Molecular epidemiology, genetic characteristics, and antimicrobial resistance of Staphylococcus capitis clinical isolates: First identification of the NRCS-A and proto-NRCS-A clones in Japan.

BACKGROUND: A pathogenic clone of Staphylococcus capitis, NRCS-A, possesses specific virulence factors and shows broader antimicrobial resistance (AMR). The present study aimed to analyze the genetic characteristics and AMR profiles of S. capitis clinical isolates and determine the prevalence of the NRCS-A clone in Japan. METHODS: S. capitis isolates from clinical specimens were analyzed for the presence of virulence factors and AMR-associated genes by PCR and sequencing. Genetic classification of S. capitis isolates was performed by an in-house multilocus sequence typing (MLST) based on four loci (arcC-rpoB-gap-tuf). RESULTS: A total of 194 S. capitis isolates (44 subsp. capitis and 150 subsp. urealyticus) were collected for 7 months. mecA was detected in 33% (63/194) of isolates (only subsp. urealyticus), while the most common AMR determinants identified were fosSC (77%, n = 150) and blaZ (59%, n = 114). Virulence factors associated with the NRCS-A clone, nsr and tarJ, were found in 20% (n = 39) and 37% (n = 71) of isolates, respectively. Both nsr and tarJ were present in 13 isolates (7%), among which three isolates had the traits of the NRCS-A clone (SCCmec-V with CRISPR/Cas-IIIA; SCCcad/ars/cop in two isolates), whereas the remaining 10 isolates were considered presumptive proto-NRCS-A clone (nsr+, tarJ+, CRISPR-Cas-IIIA/SCCmec-negative). By the MLST scheme, all the S. capitis isolates were differentiated into 48 STs and six major clonal complexes (CCs). Isolates assigned to the NRCS-A clone were classified as ST13 or ST14 in CC1, which was a minor lineage of S. capitis subsp. urealyticus. Similarly, most isolates of proto-NRCS-A clone were grouped into CC1, with ST13 being dominant. CONCLUSION: The present study first revealed the presence of NRCS-A and proto-NRCS-A clones among S. capitis clinical isolates in Japan. Careful monitoring and attention to these clones may be necessary in clinical settings.