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. 2015 Sep 17;10(9):e0138079. doi: 10.1371/journal.pone.0138079

Table 1. MLST clonal complexes and sequence types and SCCmec- associated genes detected in S. epidermidis and S. haemolyticus isolates recovered from infections in humans and companion animals.

MR phenotype & species [n] CC ST a [n] SCC/SCCmec type/genes detected b [n] mecA alleles d [n] dru types[n]
MRSE [22 Hu, 11 CpA] 2-I 2 [9 Hu, 9 CpA] IVc [Class B mec (mecA, ΔmecR1, ugpQ) dcs & ccrAB2] [6 Hu] ABSA01000066 [6 Hu] dt9bd [3 Hu]
Non-typeable [2 Hu]
dt10h [1Hu]
IVc [Class B mec (mecA, ΔmecR1, ugpQ) dcs & ccrAB2] [6 CpA] ABSA01000066 [2 CpA] dt9g [1 CpA]
Non-typeable [1 CpA]
AY786579 [2 CpA] dt9bd [1 CpA]
dt5l [1 CpA]
BA000018 [1 CpA] Non-typeable [1 CpA]
AB037671 [1 CpA] Non-typeable [1 CpA]
III [Class A mec (mecA, mecR1,mecI, ugpQ, xylR) dcs & ccrAB3] [2 Hu] GU235984 [1 Hu] dt7ah [1 Hu]
EU929081 [1 Hu] dt7ah [1 Hu]
III [Class A mec (mecA, mecR1,mecI, ugpQ, xylR) dcs & ccrAB3] & ACME-arc [2 CpA] ABSA01000066 [1 CpA] dt9bn [1 CpA]
AY786579 [1 CpA] dt5l [1 CpA]
NT6 [Class A mec (mecA, mecI, mecR1, ugpQ, xylR), dcs & ccrAB3, ccrB4, ccrC] [1 Hu] BA000018 [1 Hu] dt9a [1 Hu]
NT8 [Class A mec (mecA, ugpQ, mecI, mecR1, xylR), dcs] & ACME-arc [1 CpA] AY786579 [1 CpA] dt8b [1 CpA]
2-II 6 [1 Hu] NT3 [Class B mec (mecA, ΔmecR1, ugpQ), dcs, kdp & ccrAB2, ccrA3, ccrB4] & ACME-arc [1 Hu] AY786579 [1 Hu] dt10ac [1 Hu]
2-I 35 [2 Hu] NT1 [Class B mec (mecA, ΔmecR1, ugpQ) & ccrAB2, ccrC (IVc)] & ACME-arc [1 Hu] AY786579 [1 Hu] dt10g [1 Hu]
NT2 [Class B mec (mecA, ΔmecR1, ugpQ), dcs & ccrAB2, ccrA1 (IVa)] & ACME-arc [1 Hu] EU929081 [1 Hu] dt9g [1 Hu]
2-II 69 [1 CpA] NT7 [Class C mec (mecA, ugpQ), dcs & ccrAB2 (IVh)] & ACME-arc [1 CpA] BA000018 [1 CpA] dt10a [1 CpA]
2-II 83 [2 Hu] IV c [Class B mec (mecA, ΔmecR1, ugpQ) dcs & ccrAB2] [1 Hu] GU235984 [1 Hu] dt8am [1 Hu]
NT4 [Class B mec (mecA, ΔmecR1, ugpQ) & ccrAB2, ccrAB4] [1 Hu] AY786579 [1 Hu] dt11b [1 Hu]
2-II 85 [1 Hu] IV c [Class B mec (mecA, ΔmecR1, ugpQ) dcs & ccrAB2] & ACME-arc [1 Hu] ABSA01000066 [1 Hu] dt10a [1 Hu]
2-II 87 [2 Hu] IV c [Class B mec (mecA, ΔmecR1, ugpQ) dcs & ccrAB2] [2 Hu] ABSA01000066 [1 Hu] dt10a [1 Hu]
BA000018 [1 Hu] dt10a [1 Hu]
2-II 125 [1 CpA] IVg [Class B mec (mecA, ΔmecR1, ugpQ) dcs & ccrAB2] & ACME-arc [1] ABSA01000066 [1 CpA] dt10a [1 CpA]
S 539 [1 Hu] IV c [Class B mec (mecA, ΔmecR1, ugpQ) dcs & ccrAB2] [1 Hu] AY786579 [1 Hu] dt10a [1 Hu]
S 264 [1 Hu] VI [class B mec (mecA, ΔmecR1, ugpQ), ccrAB4] [1 Hu] AB037671 [1 Hu] dt10a [1 Hu]
9 490 [1 Hu] NT5 [mecA, mecI, mecR1, ugpQ, dcs & ccrAB1] [1 Hu] BA000018 [1 Hu] dt8f [1 Hu]
2-I 592 [2 Hu] IV c [Class B mec (mecA, ΔmecR1, ugpQ) dcs & ccrAB2] [1 Hu] ABSA01000066 [1 Hu] dt9bd [1 Hu]
IVc [Class B mec (mecA, ΔmecR1, ugpQ) dcs & ccrAB2] [1 Hu] ABSA01000066 [1 Hu] dt9bd [1 Hu]
MSSE [6 Hu, 1 CpA] 2-I 35 [2 Hu] SCC1 [ccrAB2] [2 Hu] NA [2 Hu] NA [2 Hu]
2-II 152 [1 Hu] None [1 Hu] NA [1 Hu] NA [1 Hu]
2-II 166 [1 CpA] SCC 2 [ccrB1 & ccrAB2] & ACME-arc [1 CpA] NA [1 CpA] NA [1 CpA]
2-II 256 [1 Hu] SCC1 [ccrAB2] [1 Hu] NA [1 Hu] NA [1 Hu]
13 357 [2 Hu] None [2 Hu] NA [2 Hu] NA [2 Hu]
MRSH [7 Hu, 13 CpA] 1 1 [5 Hu, 3 CpA] NT9 [class C mec (mecA, ugpQ), ccrB4] [4 Hu, 1 CpA] ABSA01000066 [2 Hu] dt11v [2 Hu]
AY786579 [2 Hu, 1CpA] dt11v [2 Hu], dt11ca [1 CpA]
NT12 [class B mec (mecA, ΔmecR1, ugpQ), ccrAB4, ccrA1, dcs] & ACME-arc [1 Hu] AY786579 [1 Hu] dt10a [1 Hu]
VT [Class C mec (mecA, ugpQ), pls, kdp & ccrAA, ccrC (ccrC2 & ccrC8)] [1 CpA] GQ902038 [1 CpA] dt10a [1 CpA]
VT [Class C mec (mecA, ugpQ) & ccrAA, ccrC (ccrC2 & ccrC8)] [1 CpA] GQ902038 [1 CpA] dt11cu [1 CpA]
1 2 [5 CpA] NT10 [class C mec (mecA, ugpQ)] [4 CpA] AY786579 [4 CpA] dt11a [4 CpA]
NT11 [class C mec (mecA, ugpQ), ccrA3, ccrB4] [1 CpA] AY786579 [1 CpA] dt9bd [1 CpA]
1 3 [2 CpA] VT [Class C mec (mecA, ugpQ) & ccrAA, ccrC (ccrC2 & ccrC8)] [2 CpA] GQ902038 [2 CpA] dt11a [2 CpA]
1 4 [1 CpA] V [Class C mec (mecA, ugpQ), pls, kdp & ccrAA, ccrC (ccrC2 only)] [1 CpA] GQ902038 [1 CpA] dt11a [1 CpA]
1 5 [1 CpA] NT10 [class C mec (mecA, ugpQ)] [1 CpA] BA000018 [1 CpA] dt11a [1 CpA]
1 6 [1 CpA] VT [Class C mec (mecA, ugpQ) & ccrAA, ccrC (ccrC2 & ccrC8)] [1 CpA] GQ902038 [1 CpA] dt11a [1 CpA]
1 8 [1 Hu] NT9 [class C mec (mecA, ugpQ), ccrB4] [1 Hu] AY786579 [1 Hu] dt11v [1 Hu]
S 9 [1 Hu] V [Class C mec (mecA, ugpQ) & ccrAA, ccrC (ccrC2)] [1 Hu] GQ902038 [1 Hu] dt5i [1 Hu]
MSSH [1 Hu] 1 1 [1 Hu] SCC 3 [ccrAA, ccrA4] [1 Hu] NA [1 Hu] NA [1 Hu]

a Sequence types (STs) were determined using species-specific multilocus sequence typing (MLST) schemes as previously described [32, 55].

b Genes commonly associated with SCCmec elements were detected using the StaphyType DNA array kit (Alere Technologies GmbH, Jena, Germany). Any isolates found to carry unusual combinations of SCC or SCCmec genes using the DNA microarray were further characterized using multiplex PCRs as previously described [44, 45, 50, 52].

c These isolates could not be subtyped by PCR [52] despite harboring mec and/or ccr genes indicative of SCCmec IV.

d MR isolates were subjected to DNA microarray analysis to detect the alleles of mecA present as previously described [42]. The mecA alleles detected are described according to their GenBank accession numbers.

Abbreviations: Hu, Human; CpA, Companion animal; MR, Methicillin resistance, CC, Clonal complex; ST, Sequence type; SCC, staphylococcal cassette chromosome; dt, dru type; MRSE, methicillin-resistant S. epidermidis; MSSE, methicillin-susceptible S. epidermidis; MRSH, methicillin-resistant S. haemolyticus; MSSH, methicillin-susceptible S. haemolyticus; ACME, arginine catabolic mobile element; NT, Non-typeable SCCmec type; S, singleton; NA, Not applicable.