Table S1

Supplemental Table S1. Details of ORFs identified in SCCmec XIa of ST130 MRSA isolate M10/0061 ORF/DR ORF_100 (orfX) DR-1 ORF_101 (blaZM10/0061)

ORF _102 (mecAM10/0061)

ORF _103 (mecR1M10/0061)

ORF _104 (mecIM10/0061)

ORF _105

Nucleotide coordinatesb

Comparative ORF (GenBank accession number)c

1-480

orfX MRSA strain MW2 (BA000033.2)

462-480 796-1647 (complement)

n/a blaZ S. aureus plasmid SAP015A (GQ900380.1) blaZm Macrococcus caseolyticus JCSC7096 (AB498756.1) blaZ Staphylococcus saprophyticus ATCC 15305 (NC_007350) mecA Staphylococcus kloosii CSCA8 (AM048808.2) mecA Staphylococcus vitulinus CSWY15 (AM048811.2) mecA MRSA N315 (D86934) mecA Staphylococcus sciuri ATCC29062 (AB547234.1) mecA M. caseolyticus JCSC7096 (AB498756.1) mecR1 MRSA N315 (D86934) mecR1 M. caseolyticus JCSC7096 (AB498756.1) blaR1 MRSA252 (BX571856.1) blaR1 Staphylococcus haemolyticus plasmid NVH96 (AJ302698) mecI MRSA N315 (D86934) mecIm M. caseolyticus JCSC7096 (AB498756.1) blaI MRSA N315 plasmid pN315 (NC_003140) blaR1 MRSA252 (BX571856.1) ORF MCCL_plsB0028 M. caseolyticus JCSC5402 plasmid pMCCL2 (AP009486.1)

1741-3738 (complement)

3839-5593

5590-5964


Protein accession number BAA82243.1

% amino acid identityd 99%

n/a ADA61365

n/a 67%

BAI83352.1

44%

BAE19331.1

49%

CAJ15584.2

63%

CAJ15587.2

63%

BAA82220.1 BAJ15061.1

62% 62%

BAI83351.1

21%

BAA82219.2 BAI83350.1

45% 35%

CAG40821.1 CAC16666.1

38% 37%

BAA82218.1 BAI83349.1

66% 40%

BAB43881.1

52%

CAG40820.1 BAH18706.1

51% 49%

Gene product/DR nucleotide sequence (5'-3') 23S rRNA methyltransferase (formerly known as open reading frame X conserved hypothetical protein)e AGAAGCGTATCACAAATGA β-lactamase protein BlaZ

Penicillin binding protein 2a

Signal transducer protein MecR1 Beta-lactamase regulatory protein BlaR1

Methicillin resistance regulatory protein MecI Beta-lactamase regulatory protein BlaI

Hypothetical protein

ORF _106


ORF _107


ORF _108

8108-8527 (complement) 8548-9054 (complement)

ORF _109 ORF _110


ORF _111

9477-9815 (complement) 10290-11918 (complement) 11939-13288 (complement) 13791-15584 (complement)

ORF _112 (ccrB-3M10/0061) ORF _113 (ccrA-1M10/0061) ORF_114 (cchM10/0061) ORF _115

ORF _117

15584-15877 (complement) 16060-17052 (complement) 17171-19102

ORF_118

19196-19975

ORF_119

20388-22553 (complement) 22852-24501

ORF_116

ORF_120

EFE10767.1

21%

Transposase

EFM07337.1

90%


ORF 12873-13292 S. saprophyticus SCCmec strain TSU 33 (AB353724.1) ORF CZ120 MRSA SRImec-III and SCCmec-III region, strain 85/2082 (AB038513.1) ORF8 MRSA SCCmecZH47 (AM292304.1)

BAG24384.1

91%


BAC53831.1

88%


CAL22885.1

82%


0RF23 MRSA BK16691 transposon Tn6072 (GU235985.1) ccrB3 MRSA 85/2082(AB014436.1)

ADC53390.1

92%


BAA88755.1

93%

Cassette chromosome recombinase B3

ccrA S. saprophyticus SCCmec strain TSU 33 (AB353724.1) ORF GU370073.1 7356-9149 SCCmec Staphylococcus cohnii strain WC28 (GU370073.1) ORF no. C16 SCCmec IV MRSA JCSC6670 (AB425824.1) ORF11 SCCmec Staphylococcus hominis strain GIFU12263 (AB063171.1) ORF FP2_13010 (FP929045.1) Faecalibacterium prausnitzii L2/6 ORF HMPREF0789_1672 Staphylococcus epidermidis BCM-HMP0060 (ACHE01000062.1) geh1 S. epidermidis (AF053006.1)

BAG24390.1

86%

Cassette chromosome recombinase A1

ADM43452.1

77%

Cassette chromosome helicase

BAG84216.1

62%


BAB83482.1

64%


CBK98818.1

32%

DNA helicase protein

EES57797.1

48%


AAC38597.1

39%

Lipase precursor protein

BAE03522.1

75%

FAD-binding dehydrogenase

EES41411.1

75%

ORF 21617-22813 Clostridium sp. M62/1C_sp_M621-1.0.1 (ACFX02000052.1) ORF HMPREF0783_1004 S. aureus ATCC BAA-39 (AEEK01000038.1)

ORF no. SH0213 S. haemolyticus strain JCSC1435 (AP006716.1) ORF ACJB01000028.1 S. epidermidis M23864:W1 contig00029

ORF_120

22852-24501

ORF_125 (arsCM10/0061)


ORF_126 (arsBM10/0061)


ORF_127 (asrRM10/0061)


ORF no. SH0213 S. haemolyticus strain JCSC1435 (AP006716.1) ORF ACJB01000028.1 S. epidermidis M23864:W1 contig00029 (ACJB01000028.1) ORF no. SSP0088 S. saprophyticus strain ATCC15305 (AP008934.1) OFR no. SSP0089 S. saprophyticus strain ATCC15305 (AP008934.1) ORF STACA0001_1525 Staphylococcus capitis SK14 (ACFR01000014.1) ORF GG730274.1:513166-513858 S. aureus C160 (GG730274.1) ORF STAWA0001_0106 Staphylococcus warneri L37603 (ACPZ01000067.1) ORF GL545278.1:540491-541666 Staphylococcus caprae C87 (GL545278.1) arsC S. capitis SK14 (ACFR01000004.1) arsC S. haemolyticus JCSC1435 (AP006716.1) arsC MRSA252 (BX571856.1) arsB Staphylococcus xylosus plasmid pSX267 (M80565.1) arsB MRSA 252 (BX571856.1) asrR S. aureus IMCJ1379 plasmid pSA1379 (AB255366.1)

DR-2

29884-29902

n/a

ORF_128

29941-30855

ORF_121

24867-25916

ORF_122

25934-26602

ORF_123


ORF_124


BAE03522.1

75%

FAD-binding dehydrogenase

EES41411.1

75%

BAE17233.1

84%

ABC transporter permease protein LolE

BAE17234.1

89%

ABC transporter ATP-binding protein

EEE48440.1

93%

Flavin reductase like domain protein

EFC01991.1

93%

EEQ79095.1

41%

EFS16465.1

41%

EEE49308.1

92%

Arsenate reductase

BAE03410.1 CAG39708.1 AAA27588.1

92% 91% 93%

Arsenic efflux pump protein

CAG39707.1 BAE92849.1

93% 79%

Arsenic resistance operon repressor protein

n/a

n/a

DUF1837 superfamily protein

AGAGGCGTATCATAAGTAG

EFV36237.1 52% Hypothetical protein ORF HMPREF0432_00311 Gemella moribillum M424 (ACRX01000004.1) ORF _129 30855-31700 53% DNA helicase protein ORF Sez_1540 Streptococcus equi subsp. ACG62873.1 zooepidemicus MGCS1056 (ACG62873.1) a _130 31697-32962 ACG62873.1 39% DNA helicase protein XI in M10/0061 and ORF Sez_1540 Streptococcus equi and subsp. TheORF final three ORFs listed in the table (ORF_128, ORF_129 ORF_130) are located downstream of SCCmec zooepidemicus MGCS1056 (ACG62873.1) n/a ORFs is flanked n/a AGGAGCGTATCATAAATAG n/a However the region harboring these three are notDR-3 part of the 33024-33042 SCCmec element. by direct repeat (DR) sequences and is

considered to be a remnant of a SCC element and is therefore included in the table.

b

Nucleotide coordinates based on the nucleotide sequence of SCCmec XI of M10/0061 (GenBank accession number FR823292).

c

For all ORFs identified within M10/0061, apart form the mec complex genes, only the top hit identified using BLAST is shown.

d

Amino acid identities between two sequences were calculated from global sequence alignments. The sequences were aligned with the

needle global alignment program from the EMBOSS software package (45). Relative identities were calculated from the number of identical amino acids in the alignment with respect to the length of the new sequence from SCCmecXI. These overall amino acid identities were calculated for the best matching BLAST sequence and for some other staphylococcal sequences which represent different allotypes or paralogs of that gene. d

orfX has been annotated as a 23S rRNA methyltransferase (http://www.uniprot.org/uniprot/P0C1V0).

n/a, not applicable