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. 2001 Jun;39(6):2237–2242. doi: 10.1128/JCM.39.6.2237-2242.2001

TABLE 1.

Oligonucleotide primers and probes used in PCR and hybridization assays

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
a

The SL probe targets the spacer and the first eight bases of the 23S gene sequence (rrlB). 

b

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.