TABLE 1.
Oligonucleotide primers and probes used in PCR and hybridization assays
| Oligonucleotide name | Oligonucleotide sequencea | Target organism | Target gene | Nucleotide position | Reference |
|---|---|---|---|---|---|
| Primer | |||||
| 5SCB | 5′-biotin-GAGAGTAGGTTATTGCCAGGG | B. burgdorferi sensu lato | 23S-5S spacer | 243–263 | 25 |
| 23SN2 | ACCATAGACTCTTATTACTTTGACCA | B. burgdorferi sensu lato | 23S-5S spacer | 469–444 | 25 |
| Probes | |||||
| SL | 5′-amino-CTTTGACCATATTTTTATCTTCCA | B. burgdorferi sensu lato | 23S-5S spacer | 453–430 | 25 |
| SS | 5′-amino-AACACCAATATTTAAAAAACATAA | B. burgdorferi sensu stricto | 23S-5S spacer | 322–299 | 25 |
| GA | 5′-amino-AACATGAACATCTAAAAACATAAA | B. garinii | 23S-5S spacer | 322–298 | 25 |
| AF | 5′-amino-AACATTTAAAAAATAAATTCAAGG | B. afzelii | 23S-5S spacer | 305–278 | 25 |
| VS | 5′-amino-CATTAAAAAAATATAAAAAATAAATTTAAGG | B. valaisiana | 23S-5S spacer | 303–278 | 25 |
| Primers | |||||
| 16S8FE | GGAATTCAGAGTTGGATCMTGGYTCAG | Eubacteria | 16S rRNA gene | 8–27 | 4 |
| 16S1523RM | CAGGAAACAGCTATGACCAAGGAGGTGATCCADCCVCA | Eubacteria | 16S rRNA gene | 1543–1523 | This study |
| B-GA1B | 5′-biotin-CGGGATCCCGAGTTTGCCGGGACTTCTTCT | Ehrlichia genus | 16S rRNA gene | 476–456 | This study |
| GA1IC | AGAAGAAGTCCCGGCAAACTC | Ehrlichia genus | 16S rRNA gene | 456–476 | This study |
| Probes | |||||
| A-EhrAll | 5′-amino-TTATCGCTATTAGATGAGCC | Ehrlichia genus | 16S rRNA gene | 203–222 | This study |
| A-HGE | 5′-amino-GCTATAAAGAATAGTTAGTGG | HGE | 16S rRNA gene | 87–107 | This study |
| A-Phago | 5′-amino-TTGCTATAAAGAATAATTAGTGG | E. phagocytophila | 16S rRNA gene | 85–107 | This study |
| A-D-HGE | 5′-amino-GCTATGAAGAATAGTTAGTG | HGE variant | 16S rRNA gene | 87–106 | This study |
| A-D-Phago | 5′-amino-TTGCTATGAAGAATAATTAGTG | E. phagocytophila variant | 16S rRNA gene | 87–106 | This study |
| A-ESchot | 5′-amino-GCTGTAGTTTACTATGGGTA | Ehrlichia-like organism | 16S rRNA gene | 76–95 | This study |
| A-ECan | 5′-amino-TCTGGCTATAGGAAATTGTTA | E. canis | 16S rRNA gene | 85–105 | This study |
| A-EChaf | 5′-amino-ACCTTTTGGTTATAAATAATTGTTA | E. chaffeensis | 16S rRNA gene | 83–107 | This study |
| Primers | |||||
| P24E | GGAATTCCCTCCTTCAGTTAGGCTGG | Bartonella | 16S rRNA gene | 966–982 | 22 |
| P12B | CGGGATCCCGAGATGGCTTTTGGAGATTA | Bartonella | 16S rRNA gene | 1224–1243 | 22 |
| Probes | |||||
| A-BartAll | 5′-amino-GTTGGGCACTCTARGG | Bartonella genus | 16S rRNA gene | 1084–1099 | This study |
| A-Hens | 5′-amino-TGCCAGCATTTGGTTGG | B. henselae | 16S rRNA gene | 1072–1088 | This study |
| A-Quin | 5′-amino-TTGCCATCATTAAGTTGGG | B. quintana | 16S rRNA gene | 1071–1089 | This study |
a
The underlined sequences represent the EcoRI and BamHI restriction sites. The double underlined sequence denotes the M13 sequence which was used for DNA sequencing.