TABLE 1.
Primer sequences used in this study
| Primer type and serogroup specificity | Amplicon size (bp) | Primer name | Multiplex assay | Sequence (5′→3′) | Reference |
|---|---|---|---|---|---|
| Serogroup-specific capsule biosynthesis gene primers | |||||
| A | 400 | orf-2 F | First | CGCAATAGGTGTATATATTCTTCC | 29 |
| orf-2 R | First | CGTAATAGTTTCGTATGCCTTCTT | 29 | ||
| B | 170 | siaD BF | First | TGCATGTCCCCTTTCCTGA | 13 |
| siaD BRa | First | AATGGGGTAGCGTTGACTAACAA | 13 | ||
| C | 442 | siaD CFa | First | GCACATTCAGGCGGGATTAG | 13 |
| siaD CR | First | TCTCTTGTTGGGCTGTATGGTGTA | 13 | ||
| Y | 330 | siaD YF | First | CATCTCAAAGCGAAGGCTTTGG | This study |
| siaD YWR | First | TTGGAATTCGTCCAATTCTTTTCG | This study | ||
| W135b | 300 | siaD W135F | First | GGTGTATGATATTCCAATCGTTGTA | This study |
| ctrA primersc | |||||
| B, C, H, W135, Y | 89 | ctrA 1F | First | TTGTGTGGAAGTTTAATTGTAGGATGC | 13 |
| ctrA 1R | First | CAGCTTGTTGCCCTAAAGAGACA | 13 | ||
| A, B, C, 29E, H, W135, X, Y, Z | 110 | ctrA UF | First and second | GCTGCGGTAGGTGGTTCAA | 6 |
| ctrA UR | Second | TTGTCGCGGATTTGCAACTA | 6 | ||
| Other serogroup-specific primers | |||||
| X | 525 | Sg XF3 | First | GTCTTTGTATAAGGCCCAAG | 1 |
| 29E | 667 | Sg 29EF2 | Second | ATTACGCTGACGGCATGTGGA | 1 |
| Z | 667 | Sg ZF | Individual (with ctrA UR) | TATGCGGTGCTGTTCGCTATG | 1 |
| H | 1,363 | Sg H ctrAF | Individual | GTTGAAATAGTCACGAAAGAA | 27 |
| ctrA rev 01 | Individual | GCTCAGACATCTTAATTACTC | 27 | ||
| N. meningitidis-specific primers | |||||
| A, B, C, 29E, H, W135, X, Y, Z, NG | 251 | porA 2F | First | GCGGTTTTGCCGGGAACTAT | This study |
| porA 15R | First | AGTGGCGGCAATTTCGGTCGTACT | 11 | ||
| Nongroupable isolate-specific primers | |||||
| cnl-3/cnl-1 liked,e,F | 432 | HC344 | Second | GGATTGGACGAGCGAGAC | 5 |
| GH26R | Second | GGTCGTCTGAAAGCTTGCCTTGCTC | 5 | ||
| cnl-1 liked | 103 | IGS F | Second | TGCCTCCGTGATGCCGTCTG | This study |
| cnl-3/cnl-1 likee | IGS R | Second | CCTTTCAGATTGTATCGTGC | This study |
a
Amplification with siaD BR and siaD CF generates a serogroup C-specific 104-bp band.
b
Amplification with siaD W135F and siaD YWR generates the 300-bp serogroup W135-specific product.
c
Readthrough amplification with ctrA 1F and ctrA UF generates a 678-bp ctrA gene product in serogroup B, C, W135, and Y isolates.
d
Readthrough amplification with HC344 and IGS F generates an NG cnl-1-like-specific 179-bp product.
e
Readthrough amplification with GH26R and IGS R generates a 377-bp product in both NG cnl-3-like and NG cnl-1-like isolates, but this is predominantly observed in NG cnl-3 isolates.
f
Readthrough amplification with HC344 and GH26R generates a 432-bp product in both NG cnl-3-like and NG cnl-1-like isolates.