Table 3.
Clades and Strains and their genotypic characterization, as identified in this study or when analyzing published genome sequences.
| Clade | Strain/isolate name, reference strain or description | Reference sequence | PS | SI | SCCmec element | cadX | blaZ+R+I | erm(A) | erm(C) | aacA-aphD | aadD | aadE | ant9 | aphA3+sat | ble | dfrA | dfrG | mupA | tet(K) | tet(M) | cat | qacA | qacC | sek+seq | sesX/sesI | Hlb-integrating phage | Other notable features |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Eurasian | TUR1 | SAMEA1029552 | 2 | 0 | SCC [mec III+Cd+ccrC] (TUR1) |  |
 |
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 |
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sea+sak+scn | splE and fnbB absent |
| T0131 | CP002643.1 | 4 | 1 | SCC [mec III+Cd+ccrC] (T0131) | |
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|
sea+sak+scn | splE and fnbB absent | |
| arsC-SCC-pos. strains from Romania | – | 0 | 2 | SCC [mec III+As/Cd+ccrC] (Unknown, ST239−1) SCC [mec III+As/Cd+ccrC] (Unknown, ST239−2) | |
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sea+ sak+ scn | splE and fnbB absent | |
| 16K/CN79 | GenBank ANCJ, BABZ | 60 | 28 | SCC [mec III+Cd+ccrC] (CN79) | |
|
 |
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 |
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sea+sak+scn (comm.); sea(N315)+ sak + chp + scn (rare, Saint Petersburg only); none (rare) | splE and fnbB absent | |
| IU17 | GenBank CTXB | 2 | 0 | SCC [mec III+Cd+ccrC] (IU17) | |
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sea+sak+scn | splE and fnbB absent | |
| Sporadic strains from Saxony | – | 0 | 2 | SCC [mec III+Cd+ccrC] (Unknown, ST239−2) SCC [mec III+Cd+ccrC] (Unknown, ST239−3) | |
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sea | splE and fnbB absent | |
| Kuwaiti ACME II-pos. Strain | – | 0 | 2 | SCC [mec III+ ACME II+Cd+ccrC] (Unknown, ST239) | |
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sea | splE and fnbB absent. ACME II present | |
| European | “Greek Epidemic Strain” | SAMEA1029513, SAMEA1029532 | 3 | 7 | SCC [mec III+Cd/Hg+ccrC] (SK1585) | |
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sea+sak+scn | fnbA commonly absent |
| Irish AR01/UK EMRSA-01 | SAMEA1029537, AB037671.1 (SCCmec only) | 2 | 5 | SCC [mec III (Delta mecR1-)+ Cd/Hg+ccrC] (85/2082) | |
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sea+sak+scn | bbp absent from UK1 and Irish isolates | |
| BK2421 | SAMEA1029510 | 1 | 0 | SCC [mec III (Delta mecR1-)+ Cd/Hg+ccrC] (BK2421) | |
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sea+sak+scn | - | |
| Australian/NZ | JKD6008 | CP002120.1 | 2 | 29 | SCC [mec III+Cd] (JKD6008) | |
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sea+sak+scn (var.); or none | splA+B+E variable |
| ACME-pos. variant of JKD6008 | – | 0 | 3 | SCC [mec III+ ACME II+Cd](Unknown, ST239−1) | |
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sea+sak+scn | ACME II present | |
| South-East Asian | TW20 (Irish AR44) | GenBank FN433596.1 | 37 | 36 | SCC [mec III+Cd/Hg+ccrC] (TW20) | |
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sea+sak+scn (comm.); sak+chp+scn (var.); sak+scn (rare) none (rare) | splE absent from Mideastern isolates and Syrian sequence M592, SAMEA862550 |
| Strain with a TW20-derived pseudoelement | GenBank JBMO | 1 | 1 | PseudoSCCmec [class A+Cd/Hg+ccrC] (UCIM6015) | |
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sea+sak+scn or none | – | |
| Z172 | GenBank CP006838.1 | 1 | 1 | SCC [mec III+Cd/Hg+ccrC] (Z172) | |
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sea+sak+scn (var.); or none | splE variable | |
| mvaS-deletion variant of Z1721 | 0 | 1 | SCC [mec III+Cd/Hg+ccrC] (UnknownST239) | |
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sea+sak+scn | – | ||
| XN108 | GenBank CP007447.1 | 4 | 9 | SCC [mec III+Cd+ccrC] (XN108) | |
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sea+sak+scn (var.); sak+chp+scn (rare); none (rare) | – | |
| S85 | SAMEA1029529 | 2 | 3 | SCC [mec III+Cd+ccrC] (S85) | |
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sak+chp+scn | – | |
| PPUKM-775-2009- | GenBank AMRE | 1 | 1 | SCC [mec III+Cd+ccrC] (PPUKM−775−2009) | |
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sea+sak+scn or sak+chp+scn | – | |
| sasX-pos. mer+/ccrC neg. isolates from Kuwait | – | 0 | 2 | SCC [mec III+Hg] (Unknown, ST239) | |
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sea+sak+scn or none | – | |
| sasX-pos. strain with a Bmb9393-like SCC element | GenBank CP013957.1 | 18 | 17 | SCC [mec III+Cd/Hg+ccrC] (Bmb9393) | |
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sea+sak+scn (var.); sak+chp+scn (rare); sak+scn (rare) none (rare) | – | |
| M418 | GenBank CTXS | 1 | 0 | SCC [mec III+Cd/Hg+ccrC] (M418/UK−9) | |
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sea+sak+scn | – | |
| NMR08 | GenBank CP023560.1 | 2 | 1 | SCC [mec III+Cd+ccrC] (NMR08) | |
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sea+sak+scn | – | |
| sasX-pos. ACME-pos. strain | – | 0 | 1 | SCC [mec III+ ACME II+Cd/Hg] (Unknown, ST239) | |
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sea+sak+scn | ACME II present | |
| sasX-pos/czrC-pos. strains | – | 0 | 5 | SCC [mec III+speG+Cd/Hg/czrC +ccrAB4C] (Unknown, ST239) SCC [mec III+speG+Cd/czrC+ccrAB4C] (Unknown, ST239) | |
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none | – | |
| sasX-pos. sporadic strains from Kuwait and Hong Kong | 0 | 5 | SCC [mec III+Cd/Hg] (Unknown, ST239−1) SCC [mec III+Cd/Hg] (Unknown, ST239−2) | |
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sea+sak+chp+scn sea+sak+scn or none | ssl01 to ssl05 absent in HK isolate | ||
| P32 | GenBank CTXV | 1 | 0 | SCC [mec III+Cd] (HSA10/ATCC33592) | |
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none | sdrD absent | |
| ACME-pos. strain similar to P32 | 1 | SCC [mec III+ACME II+Cd] (Unknown, ST239−2) | |
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sak+scn | – | |||
| hla-negative South-East Asian | DEN907 | SAMEA1029548 | 1 | 0 | SCC [mec III+Cd/Hg] (DEN907) | |
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sea+sak+scn | hla absent |
| S2/M116 | SAMEA1029563 GenBank CTXQ | 12 | 0 | SCC [mec III+Cd] (S2) | |
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sea+sak+scn | hla absent | |
| Portuguese | Portuguese & ATCC 33592 strain | GenBank JXZH | 8 | 5 | SCC [mec III+Cd] (HSA10/ATCC33592) | |
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sea+sak+scn (rare); sak+chp+scn (rare); sak+scn (var) or none (var) | spl genes variably absent, bbp and sdrD sporadically absent |
| South American/ Middle Eastern | Bmb9393/UK EMRSA-11 | GenBank CP005288.1 | 34 | 4 | SCC [mec III+Cd/Hg+ccrC] (Bmb9393) | |
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||
| BRA2-Strain | SAMEA1029514 | 6 | 0 | SCC [mec III+Cd/Hg] (BRA2) | |
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sak+chp+scn (comm.) or none | ||
| Strain with a BRA2-derived pseudoelement | GenBank MIHO | 1 | 0 | PseudoSCCmec [class A+Cd/Hg] (UP1073) | |
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sak+chp+scn | ||
| MRSA_PR1 | GenBank ANPO | 2 | 3 | SCC [mec III+Cd+ccrC] (XN108) | |
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sea+sak+scn (var.); sak+chp+scn (var.) | bbp absent in MRSA_PR1 but present in others | |
| sasX-negative strain with a S85-like SCC element | – | 0 | 2 | SCC [mec III+Cd+ccrC] (S85) | |
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sak+chp+scn | splE absent | |
| UK EMRSA-09 | – | 0 | 1 | SCC [mec III+Cd/Hg+ccrC] (UK−EMRSA−9) | |
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sak+scn | ||
| Isolate from Togo | – | 0 | 1 | SCC [mec III+Cd/Hg] (Unknown, ST239−3) | |
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sea+sak+scn | ||
| Irish AR09/ UK EMRSA-04 and−07 | GenBank AEEK | 7 | 20 | SCC [mec III+Cd/Hg+ccrC] (TW20) | |
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sea+sak+scn (var); sak+chp+scn (var.) sea(N315)+sak+chp+ scn (rare, Algeria only); none (rare) | splE variably absent, ssl01 to ssl06 absent in HK isolates | |
| Irish AR23 | – | 0 | 1 | SCC [mec III+Hg+ccrC] (AR23) | |
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sea+sak+scn | ||
| Related to South American/ Middle Eastern | Krasnoyarsk tst1+ Strain | GenBank BBKC | 1 | 4 | SCC [mec III+Cd/Hg+ccrC] (Bmb9393) with mecA(BA000018) | |
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sak+scn | tst1 positive |
| URU110 | SAMEA1029540 | 1 | 0 | SCC [mec III+Cd/Hg+ccrC] (Bmb9393) with mecA(BA000018) | |
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sea+sak+scn | ||
| DS_014 | GenBank FQPU | 1 | 0 | SCC [mec III+Cd+ccrC] (XN108) with mecA(BA000018) | |
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sak+chp+scn | ||
| Unassigned | Unassigned Middle Eastern Strain | – | 0 | 4 | SCC [mec III+Cd+ccrC] (Unknown, ST239−1) | |
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sea+sak+scn | hla absent |
Bold font of element designations indicates those elements that were found in study isolates. Column “PS” indicates the number of (non-duplicate) previously published sequences analyzed, the Column “SI” indicates the number of study isolates. Symbols/abbreviations for frequencies of variable genes: , always absent; , rare, i.e., present in < 20% of analyzed sequences and/or characterized isolates; , variable, i.e., present in 20–80%; , common, i.e., present in more than 80%; , always present.