Combination of Multiplex PCRs for Staphylococcal Cassette Chromosome mec Type Assignment: Rapid Identification System for mec , ccr , and MajorDifferences in Junkyard Regions

Abstract

ABSTRACT Staphylococcal cassette chromosome mec (SCC mec ) typing, in combination with genotyping of the Staphylococcus aureus chromosome, has become essential for defining methicillin-resistant S. aureus (MRSA) clones in epidemiological studies. We have developed a convenient system for SCC mec type assignment. The system consists of six multiplex PCRs (M-PCRs) for identifying the ccr gene complex ( ccr ), the mec gene complex ( mec ), and specific structures in the junkyard (J) regions: M-PCR with primer set 1 (M-PCR 1) identified five types of ccr genes; M-PCR 2 identified class A to class C mec ; M-PCRs 3 and 4 identified specific open reading frames in the J1 regions of type I and IV and of type II, III, and V SCC mec elements, respectively; M-PCR 5 identified the transposons Tn 554 and ΨTn 554 integrated into the J2 regions of type II and III SCC mec elements; and M-PCR 6 identified plasmids pT181 and pUB110 integrated into J3 regions. The system was validated with 99 MRSA strains carrying SCC mec elements of different types. The SCC mec types of 93 out of the 99 MRSA strains could be assigned. The SCC mec type assignments were identical to those made with a PCR system that uses numerous primer pairs to identify genes or gene alleles. Our system of six M-PCRs is thus a convenient and reliable method for typing SCC mec elements.