Correlation between SCCmec multiplex types and amplimer sizes obtained using overlapping primer pairs to amplify the novel SCCmec element variants and comparison to those expected from typical SCCmec II and SCCmec IV elements

SCCmec multiplex typeSCCmec elementAmplimer sizea (kb) with primer pairReference
L-C, IRLII F-ccrA RC-M, ccrA F-Tn554 RC-M, Tn554 F-mecR1 RM-I, mecR1 F-ugpQ RI-R, ugpQ F-dcs RI-R, dcs F-orfX RC-M, ccrA F-mecA RM-I, mecA F-ISmec RI-R, ISmec F-orfX R
II − kdpIIA5.6713*4.18.5*1.7224.78This study
II − kdpIIB5.67No amplimerc4.18.51.7134.78This study
II − kdp & mecIIIC5.676. study
II − kdp & pUB110IID5.67134.12.21.7223.72.7This study
II − kdp, mecI & pUB110IIEb5.6*7*6.5*4.1*2.2*1.7*143.72.7This study
IVIVa8.9No amplimerdNo amplimerd4.
IVIVb5.6No amplimerdNo amplimerd4.
IVIVc6.1No amplimerdNo amplimerd4.1No amplimereNo amplimere8.54.75.319
IV − dcsIVEb6.1*No amplimerdNo amplimerd4.1No amplimereNo amplimere8.5*4.7*4.7*This study
IV − dcsIVF5.6*No amplimerdNo amplimerd4.1No amplimereNo amplimere8.54.74.7*This study
  • a Amplimer sizes for SCCmec IIA, IIB, IIC, IID, IIE, IVE, and IVF were calculated either by sequencing (indicated by *) or based on electrophoretic mobility in agarose gels. Amplimer sizes for SCCmec II, IVa, IVb, and IVc were calculated from sequences in the GenBank database, accession numbers D86934, AB063172, AB063173, and AB096217, respectively. All amplimer sizes are approximate. L-C, C-M, M-I, and I-R indicate the region of the SCCmec element amplified.

  • b SCCmec elements IIE and IVE were sequenced in full from isolates AR13.1/3330.2 and AR43/3330.1, respectively.

  • c No amplimer due to no Tn554; primers ccrA F-mecR1 R were used instead, resulting in an 11.5-kb amplimer, which was sequenced.

  • d No amplimer due to no Tn554 in SCCmec IVa, IVb, IVc, IVE, and IVF.

  • e No amplimer due to no dcs region in SCCmec IVc, IVE, and IVF.