We identified two novel staphylococcal cassette chromosome mec (SCCmec) elements in sequence type 8 methicillin-resistant Staphylococcus aureus strains isolated in Japan: type II.5 SCCmec, whose J1 region was highly homologous to that of type I.2 SCCmec of strain PL72 (previously isolated in Poland), and its J1 region variant caused by the deletion/insertion of putative conjugative transposon Tn6012, identified in four S. aureus genomes.Recent advances in the field of genetics of methicillin-resistant Staphylococcus aureus (MRSA) enable us to distinguish MRSA clones by examining the genotype of the strain, e.g., by multilocus sequence typing or pulsed-field gel electrophoresis, and the type of staphylococcal cassette chromosome mec (SCCmec) integrated into the chromosome.This study was undertaken to determine the structures of two novel SCCmec elements, a type II SCCmec variant and a nontypeable SCCmec.Eight MRSA isolates, isolated in June to August 2004 from four patients at hospitals in Kochi prefecture in Japan, were investigated in this study. These isolates were susceptible to clindamycin and cefozopran, in contrast to the dominant resistant strains; belonged to the same sequence-based genotype group, Spa type t008, coagulase type 3, and sequence type 8; and showed the same pulsed-field gel electrophoresis banding patterns for SmaI digests, which were distinct from those of the dominant strains. Seven isolates from three patients (represented by JCSC6833) carried a type II SCCmec whose J1 region (the region from ccr to the right-flanking chromosome) could not be classified into known subtypes, and one isolate (JCSC6826) from one patient carried an SCCmec in which known types of ccr genes could not be identified.We have amplified DNA fragments covering entire regions of SCCmec elements of JCSC6833 and JCSC6826 by long-range PCR with the primer pairs indicated in Fig. 1 and Table 1 and determined the nucleotide sequences of the regions upstream of their mecA genes. Since a preliminary BLAST search suggested that the J1 region of the JCSC6833 SCCmec was homologous to that of the SCCmec element of strain PL72, isolated in 1991 at the University Children's Hospital in Warsaw, Poland (8), and reported to be a type I SCCmec variant (type I.2) (9), we have also resequenced parts of the SCCmec of strain PL72 for comparative purposes. Nucleotide sequences were determined as described previously (5).The overall structures of the SCCmec elements of JCSC6826, JCSC6833, and PL72 are illustrated in Fig. 1. These elements were integrated downstream of orfX, at exactly the same position as those of other known SCCmec elements, and carried characteristic sequences, direct repeats and inverted repeats, at both ends. The sizes of the three elements, calculated from the sizes of amplified DNA fragments and nucleotide sequences, are 28, 39, and 25 kb, respectively.The regions from orfX to mecA of the SCCmec elements of JCSC6833 and JCSC6826 were the same as that of the SCCmec of strain N315. They carried plasmid pUB110, which wa...