TABLE 3.
Sequences of the padlock probes used in this study
| Probea | 5′ end | Common sequenceb | Allele tagc | Locus tag | 3′ end |
|---|---|---|---|---|---|
| Probes targeting SNPs at MLST loci | |||||
| tpi-243-A | GCATCTTCAGATGTTGAT | C1 | A2 | ATTTGATCGTAACTCGGGTG | AAATGCACACATTTCATTT |
| tpi-243-G | GCATCTTCAGATGTTGAT | C1 | A1 | ATTTGATCGTAACTCGGGTG | AAATGCACACATTTCATTC |
| yqiL-333-C | AAGCGACTGTTGTTGA | C1 | A1 | TTTAGTCGTTTGCCCGAGGC | GTCCCATTTTAAAACCG |
| yqiL-333-T | AAGCGACTGTTGTTGA | C1 | A2 | TTTAGTCGTTTGCCCGAGGC | TGTCCCATTTTAAAACCA |
| gmk-129-T | ATTAAAGCTTCAAACGCA | C1 | A2 | CTTAACTATTAGCGTCGGTG | ATTCTATAAATTGGTCATCTTTA |
| gmk-129-C | ATTAAAGCTTCAAACGCA | C1 | A1 | CTTAACTATTAGCGTCGGTG | TCTATAAATTGGTCATCTTTG |
| arcC-162-T | ACGATTGTGCCTACAG | C1 | A1 | CTATATCCTTACCGCGTATG | CTACTTCCACACGTGTA |
| arcC-162-A | ACGATTGTGCCTACAG | C1 | A2 | CTATATCCTTACCGCGTATG | CTACTTCCACACGTGTT |
| arcC-210-T | GTTGGGTTATTGAATCGT | C1 | A2 | GAGTAGCCTTCCCGAGCATT | AAAAGGACCAATTGGTTTA |
| arcC-210-C | GTTGGGTTATTGAATCGT | C1 | A1 | GAGTAGCCTTCCCGAGCATT | AAAGGACCAATTGGTTTG |
| aroE-132-A | TCTTTATGAGGAATTGTGAT | C1 | A2 | AACAACGATGAGACCGGGCT | TAAATACGGTATGATACGT |
| aroE-132-G | TCTTTATGAGGAATTGTGAT | C1 | A1 | AACAACGATGAGACCGGGCT | AAATACGGTATGATACGC |
| gmk-318-T | TCTAAACTTGGAGGTGC | C1 | A2 | AATACGCTGAATAGAGCCCT | TCGCTCTCTCAAGTGA |
| gmk-318-A | TCTAAACTTGGAGGTGC | C1 | A1 | AATACGCTGAATAGAGCCCT | TCGCTCTCTCAAGTGT |
| pta-294-C | CCTGTTGAATGTGCTG | C1 | A1 | ACATATCCTAATACAGGCGC | GGACGCACAGTGTCG |
| pta-294-A | CCTGTTGAATGTGCTG | C1 | A2 | ACATATCCTAATACAGGCGC | GGACGCACAGTGTCT |
| tpi-36-T | TGCGCTTTTTTGTTAATTT | C1 | A2 | GACGATCCTTATACTCGATG | CCATGTTTGAAAATAGCA |
| tpi-36-C | TGCGCTTTTTTGTTAATTT | C1 | A1 | GACGATCCTTATACTCGATG | CATGTTTGAAAATAGCG |
| pta-383-T | CATCACCTTTAATCATAAAG | C1 | A2 | GAAGACAGTTATACCCATGC | TCACCAAAGATGTATTGTA |
| pta-383-A | CATCACCTTTAATCATAAAG | C1 | A1 | GAAGACAGTTATACCCATGC | CACCAAAGATGTATTGTT |
| tpi-153-C | CCTGCAACAGCTTTCT | C1 | A1 | TGTCTACCTTTCCGTCAAGA | TTTAAGTTGATCTTCAGATAAG |
| tpi-153-T | CCTGCAACAGCTTTCT | C1 | A2 | TGTCTACCTTTCCGTCAAGA | TTTAAGTTGATCTTCAGATAAA |
| tpi-087-A | TCTGTTTCACCAACACA | C1 | A1 | AAACCATCGACTCACGGGAT | CACTTTCACGCTCTTCT |
| tpi-087-C | TCTGTTTCACCAACACA | C1 | A2 | AAACCATCGACTCACGGGAT | ACTTTCACGCTCTTCG |
| yqiL-505-T | TACTGCTTTATGTTGTGAG | C1 | A1 | ATTGACCAAACTGCGGTGCG | CATTTTGCTGTGCACA |
| yqiL-505-C | TACTGCTTTATGTTGTGAG | C1 | A2 | ATTGACCAAACTGCGGTGCG | CATTTTGCTGTGCACG |
| Probes targeting genes within SCCmec (recombinase genes and mecA) | |||||
| ccrB-I | AATTTTTGACTTCCATACG | C1 | A1 | ATAAAGCTCTATACTCCGCG | GCATTAACTTGCCTGTTG |
| ccrB-III | TTGTATTGACTTCCATACG | C1 | A2 | ATAAAGCTCTATACTCCGCG | GCATCAATTTACCACTGC |
| ccrB-II | TCATGTTTACTATTAGGTATTT | C1 | A1 | AACTAGCATCTAAGCACTCG | CATGTTGATTAATCATCAGT |
| ccrB-IV | TCGTGTTTACTATCTGGTA | C1 | A2 | AACTAGCATCTAAGCACTCG | CATGTTGGTTAATCATTAGC |
| ccrC-V | ACTTTTACCACTTCTTCG | C1 | A1 | GCTCTAATGTTAAGTGCTCG | CCAATATCACATCATTTTTATC |
| ccrB-VI | TACTTTATCATAGCCTAGAG | C1 | A2 | GCTCTAATGTTAAGTGCTCG | AGCTCTTTTTTACTATCAGG |
| mecA | ATGAAGGTGTGCTTACA | C1 | A2 | ACCACAGATCGAAGGTCGGA | CATAAATGGATAGACGTCAT |
| Probes targeting staphylococcal 16S rRNA gene | |||||
| rDNA-Cy5 | CGTAGGAGTCTGGACC | C1 | A1 | AAGGCACGTATCATATCCCT | CCTACTGCTGCCTCC |
| rDNA-Cy3 | CGTAGGAGTCTGGACC | C1 | A2 | AAGGCACGTATCATATCCCT | CCTACTGCTGCCTCC |
a
Probe names are composed of gene names, SNP positions within genes, and alleles.
b
Common sequence C1, AGAGTGTACCGACCTCAGTA.
c
Allele tag A1, GCCGTGACTATCGA; allele tag A2, CATGAATCCGTAGT.