TABLE 1.
PCR primers used in this study
| Target region amplifieda | Primerb | bp positions in corresponding gene | Nucleotide sequence (5′-3′) |
|---|---|---|---|
| hmwA gene | hmwAF | 34-57 (hmwA1/A2) | CGCCTGAATGCTTTGGTTGCTGTG |
| hmwAR | 1055-1078 (hmwA1/A2) | CGCCGCGCTCGTCACCGCCAAGGT | |
| Variable internal fragment of hmwA genes | hmwMF | 1212-1235 (hmwA1/A2) | CGCTCAAGGTAGTGGTGATATCGC |
| hmwMR | 3150-3173 (hmwA1) | CCATCTTTAGCTGTAATCTCTGCT | |
| hmwA1 probe | hmw1AF | 1610-1633 | CCACCGGTGATGATACCAGAGGTG |
| hmw1AR | 2507-2530 | CGGCTTTCCTGGAGCCAAAGGTGA | |
| hmwA2 probe | hmw2AF | 1771-1794 | GTCGCCCAGGGCACTGTAACCATT |
| hmw2AR | 2478-2501 | CCGCCCAGAATGGATATGTTGTAG | |
| 5′ fragment from AAr96 | HI01598 AAr96R | 142-163 | GTTTAGCAAGAAAATGATCGGG |
| 1309-1327 | CCGGGTCTAACAACCACTC | ||
| AAr105 | HI01679 | 455-479 | CCGATATGATTTTACAGGCACAGGG |
| AAr105R | 1341-1358 | CGTCCAGCAGGAGCATCA | |
| G822 | HI01679 G822R | CCGATATGATTTTACAGGCACAGGG | |
| 1829-1849 | TCGCGCCACTAATGTTGTGTG | ||
| 3′ fragment from AAr96 | hmwR | 82-104/79-101 (3′ of hmwA1/ A2, respectively) | CAAGATGGGTAAAGCCCGTACTG |
| AAr96F | 3042-3062 | GGGTATTGATGTAGAGAGCTC | |
| AAr105 | hmwR AAr105F | CAAGATGGGTAAAGCCCCGTACTG | |
| 3049-3069 | GATGGAGAGAGCTCTGTTCCA | ||
| G822 | hmwR G822F | CAAGATGGGTAAAGCCCGTACTG | |
| 2989-3009 | GGCGTTGATGGGGAGAGTTCT |
a
Strain names are given to indicate those regions of hmwA that are strain specific.
b
F, forward primer; R, reverse primer.