TABLE 2.
Hairpin primers and SNP targets
| IDa and primer | Target [clade(s)]b | Sequence (5′→3′)c |
|---|---|---|
| ECs2357 | ||
| 539C-RHP | R (1-7, 9) | CCGAGCGTTTTCCAGTGGCTCGG |
| 539A-RHP | D (8) | ACGAGCGTTTTCCAGTGGCTCGT |
| 539-F | Common | GAATCTGCAGGCCAAAATTTC |
| ECs2521 | ||
| 1060G-FHP | R (2-9) | CGTGTAACTGCGCAACTGCCAGAACAGTTACACG |
| 1060T-FHP | D (1) | AGTGTAACTGCGCAACTGCCAGAACAGTTACACT |
| 1060-R | Common | TTCGGAGCCCCGGTTATT |
| ECs3881 | ||
| 438C-FHP | R (3-9) | GGTGCACATTACGACTAAGACGTGTGCACC |
| 438T-FHP | D (1, 2) | AGTGCACATTACGACTAAGACGTGTGCACT |
| 438-R | Common | GGACAGGCGACCATGCAG |
| ECs4130 | ||
| 630C-RHP | R (4-9) | CGGCTTAATCTGTACTGCGTTGATTAAGCCG |
| 630T-RHP | D (1, 2, 3) | TGGCTTAATCTGTACTGCGTTGATTAAGCCA |
| 630-F | Common | GGCACCGTTGTGCTGCTTAT |
a
The locus identifier (ID) is based on the published genome of E. coli O157:H7 Sakai (GenBank accession no. BA000007).
b
The target of the HP primer is for the reference (R) or the diagnostic (D) sequence; the clade(s) for which the HP primers are specific is given in parentheses. Common primers are nonspecific.
c
Primer sequences are based on the sequence of E. coli O157:H7 Sakai; HP regions are underlined, and SNPs are in boldface.