TABLE 3.
Primer pairs developed in this study and variability of the different loci
| Name | Directiona | Primer sequence (5′–3′) | Amplicon size (bp) | MLST locus location | No. of alleles | No. of polymorphic sites | % polymorphic sites | Avg G+C content (%) | Hunter-Gaston diversity indexb | 95% confidence interval |
|---|---|---|---|---|---|---|---|---|---|---|
| ppa | F | CGCTGACCAAGCCTTTCTAC | 256 | 192–440 | 2 | 1 | 0.39 | 38.4 | 0.501 | 0.470–0.533 |
| R | CACTCCAAACTTTGCACTCCC | |||||||||
| pgm | F | AGCACCTTGCACGATGAAGA | 1,072 | 456–1652 | 3 | 10 | 0.93 | 43.7 | 0.620 | 0.566–0.674 |
| R | CCTGCGCCTTCGTTAATTGG | |||||||||
| gyrB | F | TTGTCCCGGACTTTACCGTG | 429 | 524–952 | 2 | 2 | 0.47 | 39.9 | 0.505 | 0.482–0.528 |
| R | TGTTTTCGACAGCAAAGCGG | |||||||||
| gmk | F | GAGCGGTGTTGGCAAAAGTA | 394 | 189–582 | 2 | 1 | 0.25 | 40.1 | 0.505 | 0.482–0.528 |
| R | TGCATCCTCGTCATTACGCTT | |||||||||
| glyA | F | CAGAGAACTATGTGAGTAGGGACA | 676 | 74–749 | 3 | 2 | 0.30 | 45.6 | 0.560 | 0.493–0.627 |
| R | TGACAACCCGGAAAGACACC | |||||||||
| atpA | F | GTCGCTGATGGCATTGCTAAG | 796 | 100–895 | 4 | 3 | 0.38 | 44.8 | 0.557 | 0.502–0.612 |
| R | CCAGTAAACGCGAGTGCAAG | |||||||||
| arcC | F | CCCCATCAAGCCGTGTACTT | 570 | 304–873 | 2 | 1 | 0.18 | 45.5 | 0.069 | 0.000–0.158 |
| R | TTGGGCAATAATGGCCGTCT | |||||||||
| adk | F | GTAGCCAACACCACCGGATT | 473 | 70–542 | 4 | 3 | 0.63 | 47.5 | 0.199 | 0.063–0.335 |
| R | ACGGTGTCTTCGTAAAGCGT |
a
F, forward; R, reverse.
b
Hunter-Gaston diversity index (DI) ranges from 0.0 for no diversity to 1.0 for complete diversity.