Typing of SCCTyping of SCCmec elements IWG-SCC Nomenclature · 2017. 2. 2. · Typing of SCCTyping...

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

31

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

33

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


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

12

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

37


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)

38

mecRI1-987

∆IS12721458-1434

∆IS12721435-1

ISSep14,387 bp mecRI1-987

∆IS12721458-1434

∆IS12721435-1

ISSep14,387 bp


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

39


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)

40


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


675-606

mA7

IS2

IS2L (Ruppe et al. 2009)∆mecRI1-968

mecA


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)

41


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

42


43Garcia-Alvarez et al. (2011)



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


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


46Higuchi et al. (2008)



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

48

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

49

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)

50

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

52

Subtyping of SCCmec elementsSubtyping of SCCmec elementsM-PCR 3 & 4

Lane mec gene complex class

Standard strains


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

54

Subtyping of SCCmec elementsSubtyping of SCCmec elements

55Li et al. (2011)

Subtyping of SCCmec elementsSubtyping of SCCmec elements


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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Typing of SCCTyping of SCCmec elements IWG-SCC Nomenclature · 2017. 2. 2. · Typing of SCCTyping...

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