typing of scctyping of sccmec elements iwg-scc nomenclature · 2017. 2. 2. · typing of scctyping...
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Typing of SCCmec elementsTyping of SCCmec elementsIWG-SCC Nomenclature
Currently identified SCCmec types in
S.aureus strains
SCCSCCmec
types
ccr gene
complexes
mec gene
complexesstrains
I 1 (A1B1)* B NCTC10442, COL
II 2 (A2B2) A N315, Mu50, Mu3,
MRSA252, JH1, JH9
III 3 (A3B3) A 85/2082
IV 2 (A2B2) B
CA05, MW2, 8/6-3P,
81/108, 2314, cm11,
JCSC4469, M03-68, E-
MRSA 15 JCSC6668MRSA-15, JCSC6668,
JCSC6670
V 5 (C1) C2 W IS(WBG8318), TSGH17,
PM1,
VI 4 (A4B4) B HDE288
VII 5 (C1) C1 JCSC6082
VIII 4 (A4B4) A C10682, BK20781
IX 1(A1B1) C2 JCSC6943
X 7(A1B6) C1 JCSC6945
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XI 8(A1B3) E LGA251
http://www.sccmec.org/
Typing of SCCmec elementsTyping of SCCmec elementsPCR-based assays
32http://www.staphylococcus.net/
Typing of SCCmec elementsTyping of SCCmec elementsKondo et al. (2007)
M-PCR 1f f Identifies mecA and the structural features unique to
each of the types 1-5 ccr gene complexes Types 6-8 ccr gene complexes are not detected Types 6 8 ccr gene complexes are not detected
M-PCR 2 Classes A, B, and C2 mec gene complexes Classes C1, D, and E mec gene complexes are not
detecteddetected
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Typing of SCCmec elementsTyping of SCCmec elementsM-PCR 1
Currently identified ccr gene complexes in
staphylococci.
ccr gene
complexes
ccr ge-
nes
SCCmec types carrying the ccr
gene complexescomplexes nes gene complexes
Type 1 A1B1 I, IX
Type 2 A2B2 II, IV
Type 3 A3B3 III
Type 4 A4B4** VI, VIII
Type 5 C1 V, VII
Lane ccr gene Standard Gene(s) or gene allele(s) detected (primer pair) Expected size
Type 6 A5B3
Type 7 A1B6 X
Type 8 A1B3 XI
mecA(mA1-mA2) 286 bp
Lane ccr gene complex class
Standard strains
Gene(s) or gene allele(s) detected (primer pair) Expected size of product (bp)
A1 1 NCTC10442 ccrA1-ccrB (α1-βc) 695
A2 2 N315 ccrA2-ccrB (α2-βc) 937
A3 3 & 5 85/2082 ccrA3-ccrB (α3-βc) & ccrC (γR- γF) 1,791 & 518
A4 2 CA05 ccrA2-ccrB (α2-βc) 937
A5 5 WIS ccrC1 (γR- γF) 518
34A6 4 HDE288 ccrA4-ccrB4 (α4.2-β4.2) 1,287
Typing of SCCmec elementsTyping of SCCmec elementsM-PCR 2
Lane mec gene complex class
Standard strains
Gene(s) or gene allele(s) detected (primer pair) Expected size of product (bp)
B1 B NCTC10442 mecA-mecI (mA7-mI6) 2,827
B2 A N315 mecA-IS1272 upstream of mecA (mA7-IS7) 1,963
B3 A 85/2082 mecA-IS1272 upstream of mecA (mA7-IS7) 1,797
B4 B CA05 mecA-mecI (mA7-mI6) 2,827
35B5 C2 WIS mecA-IS431 upstream of mecA (mA7-IS2) 804
Typing of SCCmec elementsTyping of SCCmec elementsKondo et al. (2007)
mec classccr type SCCmectype
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ABII (2A)
I (2B)
345
C1C2D
IV (2B)III (3A)
V (5C2)567
DE
VII (5C1)VI (4B)V (5C2)
( )
IX (1C2)VIII (4A)8
36X (7C1)XI (8E)
Typing of SCCmec elementsTyping of SCCmec elements
Class B(L) mec gene complexesC ( ) Class B mec gene complexes in type IV (2B) SCCmec may contain insertion sequences, transposons, and antimicrobial resistance genesp g
The M-PCR 2 conditions (2 min elongation) may not facilitate amplification of such extra-long class B(L) mec gene complexesmec gene complexes
Use long template PCR assays
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Typing of SCCmec elementsTyping of SCCmec elements
mecA
CA05 (IV)mA7 mI6
mecA
CA05 (IV)mA7 mI6
mecRI1-987
IS12721458-1
2,827 bp
mecA
Tn4001
mA7 mI6mecRI1-987
IS12721458-1
2,827 bp
mecA
Tn4001
mA7 mI6
∆mecRI1-827
IS256 IS256 IS12721458-1
∆mecRI820-987
mZH47 (IV)7,401 bp aac aac(2')-
aph(6'')∆mecRI1-827
IS256 IS256 IS12721458-1
∆mecRI820-987
mZH47 (IV)7,401 bp aac aac(2')-
aph(6'')
mecA
IS256 ∆mecRI38-987
IS12721458-1
JCSC7158 (IV)4,159 bp ∆mecRI
1-45
mecA
IS256 ∆mecRI38-987
IS12721458-1
JCSC7158 (IV)4,159 bp ∆mecRI
1-45
mecA
40850 (IV)
mecA
40850 (IV)
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mecRI1-987
∆IS12721458-1434
∆IS12721435-1
ISSep14,387 bp mecRI1-987
∆IS12721458-1434
∆IS12721435-1
ISSep14,387 bp
Typing of SCCmec elementsTyping of SCCmec elements
Type 7 ccr gene complex in type XI (7C1) SCCmecerroneously yields a positive result for a type 1 ccrerroneously yields a positive result for a type 1 ccrgene complex in M-PCR 1
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Typing of SCCmec elementsTyping of SCCmec elements
Class C1 mec gene complexesC C ( C ) Class C1 mec gene complexes in types VII (5C1) and X (7C1) SCCmec are not amplified in M-PCR 2
Use mA7 (mecA) in combination with IS2L (IS431L Use mA7 (mecA) in combination with IS2L (IS431Lupstream of mecA) described by Ruppe et al. (2009)
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Typing of SCCmec elementsTyping of SCCmec elements
mecA
WIS (V)mec
A
WIS (V)WIS (V)WIS (V)804 bp ∆mecRI
1-91IS4311-496
IS2mA7WIS (V)804 bp ∆mecRI
1-91IS4311-496
IS2mA7WIS (V)804 bp ∆mecRI
1-91IS4311-496
IS2IS2mA7mA7
∆mecRI1-968
mecA
JCSC6082 (VII)1,256 bp IS431L
675-606
mA7
IS2
IS2L (Ruppe et al. 2009)∆mecRI1-968
mecA
JCSC6082 (VII)1,256 bp IS431L
675-606
mA7
IS2
IS2L (Ruppe et al. 2009)∆mecRI1-968
mecA
JCSC6082 (VII)1,256 bp IS431L
675-606
mA7mA7
IS2
IS2L (Ruppe et al. 2009)IS2L (Ruppe et al. 2009)
mecA
1-968 675-606
IS2mecA
1-968 675-606
IS2mecA
1-968 675-606
IS2
306 bp
JCSC6945 (X)IS431L675-606
∆mecRI1-17
mA7 IS2L (Ruppe et al. 2009)306 bp
JCSC6945 (X)IS431L675-606
∆mecRI1-17
mA7 IS2L (Ruppe et al. 2009)306 bp
JCSC6945 (X)IS431L675-606
∆mecRI1-17
mA7mA7 IS2L (Ruppe et al. 2009)IS2L (Ruppe et al. 2009)
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Typing of SCCmec elementsTyping of SCCmec elements
Type XI (8E) SCCmec-carrying MRSAS CC ( ) Ruminant-associated MRSA CC130 (spa type t843)
Phenotypically resistant to methicillin but lack mecAby using PCR- and microarray-based assaysby using PCR and microarray based assays
New mecA homolog - mecAlga251
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Typing of SCCmec elementsTyping of SCCmec elements
43Garcia-Alvarez et al. (2011)
Typing of SCCmec elementsTyping of SCCmec elements
Gene(s) or gene allele(s) detected (primer pair) Expected size of product (bp)
Referenceof product (bp)
mecAlga251 (Fw-Rv)mecAlga251 (mecAlga251MultiFP-mecAlga251MultiRP)
356138
Garcia-Alvarez et al. (2011)Stegger et al. (in press)
mecI (mecIF-mecIR) 229 Garcia-Alvarez et al. (2011
mecR1 (mecR1F-mecR1R) 663 Garcia-Alvarez et al. (2011
ccrA1 (ccrAF-ccrAR) 887 Garcia-Alvarez et al. (2011
ccrB3 (ccrBF-ccrBR) 1,404 Garcia-Alvarez et al. (2011
44blaZ (blaZF-blaZR) 763 Garcia-Alvarez et al. (2011
Typing of SCCmec elementsTyping of SCCmec elements
SCCmec V (5C2&5)C f SCC C SCC Composites of SCC with ccrC1 allele 8 and SCCmecwith class C2 mec gene complex and a type 5 ccr gene complex carrying ccrC1 allele 2 [i.e., V (5C2&5)] g p y g [ ( )]are not identified in M-PCR 1
45
Typing of SCCmec elementsTyping of SCCmec elements
46Higuchi et al. (2008)
Typing of SCCmec elementsTyping of SCCmec elements
Gene(s) or gene allele(s) detected (primer pair) Expected size of product (bp)
Reference
ccrC1 allele 2 (ccrC2-F2-ccrC2-R2) 257 Higuchi et al. (2008)
47ccrC1 allele 8 (ccrC8-F-ccrC8-R) 562 Higuchi et al. (2008)
Subtyping of SCCmec elementsSubtyping of SCCmec elementsJoining (J) regions
J3 (I-R) - between the left chromosome-SCC junction and the mec (ccr) gene complexand the mec (ccr) gene complex
J2 (C-M) - between the mec and ccr gene complexesJ2 (C M) between the mec and ccr gene complexes
J1 (L-C) - between the ccr (mec) gene complex and the i ht SCC h j tiright SCC-chromosome junction
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Subtyping of SCCmec elementsSubtyping of SCCmec elementsJoining (J) regions
SCCmec subtypes are defined by presence of specific DNA sequences in the J regionsDNA sequences in the J regions
Characteristic genes, pseudo-genes, or non-coding regions other than mobile genetic elementsg g
Mobile genetic elements, e.g., insertion sequences, and transposons, plasmids, and antimicrobial resistance genesresistance genes
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Subtyping of SCCmec elementsSubtyping of SCCmec elementsIWG-SCC nomenclature
Expressing the J1 region differences as small letters (e g IVa IVb IVc)(e.g., IVa, IVb, IVc)
Expressing the differences due to the presence orExpressing the differences due to the presence or absence of mobile genetic elements as capital letters (e.g., IA, IIA, IVA)
Expressing the differences in each J1, J2, and J3 region in Arabic numbers, which are given in the
d f di ( II 1 1 1 II 1 1 2 II 2 1 1)order of discovery (e.g., II.1.1.1, II.1.1.2, II.2.1.1)
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Subtyping of SCCmec elementsSubtyping of SCCmec elementsPCR-based assays
51http://www.staphylococcus.net/
Subtyping of SCCmec elementsSubtyping of SCCmec elementsKondo et al. (2007)
M-PCR 3f f f Identifies structural features unique to each of the J1
regions in SCCmec subtypes IV.1-IV.4 (IVa-IVd) Subtypes IV.1-IV.4 (IVg-IVj) are not detected Subtypes IV.1 IV.4 (IVg IVj) are not detected Use primer pairs described by Milheirico et al. (2007)
and Berglund et al. (2009)
M-PCR 4 SCCmec subtype V 1 (Va) SCCmec subtype V.1 (Va) Subtypes V.2 (Vb) and V.3 (Vc) are not detected
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Subtyping of SCCmec elementsSubtyping of SCCmec elementsM-PCR 3 & 4
Lane mec gene complex class
Standard strains
Gene(s) or gene allele(s) detected (primer pair) Expected size of product (bp)
C2 IV.1 (IVa) CA05 CQ02 (4a1-4a3) 458
C3 IV.2 (IVb) 8/6-3P M001 (4b2-4b4) 726
C4 IV.3 (IVc) 81/108 CR008 (4c4-4c5) 259
C5 IV.4 (IVd) JCSC4469 CD002(4d3-4d4) 1,242
53D6 V.1 (Va) WIS V024 (5a1-a2) 1,159
Subtyping of SCCmec elementsSubtyping of SCCmec elementsKondo et al. (2007)
M-PCR 3f f f Identifies structural features unique to each of the J1
regions in SCCmec subtypes IV.1-IV.4 (IVa-IVd) Subtypes IV.1-IV.4 (IVg-IVj) are not detected Subtypes IV.1 IV.4 (IVg IVj) are not detected Use primer pairs described by Milheirico et al. (2007)
and Berglund et al. (2009)
M-PCR 4 SCCmec subtype V 1 (Va) SCCmec subtype V.1 (Va) Subtypes V.2 (Vb) and V.3 (Vc) are not detected
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Subtyping of SCCmec elementsSubtyping of SCCmec elements
55Li et al. (2011)
Subtyping of SCCmec elementsSubtyping of SCCmec elements
Gene(s) or gene allele(s) detected (primer pair) Expected size of product (bp)
Reference
J1, subtype 2-specific orf33J1, subtype 2-specific orf35
534304
Higuchi et al. (2008)Higuchi et al. (2008)
56J1, subtype 3-specific czrC 562 Cavaco et al. (2010)
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