TABLE 1.

Primers used in this study

Test and primerSequence (5′-3′)DescriptionSource or reference
MRSA/PVL detection
    16S-FAGA GTT TGA TCA TGG CTC AG16S rRNA25
    16S-RGGA CTA CCA GGG TAT CTA AT
    mecA-FAAA ATC GAT GGT AAA GGT TGG CmecA25
    mecA-RAGT TCT GCA GTA CCG GAT TTG C
    nuc-FGCG ATT GAT GGT GAT ACG GTTnuc25
    nuc-RAGC CAA GCC TTG ACG AAC TAA AGC
    luk-FATC ATT AGG TAA AAT GTC TGG ACA TGA TCC AlukS/F (PVL)23
    luk-RGCA TCA AST GTA TTG GAT AGC AAA AGC
SCC typing
    KDP F1AAT CAT CTG CCA TTG GTG ATG CLocus B (SCCmec II)33
    KDP R1CGA ATG AAG TGA AAG AAA GTG G
    DCS F2CAT CCT ATG ATA GCT TGG TCLocus D (SCCmec II)33
    DCS R1CTA AAT CAT AGC CAT GAC CG
    IS431 P4CAG GTC TCT TCA GAT CTA CGLocus G (SCCmec II)33
    pUB110 R1GAG CCA TAA ACA CCA ATA GCC
ccr typing
    α1AAC CTA TAT CAT CAA TCA GTA CGTccrA1 (SCCmec I)22
    α2TAA AGG CAT CAA TGC ACA AAC ACTccrA2 (SCCmec II)22
    βcATT GCC TTG ATA ATA GCC ITC TccrB1 (SCCmec I) and ccrB2 (SCCmec II)22
spa typing
    932-FGCC AAA GCG CTA ACC TTT TAProtein A (spa)B. Kreiswirth, unpublished
    1740-RTCC AGC TAA TAA CGC TGC AC    data
J1 PCR
    LIR2-FCGA ATT AAA CAC GCT TGC TCJ1 (SCCmec II)This study
    LIR2-RCAG AAG TCT ACA GGT CTT GC
Long-range PCR
    3.0-RCTC AGA CAG CAA TTT CCC GDownstream of SCCmecThis study
    4.2-RCCC TAA AAA TAC CTG TAG GGG
Detection of MGE targets
    MW756-FTGG TTA GCT ATG AAT GTA GTT GCHypothetical protein (νSa3),45
    MW756-RGTC CAT CCT CTG TAA TTT TGC    unique to MW2
    sel2-FATC ATA CAG TCT TAT CTA ACG GCGsel2 (νSa3)This study
    sel2-RTCT GGA AGA CCG TAT CCT GTG
    SAS0898-FGAA GTA GCA GAT ATA TTG GGC GIntergenic region of SAS0898/0899This study
    SAS0899-RATC ACT GGC AAG TCC TAC C    (φSa4)
    SAS0922-FGAG GGA TAA ACT AAT GAA AGA ACGHypothetical phage proteinThis study
    SAS0922-RTCA TAG AAC CTA AAC GTC CCG    (φSa4), unique to MSSA476
SCCmec/orfX junction detection
    Xsau325GGA TCA AAC GGC CTG CAC AorfX15
    mecii574GTC AAA AAT CAT GAA CCT CAT TAC TTA TGSCCmec I, II, IV15
SCCmec II gene elements detection and sequencing
    kdpB2TAA ACT GTG TCA CAC GAT CCA TkdpB22
    II-48600RTCT TAG ATA GTA GCC AAC GGCJ3 of SCCmec IIThis study