TABLE 2.
LC-PCR primers and the LC-PCR sensitivities
| Species and subgroups | Target gene (description) | PCR primer and sequence (5′-3′) | Product size (bp) | Tma | Sensitivityb
|
Reference | |
|---|---|---|---|---|---|---|---|
| Direct LC-PCR | LC-PCR after enrichment | ||||||
| Escherichia coli | |||||||
| EPEC and EHEC | eaeA (E. coli attaching and effacing) | EAE-a, ATGCTTAGTGCTGGTTTAGG | 248 | 78.2 ± 0.2 | 3 | 3.3 | 37 |
| EAE-b, GCCTTCATCATTTCGCTTTC | |||||||
| EHEC | stx1 (Shiga toxin) | JMS1F, GTCACAGTAACAAACCGTAACA | 95 | 81.4 ± 1.0 | 4.1 | 2.6 | 14 |
| JMS1R, TCGTTGACTACTTCTTATCTGGA | |||||||
| stx2 | JMS2F, CGACCCCTCTTGAACATA | 108 | 81.4 ± 0.3 | 4 | 2 | 14 | |
| JMS2R, GATAGACATCAAGCCCTCGT | |||||||
| ETEC (LT) | LT (heat-labile enterotoxin) | LT-1, AGCAGGTTTCCCACCGGATCACCA | 132 | 81.4 ± 0.3 | 4.3 | 2.3 | 12 |
| LT-2, GTGCTCAGATTCTGGGTCTC | |||||||
| ETEC (ST) | ST (heat-stable enterotoxin) | STa-F, GCTAATGTTGGCAATTTTTATTTCTGTA | 190 | 76.6 ± 0.2 | 4.5 | 3.5 | 6 |
| STa-R, AGGATTACAACAAAGTTCACAGCAGTAA | |||||||
| EAEC | astA (EAECheat-stable enterotoxin) | EAST-1S, GCCATCAACACAGTATATCC | 106 | 84.9 ± 0.6 | 3.6 | 2 | 40 |
| EAST-1AS, GAGTGACGGCTTTGTAGTCC | |||||||
| aggR (transcriptional activator for EAEC aggregative adherence fimbria I expression) | aggRks1, GTATACACAAAAGAAGGAAGC | 254 | 78.9 ± 0.2 | 4.6 | 2 | 27 | |
| aggRkas2, ACAGAATCGTCAGCATCAGC | |||||||
| EIEC | virA (virulence of plasmid) | virA-F, CTGCATTCTGGCAATCTCTTCACA | 215 | 81.4 ± 0.3 | 3.3 | 6 | 34 |
| virA-R, TGATGAGCTAACTTCGTAAGCCCTCC | |||||||
| Shigella spp. | virA | 4.8 | 6 | ||||
| Salmonella spp. | invA (invasion) | invA 139, GTGAAATTATCGCCACGTTCGGGCAA | 284 | 85.8 ± 0.4 | 5 | 1.3 | 26 |
| invA 141, TCATCGCACCGTCAAAGGAACC | |||||||
| Yersinia enterocolitica | yadA (Yersinia adhesion) | yadA667-F, TGTTCTCATCTCCATATGC | 203 | 85.5 ± 0.8 | 4.5 | 2.9 | This study |
| yadA851-R2, TCCTTTCGCTGCTTCAGCA | |||||||
| Y. pseudotuberculosis | yadA | >203 | 84.3 ± 0.3 | 5.7 | 1.6 | ||
| Campylobacter jejuni | gyrA (DNA gyrase: a primary target of the fluoroquinolone antibiotics) | JL238, TGGGTGCTGTTATAGGTCGT | 192 | 80.3 ± 0.3 | 3 | 2 | 39 |
| JL239, GCTCATGAGAAAGTTTACTC | |||||||
| Vibrio cholerae | RTX toxin (repeat in toxin) | rtxC-F, CGACGAAGATCATTGACGAC | 265 | 85.8 ± 0.5 | 5 | 2 | 3 |
| rtxC-R, CATCGTCGTTATGTGGTTGC | |||||||
| CT (cholera toxin) | CT-F, ACAGAGTGAGTACTTTGACC | 308 | 80.4 ± 0.3 | 4.8 | 2.3 | 22 | |
| CT-R, ATACCATCCATATATTTGGGAG | |||||||
| V. parahaemolyticus | tdh (thermostable direct hemolysin) | Tdh199-F, GGTACTAAATGGCTGACATC | 251 | 80.4 ± 0.4 | 4.7 | 2 | 24 |
| Tdh199-R, CCACTACCACTCTCATATGC | |||||||
| trh (tdh-related hemolysin) | Trh250-F, GGCTCAAAATGGTTAAGCG | 250 | 79.6 ± 0.1 | 4.7 | 2 | 24 | |
| Trh251-R, CATTTCCGCTCTCATATGC | |||||||
| V. vulnificus | Cytotoxin hemolysin | VV-1, CTCACTGGGGCAGTGGCT | 383 | 84.4 ± 0.3 | 5 | 1.9 | 38 |
| VV-2, CCAGCCGTTAACCGAACCA | |||||||
| Aeromonas hydrophila | Cytolytic enterotoxin | AHCF1, GAGAAGGTGACCACCAAGAACA | 232 | 89.0 ± 0.5 | 4.7 | 4 | 16 |
| AHCR1, AACTGACATCGGCCTTGAACTC | |||||||
| Clostridium perfringens | Enterotoxin | GAP11, GGTTCATTAATTGAAACTGGTG | 154 | 76.0 ± 0.6 | 3.9 | 3.8 | 15 |
| GAP12, AACGCCAATCATATAAATTACAGC | |||||||
| Staphylococcus aureus | Nuclease | SA-1, GCGATTGATGGTGATACGGTT | 276 | 79.0 ± 0.3 | 4.5 | 6.9 | 2 |
| SA-2, CAAGCCTTGACGAACTAAAGC | |||||||
| Bacillus cereus | Hemolysin | BC-1, CTGTAGCGAATCGTACGTATC | 185 | 79.8 ± 0.9 | 3.9 | 8 | 38 |
| BC-2, TACTGCTCCAGCCACATTAC | |||||||
a
Values represent means ± standard deviations of 10 to 18 tests.
b
Sensitivity values represent the minimum numbers of cells necessary for the assay to yield positive LC-PCR results. Values are given as number of cells log10 per gram.