โ Maintenance: A BIGSdb-Pasteur maintenance is scheduled on Friday, July 04th and Saturday, July 05th. All services will be offline until late in the evening (Central European Time). During this period, the server and API will be unavailable. Please note that job submission not be available and all unfinished jobs will be killed. Sorry for any inconvenience. If any questions, contact us
Data access policy note: since January 1st, 2025, registration and authentication are mandatory to access all data curated after this date, either via the web interface or via the application programming interface (API authentication help link). Please contact us if you have any questions.
Primers used for MLST ofย Bordetella
Genes
The Bordetella MLST scheme uses internal fragments of the following seven housekeeping genes:
adk (Adenylate kinase)
fumC (fumarate hydratase class II)
glyA (serine hydroxymethyltransferase)
tyrB (aromatic amino-acid aminotransferase)
icd (isocitrate dehyrogenase)
pepA (cytosol aminopeptidase)
pgm (phosphoglucomutase)
PCR amplification
The PCR conditions were optimized using HotStar Taq mastermix (Qiagen) and 1M betaine final concentration. The cycling conditions were as follows:
- 1 cycle:
- 95ยฐC for 15 min
- 30 cycles:
- 95ยฐC for 30 s
- 54ยฐC for 30 s
- 1 cycle:
- 72ยฐC for 1 min
Allele templates
Gene | Direction | Primer Sequence |
---|---|---|
adk | F | AGCCGCCTTTCTCACCCAACACT |
R | TGGGCCCAGGACGAGTAGT | |
fumC | F | CGTGAACCGGGGCCAGTCGTC |
R | GGCCAGCCAGCGCACATCGTT | |
glyA | F | CAACCAGGGCGTGTACATGGC |
R | CCGCGATGACGTGCATCAG | |
tyrB | F | CGAGACCTACGCTTATTACGAT |
R | TGCCGGCCAGTTCATTTT | |
icd | F | CTGGTCCACAAGGGCAACAT |
R | ACACCTGGGTGGCGCCTTC | |
pepA | F | CGCCCCAGGTTGAAGAAAATCGTC |
R | ATCAGGCCCACCACATCCAG | |
pgm | F | CGCCCATGTCACCAGCACCGA |
R | CGCCGTCTATCGTAACCAG |