USE OF CLEAVED AMPLIFIED POLYMORPHIC SEQUENCES TO DISTINGUISH STRAINSOF STAPHYLOCOCCUS-EPIDERMIDIS

We examined the utility of a PCR-based termed cleaved amplified polymo rphic sequences (CAPS) to type 35 well-characterized isolates of Staph ylococcus epidermidis. The results were compared with detailed epidemi ologic information and typing obtained by using pulsed-field gel elect rophoresis (PFGE). To identify CAPS markers for this study, eight pair s of oligonucleotide primers corresponding to five previously sequence d S. epidermidis genes were synthesized and then used to amplify DNA s equences from the S. epidermidis strains by using PCR. Amplified produ cts were reproducibly obtained for seven of eight primer pairs from ch romosomal DNA of 33 of the 35 isolates. Seven restriction site polymor phisms were found in five of the amplified products when they were sub jected to digestion with a panel of restriction endonucleases. Each fr agment-enzyme combination that was polymorphic demonstrated only two a lleles in the 33 S. epidermidis isolates analyzed, corresponding to th e presence or absence of a single restriction site. Overall, five dist inct combinations of alleles were detected and were designated CAPS ty pes A through E. There was a close correlation between the CAPS groupi ng, the epidemiologic information for the strains, and grouping by PFG E following SmaI digestion of chromosomal DNA. Although PFGE analysis was more discriminatory than typing based on the limited number of CAP S markers used in this study (isolates from the same CAPS group were s ometimes distributed into more than one PFGE group), no isolates from the same PFGE group were found in more than one CAPS group. The CAPS p rocedure was highly reproducible, in contrast to published experience with arbitrarily primed PCR. These preliminary data suggest that CAPS represents a PCR-based technique for strain typing that is highly repr oducible, rapid, utilizes widely available technologies, and provides results that are relatively easy to interpret and express.