TABLE 1.
Oligonucleotide primer or probe | Sequence | Target organism | Target gene | Nucleotide position | Reference or source |
---|---|---|---|---|---|
Borrelia-specific primers | |||||
B-5SBor | 5′biotin-GAGTTCGCGGGAGAGTAGGTTATT | B. burgdorferi sensu lato | 5S rRNA (rrfA) | 82–105 | This study |
23SBor | TCAGGGTACTTAGATGGTTCACTT | B. burgdorferi sensu lato | 23S rRNA (rrlB) | 208–185 | This study |
Probes | |||||
SL | 5′amino-CTTTGACCATATTTTTATCTTCCA | B. burgdorferi sensu lato | 23S-5S spacera | 182–167 | 24 |
SS | 5′amino-AACACCAATATTTAAAAAACATAA | B. burgdorferi sensu stricto | 23S-5S spacer | 59–36 | 24 |
GA | 5′amino-AACATGAACATCTAAAAACATAAA | B. garinii | 23S-5S spacer | 58–35 | 24 |
AF | 5′amino-AACATTTAAAAAATAAATTCAAGG | B. afzelii | 23S-5S spacer | 44–21 | 24 |
VS | 5′amino-CATTAAAAAAATATAAAAAATAAATTTAAGG | B. valaisiana | 23S-5S spacer | 51–21 | 24 |
Ruski | 5′amino-GAATAAAACATTCAAATAATATAAAC | B. afzelii like | 23S-5S spacer | 67–42 | This study |
Ehrlichia-specific primers | |||||
16S8FE | GGAATTCAGAGTTGGATCMTGGYTCAG | Eubacteria | 16S rRNA gene | 8–27 | 27 |
B-GA1B | 5′biotin-CGGGATCCCGAGTTTGCCGGGACTTCTTCT | Ehrlichia genus | 16S rRNA gene | 476–456 | 27 |
Probes | |||||
A-EhrAll | 5′amino-TTATCGCTATTAGATGAGCC | Ehrlichia genus | 16S rRNA gene | 203–222 | 27 |
A-HGE | 5′amino-GCTATAAAGAATAGTTAGTGG | HGE agent | 16S rRNA gene | 87–107 | 27 |
A-Phago | 5′amino-TTGCTATAAAGAATAATTAGTGG | E. phagocytophila | 16S rRNA gene | 85–107 | 27 |
A-D-HGE | 5′amino-GCTATGAAGAATAGTTAGTG | HGE agent variant | 16S rRNA gene | 87–106 | 27 |
A-D-Phago | 5′amino-TTGCTATGAAGAATAATTAGTG | E. phagocytophila variant | 16S rRNA gene | 87–106 | 27 |
A-ESchot | 5′amino-GCTGTAGTTTACTATGGGTA | Ehrlichia like | 16S rRNA gene | 76–95 | 27 |
A-ECan | 5′amino-TCTGGCTATAGGAAATTGTTA | Ehrlichia canis | 16S rRNA gene | 85–105 | 27 |
A-EChaf | 5′amino-ACCTTTTGGTTATAAATAATTGTTA | E. chaffeensis | 16S rRNA gene | 83–107 | 27 |
A-EmurisC | 5′amino-GCTATAGGTTCGCTATTAG | E. muris C variant | 16S rRNA gene | 85–103 | This study |
A-EmurisT | 5′amino-AGCTATAGGTTTGCTATTAGT | E. muris T variant | 16S rRNA gene | 86–104 | This study |
Spike primers | |||||
23SBortmpA | CGGGATCCC-TCAGGGTACTTAGATGGTTCACTT-ACCCCGAACTTTTCTCCb | T. pallidum | tmpA | 199–215 | This study |
5SBortmpA | GGAATT-CGAGTTCGCGGGAGAGTAGGTTATT-CTTCCCCAGTTCTGTGTAGA | T. pallidum | tmpA | 725–706 | This study |
EhrFtmpB | GCTCTAGAG-AGAGTTTGATCCTGGCTCAG-CGCCTATCCGACCGAGTAT | T. pallidum | tmpB | 308–326 | This study |
EhrRtmpB | CGGGATCCC-GAGTTTGCCGGGACTTCTTCTA-CCACGTAGTCACCTTGTATT | T. pallidum | tmpB | 756–736 | This study |
Probes | |||||
A-TmpABor | 5′amino-TACAATCTAAGATCCAGACT | T. pallidum | tmpA | 346–365 | This study |
A-TmpBEhr | 5′amino-GAAAACTCGAAGAACAAAGAA | T. pallidum | tmpB | 502–522 | This study |
The SL probe targets the spacer and the first eight bases of the 23S gene sequence (rrlB).
The dashes in the spike primers indicate the separation between the restriction site sequences, the Borrelia or Ehrlichia sequence, and the tmpA- or tmpB-specific sequence.