TABLE 3.
Multiplex PCR for detection of the five prophages harbored by S. enterica serovar Typhimurium DT104 (NCTC 13348) and SGI1
| Primer | Sequence (5′-3′) | Genome coordinates of product (DT104 [NCTC13348]) | Product size (bp) | Target |
|---|---|---|---|---|
| P1For | CGGAAGAGCTGGATAACGAGTTTCTG | 365087-367366 | 2,179 | Prophage 1/ST104 |
| P1Rev | GCGAATTATGTTCCGGGAGTATGAC | |||
| P2For | TCACAAGCAATGCGTGGTGTGCAAC | 381790-382891 | 1,101 | Prophage 1/ST104 |
| P2Rev | GCAGCACGAACACATGACATTACTAG | |||
| P3For | GGTGAAACGCGCATTGGCATAGAAG | 406501-407203 | 702 | Prophage 1/ST104 |
| P3Rev | ACGCGGGTAGGATCAGAGTACATAG | |||
| P4For | GCAGTACGAACCGTACCCGATACAG | 1111820-1112670 | 850 | Prophage 2 |
| P4Rev | CAGTCCGTCACGCCATGCTCAAACT | |||
| P5For | GCTTTCTCGTAACGCCTGCGATTTT | 1953476-1954662 | 1,186 | Prophage 3 |
| P5Rev | CGAATTTATTGGGGCAGGTGATGCG | |||
| P6For | TGAAGGCTCTCAGCATATCACCCGTA | 1965128-1965939 | 811 | Prophage 3 |
| P6Rev | ATCCACTGCCGAACGTTATCGTGGT | |||
| P7For | AATAGCCCGACCGGGAATATTCATC | 1995172-1995776 | 604 | Prophage 3 |
| P7Rev | GCTTTGTGATCCATCCAATAGCTGAC | |||
| P8For | ATGCTGACGGAAGCGTTCGGGATT | 2129791-2128102 | 1,689 | Prophage 4 |
| P8Rev | GATGCGTGGAGATCAGCTTATGCA | |||
| P9For | TAATACCGCGCTCACGCTCAAGATC | 2796632-2797808 | 1,176 | Prophage 5 |
| P9Rev | CTATAACAGTACCGGGAACTGTTCG | |||
| P10For | CTGGCGCTTAGTCATGTCGGTAATT | 2827013-2827557 | 544 | Prophage 5 |
| P10Rev | ACGTTTGGTAAACGCCTTACGCCTT | |||
| P11For | AGTGAAGTAAACGGTCACTCACTGG | 4083151-4083812 | 661 | SGI1 |
| P11Rev | ATTGTGCTGACGCTCTGCTTGTGTC | |||
| P12For | CAACTTCCGTAAGTTCAGCTACAGC | 4096995-4097976 | 981 | SGI1 |
| P12Rev | TAGCTCTATCCAGCAATGCGGATTG | |||
| P13For | AATTAGTCGGGCTACTTGCATTTGCT | 4129495-4129852 | 357 | SGI1 |
| P13Rev | ACTTATCTACAGCGTTCTGTCTGCC |