA Tibor STAŇKOVÁ Eva DOŠKAŘ Jiří PANTŮČEK Roman

Year of publication 2023
Type Article in Periodical
Magazine / Source Microbiology Spectrum
MU Faculty or unit

Faculty of Science

Citation
Web https://doi.org/10.1128/spectrum.01342-23
Doi http://dx.doi.org/10.1128/spectrum.01342-23
Keywords coagulase-negative staphylococci; phylogenetic analysis; comparative genomics; mobile genetic elements; genomic islands; cassette chromosome recombinase; polyphasic taxonomy; gram-positive pathogens
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Description Novel species of coagulase-negative staphylococci, which could serve as reservoirs of virulence and antimicrobial resistance factors for opportunistic pathogens from the genus Staphylococcus, are recognized in human and animal specimens due to advances in diagnostic techniques. Here, we used whole-genome sequencing, extensive biotyping, MALDI-TOF mass spectrometry, and chemotaxonomy to characterize five coagulase-negative strains from the Staphylococcus haemolyticus phylogenetic clade obtained from human ear swabs, wounds, and bile. Based on the results of polyphasic taxonomy, we propose the species Staphylococcus brunensis sp. nov. (type strain NRL/St 16/872T = CCM 9024T = LMG 31872T = DSM 111349T). The genomic analysis revealed numerous variable genomic elements, including staphylococcal cassette chromosome (SCC), prophages, plasmids, and a unique 18.8 kb-long genomic island SbCIccrDE integrated into the ribosomal protein L7 serine acetyltransferase gene rimL. SbCIccrDE has a cassette chromosome recombinase (ccr) gene complex with a typical structure found in SCCs. Based on nucleotide and amino acid identity to other known ccr genes and the distinct integration site that differs from the canonical methyltransferase gene rlmH exploited by SCCs, we classified the ccr genes as novel variants, ccrDE. The comparative genomic analysis of SbCIccrDE with related islands shows that they can accumulate virulence and antimicrobial resistance factors creating novel resistance elements, which reflects the evolution of SCC. The spread of these resistance islands into established pathogens such as Staphylococcus aureus would pose a great threat to the healthcare system.
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