Table 1.
Summary of oligonucleotide primers and probes for PCR and TaqMan qPCR
| Target organism(s) | Assaya | Primer | P sequence (5′ to 3′) | Ta (°C)b | Size (bp)c | Reference or source |
|---|---|---|---|---|---|---|
| Enterococcus spp. | Entero1 | ECST748F | AGAAATTCCAAACGAACTTG | 60 | 92 | 18 |
| ENC854R | CAGTGCTCTACCTCCATCATT | |||||
| GPL813TQ | 6FAM-TGGTTCTCTCCGAAATAGCTTTAGGGCTA-TAMRA | |||||
| Ent1 | Ent151F | ACACTTGGAAACAGGTGC | 65 | 243 | This study | |
| Ent376R | TCGGTCAGACTTKCGTCC | |||||
| Ent2 | Ent151F | ACACTTGGAAACAGGTGC | 65 | 445 | This study | |
| Ent578R | TTAAGAAACCGCCTGCGC | |||||
| Ent3 | Ent240F | TGCATTAGCTAGTTGGTG | 63 | 356 | This study | |
| Ent578R | TTAAGAAACCGCCTGCGC | |||||
| Ent4 | Ent376F | GGACGMAAGTCTGACCGA | 65 | 220 | This study | |
| Ent578R | TTAAGAAACCGCCTGCGC | |||||
| Enterococcus faecalis | Faecalis1 | FaecalF | CGCTTCTTTCCTCCCGAGT | 60 | 143 | 32 |
| FaecalR | GCCATGCGGCATAAACTG | |||||
| FaecalP | 6FAM-CAATTGGAAA GAGGAGTGGCGGACG-TAMRA | |||||
| Faecalis2 | Ent151F | ACACTTGGAAACAGGTGC | 64 | 318 | This study | |
| Faecal449R | AGTTACTAACGTCCTTGTTC | |||||
| Faecalis3 | Ent240F | TGCATTAGCTAGTTGGTG | 63 | 229 | This study | |
| Faecal449R | AGTTACTAACGTCCTTGTTC | |||||
| Enterococcus casseliflavus | Casseli1 | CasselF | GGAGCTTGCTCCACCGAA | 60 | 132 | This study |
| CasselR | TTTCTTCCATGCGGAAAATAGT | |||||
| CasselP | 6FAM-CGAACGGGTGAGTAACACGTGGGTAA-TAMRA | |||||
| Casseli2 | Cassel190F | GGAAGAAAGTTGAAAGGC | 60 | 204 | This study | |
| Ent376R | TCGGTCAGACTTKCGTCC | |||||
| Casseli3 | Cassel190F | GGAAGAAAGTTGAAAGGC | 60 | 406 | This study | |
| Ent578R | TTAAGAAACCGCCTGCGC | |||||
| Enterococcus faecium | Faecium1 | CiumF | TTCTTTTTCCACCGGAGCTT | 60 | 141 | This study |
| CiumR | AACCATGCGGTTTYGATTG | |||||
| CiumP | 6FAM-AGTAACACGTGGGTAACCTGCCCATCAGA-TAMRA | |||||
| Faecium2 | Cium84F | TGCTCCACCGGAAAAAGA | 63 | 174 | This study | |
| Ent240R | CACCAACTAGCTAATGCA | |||||
| Faecium3 | Cium84F | TGCTCCACCGGAAAAAGA | 64 | 310 | This study | |
| Ent376R | TCGGTCAGACTTKCGTCC | |||||
| Faecium4 | Cium84F | TGCTCCACCGGAAAAAGA | 65 | 512 | This study | |
| Ent578R | TTAAGAAACCGCCTGCGC |
a
Entero1 targets the 23S rRNA gene, whereas the other assays target the 16S rRNA gene.
b
Optimum annealing temperatures determined using temperature-gradient PCR.
c
Approximate product size determined from in silico data.