Table 1.
Primers and TwistAmp exo probes used in multiplex and singleplex RPA reactions to identify orfX-SCCmec junction types in MRSA isolates.
Figure 1.
Level of homology between 24 sequenced SCCmec elements using the Circos tool [52].
All-against-all BLASTN using E value of 10−300 as cut-off. 4738 local alignments produced in total, internal ribbons show 2465 alignments to preserve clarity. Histograms around circumference of circle show distribution of all 4738 alignments. Colours correspond to SCCmec type: red, IVh-CMFT3119; light purple, IVj; blue, IVa; purple, IVk; orange, IIa-CMFT2-like; yellow, IIa-CMFT492-like; dark orange, II.5; dark red, IVe; black, XI; green, V. Very little homology seen for CMFT540 (type XI) and region of CMFT3119 containing arc gene complex and ccrC.
Table 2.
Further characterisation of isolates undetectable by recombinase polymerase amplification: MLST and spa typing for the 28 isolates and sequencing data for the 24 isolates for which DNA could be recovered.
Figure 2.
a) SCCmec for archetypal type II, MRSA252 (NC_002952), compared to isolates CMFT2 and CMFT492. The cassette of CMFT2 shows the typical features of a type II SCCmec; a class A mec complex and a class 2 ccr complex. However, there is an additional SCC carrying type I ccr genes situated at the 5′ end of the element. CMFT492 is superficially similar and contains the same additional class 1 ccr complex. However, it lacks two of the major features of most type II SCCmec elements; the plasmid vector pUB110 and transposon Tn554. b) SCCmec type IVk: SCCmec for CMFT201 compared to CA05 (AB063172, type IV(2B)) and 45394F (GU122149). The cassette of CMFT201 shows the typical features of a type IV SCCmec (CA05); a class B mec complex and a class 2 ccr complex. However, there are additional SCC elements with an SCC carrying type I ccr genes situated at the 5′ end of the cassette. This is a similar structure to that shown by strain 45394F (unpublished). c) Type IVh variant SCC-SCCmec element for CMFT3119 compared to strains ZH47 (AM292304) and M1 (HM030720). The cassette of CMFT3119 shows the typical features of a type IV SCCmec; a class B mec complex and a class 2 ccr complex. However CMFT3119 contains an additional SCC carrying a ccrC gene upstream of the mec complex, similar to the recombination seen in ZH47. In contrast to ZH47 there is not a Tn4001 but instead part of the arginine catabolic mobile element (ACME), seen in S. epidermidis, S. haemolyticus and USA300, has been inserted. This arc gene cluster is very similar to that seen in the recently identified strain M1.