TABLE 2.
Oligonucleotide sequences for primers and TaqMan MGB probes for Brucella clade identification
| SNP clade | Assay name | Primers (5′-3′) | Probes (5′-3′)a | Genome positionb | SNP identityc |
|---|---|---|---|---|---|
| B. abortus | abc_205 | F-GTTTCCGCATCCAAATGGTT | FAM-AAGCAGAATCTTGCACA | 573136 | T, B. abortus |
| R-TTCGGGCGGTGAAAAGC | VIC-AAAGCAGAAGCTTG | G, other spp. | |||
| B. suis/B. canis | abc_246 | F-AGCCTGACCTGCTGCTTCTC | FAM-ATGAGCCCACCAAC | 573177 | C, B. suis/B. canis |
| R-GAGCCAGGCTGTGGTTTCC | VIC-ATGAGCCGACCAAC | G, other spp. | |||
| B. ovis | cysW_234 | F-CCGGGAAAGCGGAATTTC | VIC-CGAAAGCGATGTTGAT | 696894 | G, B. ovis |
| R-GCTGACCGCAATCGTTGTC | FAM-CGAAAGCCATGTTGAT | C, other spp. | |||
| B. melitensis | cysW_288 | F-GGAAAAAGGTATCTCCACGAAGGT | VIC-AGCCTGCGTCCGGG | 696948 | G, B. melitensis |
| R-CGTGGCTGGTGACGAAATT | FAM-TGAGGAGCCTTCG | T, other spp. | |||
| B. canis | omp25_256 | F-GGCTGGCGCCTTTGCT | FAM-AACTTCCAGAAGGAC | 1297911 | A, B. canis |
| R-GGCCCAGGAATAACCTGCAT | VIC-ACTTCCAGCAGGACC | C, other spp. | |||
| B. neotomae | rpoB_2673 | F-CATCCTGGCGACATTCTTGTC | VIC-AAGATCACGCCGAAGG | 776263 | G, B. neotomae |
| R-GGCGTCATCGGGCTTTC | FAM-TCACGCCTAAGGG | T, other spp. | |||
| Marine mammals | trpE_290 | F-ACGAGGATTCCTTCGTCCATAC | FAM-CCAATTATTTCCACCAGAC | 468289 | A, marine mammal |
| R-AACGCACGGTGGAAACCTT | VIC-TTGCCAATTATTTCCGCCA | G, other spp. |
a
TaqMan probes with a minor groove binder (MGB). Each probe was fluorescently labeled with either VIC or FAM dye.
b
Based on the genome of B. melitensis 16M chromosome I (GenBank accession no. AE008917).
c
The SNP identities are listed for the primer letters in bold.