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

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

^bThe 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.