Table 1 Nucleotide sequences of PCR primers and probes
Oligonucleotide | Sequence (5′-3′) | Target bacteria | Source |
|---|---|---|---|
DNA microarray amplification | |||
16S27f | GAGAGTTTGATCCTGGCTCAG | Almost all eubacteria | Modified oligo fD1[38] |
16S1495r | CTACGGCTACCTTGTTACGA | Almost all eubacteria | Modified oligo fD1[38] |
qPCR amplification | |||
CbqPCR F | GGGAAACTCGGGCTAATACC | Coxiella spp. | This study |
CbqPCR R | CACGAGGTCCGAAGATCC | Coxiella spp. | This study |
CbqPCR P | FAM-CCCGCTTTGCTCCAAAGAGATTATG-TAMRA | Coxiella spp. | This study |
RcqPCR F | GCTTAACCTCGGAATTGCTT | Rickettsia spp. | This study |
RcqPCR R | CGTCAGTTGTAGCCCAGATG | Rickettsia spp. | This study |
RcqPCR P | HEX-CCTTCGCCACCGGTGTTCCT-TAMRA | Rickettsia spp. | This study |
FrqPCR F | ATTAAAGGTGGCCTTTGTGC | Francisella spp. | This study |
FrqPCR F2 | ATTAAAGGTGGCTTTCGGGC | Francisella spp. | This study |
FrqPCR R | ACCAACTAGCTAATCCAACGC | Francisella spp. | This study |
FrqPCR P | Cy5-AGGCTCATCCATCTGCGGCA-BHQ2 | Francisella spp. | This study |
Capture probes | |||
A3 | CGGCTATCTGGTCCGGTACTGAC | Anaplasma spp. | [28] |
Av | GCTGAATGTGGGGATTTTTTATCTCTGT | Anaplasma spp. | [28] |
Be | AAGGGTGGAATCTGTTGATATCAGG | Borrelia spp. | [28] |
Bg1 | CTGGTGTAAGGGTGGAATCTGTTGA | Borrelia spp. | [28] |
Bg2 | TCAGAAAGAATACCGGAGGCGAAGG | Borrelia spp. | This study |
Bsp1 | GGAATAAGCTTTGTAGGAAATGGCAAAGTGATGACG | Borrelia spp. | This study |
Bv | ACTTGGTGTTAACTAAAAGTTAGTACCGA | Borrelia spp. | [28] |
Bv2 | TATCAGGAAGAATACCGGAGGCGAA | Borrelia spp. | This study |
C1 | AATATCCTTGGGCGTTGACGTTACC | Coxiella spp. | [28] |
Cv | ACTAGCTGTTGGGAAGTTCACTTCTTAGT | Coxiella spp. | [28] |
F1v | ACTAGCTGTTGGAGTCGGTGTAAAGG | Francisella spp. | [28] |
F2 | TAGAGGAATGGGGAATTTCTGGTGT | Francisella spp. | [28] |
F2v | ACTAGCTGTTGGATTCGGTGTAAAGG | Francisella spp. | [28] |
Fa | AATAGCCTTGGGGGAGGACGTTAC | Francisella spp. | [28] |
NM | CTATTTAAACTAGAGATCGAGAGAGGATAGTGG | C. Neoehrlichia mikurensis | This study |
R1 | TAGAGTRTAGTAGGGGATGATGGAA | Rickettsia spp. | [28] |
Rv | GCTAGATATCGGAAGATTCTCTTTCGG | Rickettsia spp. | [28] |
Re | GTGGTCGCGGATCGCAGAGA | Rickettsia spp. | [28] |