Staphylococcus saprophyticus is a uropathogenic bacterium that causes acute uncomplicated urinary tract infections, particularly in female outpatients. We investigated the dissemination and antimicrobial susceptibilities of 101 S. saprophyticus isolates from the genitourinary tracts of patients in Japan. Eight of these isolates were mecA positive and showed ␤-lactam resistance. Pulsed-field gel electrophoresis showed that only some isolates were isogenic, indicating that the mecA gene was apparently acquired independently by mecA-positive isolates through staphylococcal cassette chromosome mec (SCCmec). Type determination of SCCmec by multiplex PCR showed a nontypeable element in the eight mecA-positive isolates. Sequence analysis of the entire SCCmec element from a prototype S. saprophyticus strain revealed that it was nontypeable with the current SCCmec classification due to the novel composition of the class A mec gene complex (IS431-mecAmecR1-mecI genes) and the ccrA1/ccrB3 gene complex. Intriguingly, the attachment sites of SCCmec are similar to those of type I SCCmec in S. aureus NCTC 10442. Furthermore, the genes around the mec gene complex are similar to those of type II/III SCCmec in S. aureus, while those around the ccr gene complex are similar to those of SCC15305RM found in S. saprophyticus ATCC 15305. In comparison with known SCCmec elements, this S. saprophyticus SCCmec is a novel type.Staphylococcus saprophyticus is a member of the coagulasenegative staphylococci (CoNS), which frequently cause uncomplicated urinary tract infections (UTIs) in young and middleaged female outpatients (8,12,15,18,21,22,23). Unlike most other CoNS, S. saprophyticus is rarely resistant to most antibiotics active against gram-positive organisms (10,17).Although the UTIs caused by S. saprophyticus have been well documented, the antimicrobial resistance and dissemination of this species are not well studied. The study described here investigated the current dissemination and antimicrobial resistance of S. saprophyticus isolates recovered from the urogenital tracts of Japanese patients. In addition, the characterization of a new type of staphylococcal cassette chromosome mec (SCCmec) element from a mecA-positive S. saprophyticus was carried out. MATERIALS AND METHODSBacterial isolates. From April to December 2003, a total of 101 S. saprophyticus isolates were recovered from urine specimens (94 isolates) of patients with acute cystitis with bacterial counts of Ն10 4 CFU/ml or vaginal specimens (7 isolates) of patients with from bacterial vaginosis-or candidiasis-related symptoms at the clinical microbiology laboratories of 65 different Japanese hospitals. All isolates were from different patients, and duplicate isolates from the same patient were excluded. In addition, specimens also yielding gram-negative bacteria, which are often isolated from patients with either uncomplicated or complicated UTIs, were not considered for further isolation of CoNS, including S. saprophyticus. These isolates were identified as CoNS by means...