TABLE 1.
Primers and probes used in this study
| Primer or probe | Sequence | Gene(s) | Source or reference |
|---|---|---|---|
| Primers | |||
| BORF | 5′-CGC TGG CAG TGC GTC TTA A | rrs | This study |
| 16S3B | 5′-biotin-GCG GCT GCT GGC ACG TAA TTA GC | rrs | 3 |
| 16S1 | 5′-CGA AGA GTT TGA TCC TGG CTTAG | rrs | 3 |
| 16S2 | 5′-GCT AAT TAC GTG CCA GCA GCC GC | rrs | 3 |
| 16S5 | 5′-GTG CGG GCC CCC GTC AAT TCC | rrs | 3 |
| 16S7 | 5′-CCA TGA TGA TTT GAC GTC ATC | rrs | 3 |
| 16S9 | 5′-CCT TGT TAC GAC TTC ACC CC | rrs | 3 |
| 23SN2 | 5′-ACC ATA GAC TCT TAT TAC TTT GAC CA | rrf-rrl | 69 |
| 5SCB | 5′-biotin-GAG AGT AGG TTA TTG CCA GGG | rrf-rrl | 69 |
| N1 | 5′-GAG CTT AAA GGA ACT TCT GAT AA | ospA | 35 |
| C1 | 5′-GTA TTG TTG TAC TGT AAT TGT | ospA | 35 |
| N2 | 5′-ATG GAT CTG GAG TAC TTG AA | ospA | 35 |
| C2 | 5′-CTT AAA GTA ACA GTT CCT TCT | ospA | 35 |
| FlaBorF1 | 5′-GCW TCT GAT GAT GCT GCT GG | flaB | This study |
| FlaBorF2 | 5′-GCA AMY CAR GAY GAR GCD ATT GC | flaB | This study |
| FlaBorR1 | 5′-GCY ACA AYH TCA TCK GTC | flaB | This study |
| FlaBorR2 | 5′-GCA ATH GCY TCR TCY TGR KTT GC | flaB | This study |
| C | 5′-GCA GTT CAA TCA GGT AAC GG | flaB | 27 |
| D | 5′-AGG TTT TCA ATA GCA TAC TC | flaB | 27 |
| 66F1 | 5′-GAA KTA GGC AAR GAY GAY CC | p66 | This study |
| 66F2 | 5′-GAR GRA CAA TTC TTG CAA GAG G | p66 | This study |
| 66F3 | 5′-CCA ACT TTA TCA AAT KCW KC | p66 | This study |
| 66F4 | 5′-GGT GAA AAA GAA TCH TGG | p66 | This study |
| 66R1 | 5′-TTT GAR TCC CAK CCA AG | p66 | This study |
| 66R2 | 5′-CCA DGA TTC TTT TTC ACC | p66 | This study |
| 66R3 | 5′-GMW GMA TTT GAT AAA GTT GG | p66 | This study |
| 66R4 | 5′-CCT CTT GCA AGA ATT GTY CYT C | p66 | This study |
| 1730F | 5′-CTT GGI CCI GGI GGA CTT TC | rpoB | 65 |
| 2900R | 5′-AGA AAT IAA IAT IGC ATC CTC | rpoB | 65 |
| GroEL-F | 5′-TAC GAT TTC TTA TGT TGA GGG | groEL | This study |
| GroEL-R | 5′-CGY CTA TCA CCA AAA CCR GGM G | groEL | This study |
| Probesa | |||
| 16S | 5′-a-GAG GAA TAA GCT TTG TAG GAA ATG ACA Ab | rrs | This study |
| R57 | 5′-a-AGT CAT TAA AGA TGT TTA ATG | rrs | This study |
| SL | 5′-a-CTT TGA CCA TAT TTT TAT CTT CCA | rrf-rrl | 69 |
| SS | 5′-a-AAC ACC AAT ATT TAA AAA ACA TAA | rrf-rrl | 69 |
| GA | 5′-a-AAC ATG AAC ATC TAA AAA CAT AAA | rrf-rrl | 69 |
| AF | 5′-a-AAC ATT TAA AAA ATA AAT TCA AGG | rrf-rrl | 69 |
| VA | 5′-a-CAT TAA AAA AAT ATA AAA AAT AAA TTT AAG G | rrf-rrl | 69 |
a
16S, generic probe to 16S rRNA of Borrelia spp. R57, specific probe for 16S rRNA of spirochetes similar to R57; SL, generic probe for 5S-23S rRNA of B. burgdorferi sensu lato, SS, specific probe for B. burgdorferi sensu stricto; GA, specific probe for B. garinii; AF, specific probe for B. afzelii; VA, specific probe for B. valaisiana.
b
a, aminolink modification of the oligonucleotides in 5′.