TABLE 3.
Details of primers, SNPs, and observed migration of extension products for the Salmonella serovars under study
| Panel | Serovar (key allele) | PCR primer | Amplified product length (bp) | SNP position | Extension base variation | Extension primer sequence (5′ to 3′) | Probe size (bp) | Observed migration of extension products (LIZ-120 parameter)a |
|||
|---|---|---|---|---|---|---|---|---|---|---|---|
| A | C | T | G | ||||||||
| I | Typhimurium | F-GAA GCG TTA GTG AGC CGT CTG CG | 643 | 10 | T/C | GCAAAAACCAGATCGTTTTCCG | 22 | — | 27.3 | 29.6 | — |
| (hemD12) | R-ATC AGC GAC CTT AAT ATC TTG CCA | 48 | T/C | CTGGTTTTTGCCCTTTCACAGCACGC | 26 | — | 28.4 | 31.1 | — | ||
| 100 | G/T | CCAGCTCCAGCGGGATGGTCGAAACTGGCCTGTG | 34 | — | — | 39.3 | 35.8 | ||||
| 166 | A/G | CGCACCACGGCGCTCGCCCTTCATACCGTTAGCGGGT TCGAT | 42 | 45.7 | — | — | 44.4 | ||||
| Enteritidis (thrA11) | F-GTC ACG GTG ATC GAT CCG GT | 852 | 192 | A/G/C | GCGTAATGGTGCGAGGGTGAAG | 22 | 33.2 | NA | — | 30.6 | |
| R-CAC GAT ATT GAT ATT AGC CCG | 309 | G/A/C | GTTAAGGTTAGAGATCCCTTTAACCGGCAG | 30 | 35.4 | NA | — | 25.8 | |||
| 369 | C/A/T | AAAACACGCGCCGCCATCCCAATCATCCCTTTCATTCC | 38 | 40.2 | 40.1 | 41.60 | — | ||||
| II | Virchow (thrA14) | As above for thrA11 | As above for thrA11 | 291 | C/T/A/G | TAAGGTTAGAGATCCCTTTAACCGGCAGGTTATCATCGTCGCTGG A | 46 | NA | 48.7 | 50.78 | NA |
| 339 | A/G | CCAATCATCCCTTTCATTCCAGGGCCGGAGACGCTAAACATCGCCATGTT | 50 | 53.6 | — | — | 52.3 | ||||
| Infantis (sucA21) | F-AGC ACC GAA GAG AAA CGC TGC | 666 | 69 | C/T/G/A | CGAACTGACTGCCGCTGAAGGGCTGGAACGTTATCTGGGGGCCAAATTCCCCGG | 54 | NA | 57.52 | 60.2 | 57.5 | |
| R-GGT TGT TGA TAA CGA TAC GTA | 137 | C/T | TTCTCGCTGGAAGGGGGAGATGCTCTGGTACCCATGCTGAAAGAGATGGTTCGCCATG | 58 | — | 61.3 | NA | — | |||
| 438 | C/T | GTGAGCCCGGTGGTGATGGGCTCCGTGCGCGCCCGTCTGGACAGACTGGACGAACCGAGCAG | 62 | — | 65.5 | NA | — | ||||
| Braenderup (purE11) | F-ATG TCT TCC CGC AAT AAT CC | 510 | 81 | A/G | TCACTTGATATCCGTTCTCTTCCGCCGTTTCGGCGAAGCTGAACAGTTTATCGGGGGTGCGATG | 64 | 67.6 | — | — | 66.7 | |
| R-TCA TAG CGT CCC CCG CGG ATC | 171 | C/T | GCAGCGCTTTGTACCGGCACGCCGAGTACCGGGACCAGCGTTTTTGCCGCAATCATTCCCGGCAGGTG | 68 | — | 68.8 | 69.90 | — | |||
| 360 | C/G | CATTCCGGTGGGTACGCTGGCGATCGGTAAAGCCGGTGCCGCTAACGCCGCCCTGCTCGCCGCGCAGATTCT | 72 | — | 75.17 | — | 74.3 | ||||
a
NA, extension products corresponding to these loci were not included among the study collection; —, nucleotides not covered by extension primers.