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Primers used for MLST of Bacillus Genes

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

glpF (glycerol uptake facilitator protein)
gmk (guanylate kinase, putative)
ilvD (dihydroxy-acid dehydratase)
pta (phosphate acetyltransferase)
pur (phosphoribosylaminoimidazolecarboxamide)
pycA (pyruvate carboxylase)
tpi (triosephosphate isomerase)

PCR Amplification

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

Gene Forward primer 5'-3' sequence Reverse primer 5'-3' sequence Annealing temp. ÂșC
glpF GCG TTT GTG CTG GTG TAA GT CTG CAA TCG GAA GGA AGA AG 59
gmk ATT TAA GTG AGG AAG GGT AGG GCA ATG TTC ACC AAC CAC AA 56
*gmk_F3 GAG AAG TAG AAG AGG ATT GCT CAT C 55
ilvD CGG GGC AAA CAT TAA GAG AA GGT TCT GGT CGT TTC CAT TC 58
**IlvD_2 AGA TCG TAT TAC TGC TAC GG GTT ACC ATT TGT GCA TAA CGC 58
***ilv4F GCA GAG ATT AAA GAT AAG GA 50
pta GCA GAG CGT TTA GCA AAA GAA TGC AAT GCG AGT TGC TTC TA 56
pur CTG CTG CGA AAA ATC ACA AA CTC ACG ATT CGC TGC AAT AA 56
pycA GCG TTA GGT GGA AAC GAA AG CGC GTC CAA GTT TAT GGA AT 57
tpi GCC CAG TAG CAC TTA GCG AC CCG AAA CCG TCA AGA ATG AT 58

* Alternative primer for gmk, courtesy of Katie Wheeler (Children's Hospital Oakland Research Institute, CA, USA).
** Alternative primers for ilvD (used for Bacillus cereus emetic toxin producing strains).
*** Alternative primer for ilv. Used with ilvD_2 reverse primer, works with most cereus and thuringiensis strains, including pseudomycoides and the emetic strains.x

Sequencing

We use the same primer pairs for sequencing.

Citing the database

The preferred format for citing this website in publications is:

This publication made use of the Bacillus cereus Multi Locus Sequence Typing website (https://pubmlst.org/ bcereus/) developed by Keith Jolley and sited at the University of Oxford (Jolley & Maiden 2010, BMC Bioinformatics, 11:595). The development of this site has been funded by the Wellcome Trust.

Related databases

University of Oslo

Status

Sequence database
Sequences: 1587
Profiles (MLST): 1351
Last updated: 2017-05-24

Isolate database
Isolates: 2116
Last updated: 2017-06-20