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
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 
Published: September 2023

ABSTRACT

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 16/872
T
= CCM 9024
T
= LMG 31872
T
= DSM 111349
T
). The genomic analysis revealed numerous variable genomic elements, including staphylococcal cassette chromosome (SCC), prophages, plasmids, and a unique 18.8 kb-long genomic island SbCI

ccrDE

integrated into the ribosomal protein L7 serine acetyltransferase gene
rimL
. SbCI

ccrDE

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 SbCI

ccrDE

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.

IMPORTANCE

The coagulase-negative staphylococci are important opportunistic human pathogens, which cause bloodstream and foreign body infections, mainly in immunocompromised patients. The mobile elements, primarily the staphylococcal cassette chromosome
mec
, which confers resistance to methicillin, are the key to the successful dissemination of staphylococci into healthcare and community settings. Here, we present a novel species of the
Staphylococcus
genus isolated from human clinical material. The detailed analysis of its genome revealed a previously undescribed genomic island, which is closely related to the staphylococcal cassette chromosome and has the potential to accumulate and spread virulence and resistance determinants. The island harbors a set of conserved genes required for its mobilization, which we recognized as novel cassette chromosome recombinase genes
ccrDE
. Similar islands were revealed not only in the genomes of coagulase-negative staphylococci but also in
S. aureus
. The comparative genomic study contributes substantially to the understanding of the evolution and pathogenesis of staphylococci.