Primers used for MLST of Neisseria

Genes

The neisserial MLST scheme uses internal fragments of the following seven house-keeping genes:

abcZ (putative ABC transporter)
adk (adenylate kinase)
aroE (shikimate dehydrogenase)
fumC (fumarate hydratase)
gdh (glucose-6-phosphate dehydrogenase)
pdhC (pyruvate dehydrogenase subunit)
pgm (phosphoglucomutase)

PCR Amplification

Please note: These are new primer sequences (added 10 October 2003).  Amplification primers, with the exception of those for pgm, were designed by A. Birtles at the Meningococcal Reference Unit, Health Protection Agency, UK.

The primer pairs we use for the PCR amplification of internal fragments of these genes are:

abcZ-P1C 5-TGTTCCGCTTCGACTGCCAAC-3
abcZ-P2C 5-TCCCCGTCGTAAAAAACAATC-3

adk-P1B 5-CCAAGCCGTGTAGAATCGTAAACC-3
adk-P2B 5-TGCCCAATGCGCCCAATAC-3

aroE-P1B 5-TTTGAAACAGGCGGTTGCGG-3
aroE-P2B 5-CAGCGGTAATCCAGTGCGAC-3

fumC-P1B 5-TCCCCGCCGTAAAAGCCCTG-3
fumC-P2B 5-GCCCGTCAGCAAGCCCAAC-3

gdh-P1B 5-CTGCCCCCGGGGTTTTCATCT-3
gdh-P2B 5-TGTTGCGCGTTATTTCAAAGAAGG-3

pdhC-P1B 5-CCGGCCGTACGACGCTGAAC-3
pdhC-P2B 5-GATGTCGGAATGGGGCAAACA-3

pgm-P1 5'-CTTCAAAGCCTACGACATCCG-3' 
pgm-P2 5'-CGGATTGCTTTCGATGACGGC-3'

Sequencing

We use the following primer pairs for sequencing:

abcZ-S1A (P1A) 5'-AATCGTTTATGTACCGCAGR-3'
abcZ-S2 5'-GAGAACGAGCCGGGATAGGA-3'

adk-S1A 5'-AGGCWGGCACGCCCTTGG-3'
adk-S2 5'-CAATACTTCGGCTTTCACGG-3'

aroE-S1A 5-GCGGTCAAYACGCTGRTK-3 
aroE-S2 5-ATGATGTTGCCGTACACATA-3

fumC-S1 5-TCCGGCTTGCCGTTTGTCAG-3
fumC-S2 5-TTGTAGGCGGTTTTGGCGAC-3

gdh-S3 5'-CCTTGGCAAAGAAAGCCTGC-3'
gdh-S4C 5-RCGCACGGATTCATRYGG-3

pdhC-S1 5'-TCTACTACATCACCCTGATG-3'
pdhC-S2 5'-ATCGGCTTTGATGCCGTATTT-3'

pgm-S1 5'-CGGCGATGCCGACCGCTTGG-3'
pgm-S2A 5'-GGTGATGATTTCGGTYGCRCC-3'