Home page > Bacillus anthracis > Archived, 2013 version of Bacillus anthracis MLVA database

Archived, 2013 version of Bacillus anthracis MLVA database

Warning added june 2016: this article is valid for the database hosted at http://mlva.u-psud.fr last updated in 2013. We strongly recommend the use of the database hosted at http://microbesgenotyping.i2bc.paris-saclay.fr. In particular the coding convention has been modified for vrrA (minus 6), vrrB1 (plus 4) and vrrB2 (plus seven) in 2014 for reasons given in Thierry et al. PlosOne 2014. The 2013 version does not take into account these changes.

The Bacillus anthracis MLVA database presents published genotyping data compiled from the litterature. While we have done our best to harmonize the typing conventions, the database is provided as is.

The cooperative database format allows to aggregate multiple independant databases, including B_anthracis_CG (derived from in silico analysis of complete genome sequence data), B_anthracis_2000_2011 presenting published data up to year 2011, B_anthracis_2012 presenting data published in 2012.

Two categories of data are included, MLVA data derived from the analysis of variable number of tandem repeats (VNTRs), and single nucleotide polymorphisms (SNPs).

Data from one collection of 13 SNPs is presented, canSNP13 set-up by van Ert et al., 2007, comprising 13 SNPs.

A number of MLVA panels are defined in the database, selected among 31 VNTR loci:

MLVA8Keim2000, MLVA15vanErt2007, MLVA25Lista2006, MLVA31Beyer2012.

The typing convention for each of the 31 loci is summarized in the list below:

vrrA_12bp_10U

vrrB1_9bp_16U

vrrB2_9bp_6U

vrrC1_9bp_53U

vrrC2_18bp_17U

CG3_5bp_2U

pXO1_aat_3bp_7U

pXO2_at_2bp_10U

Bavntr12_2bp_6U

Bavntr16_8bp_20U

Bavntr17_8bp_4U

Bavntr19_3bp_4U

Bavntr23_12bp_4U

BAMS01 (alias Bavntr32)_21bp_16U

Bavntr35_6bp_5U

BAMS03_15bp_26U

BAMS05_39bp_5U

BAMS13_9bp_70U

BAMS15_9bp_24U

BAMS21_45bp_10U

BAMS22_36bp_16U

BAMS23_42bp_11U

BAMS24_42bp_11U

BAMS25_15bp_13U

BAMS28_24bp_14U

BAMS30_9bp_57U

BAMS31_9bp_64U

BAMS34_39bp_11U

BAMS44_39bp_8U

BAMS51_45bp_9U

BAMS53_12bp_8U

This list indicates for each locus the repeat unit size and the corresponding repeat copy number in the Ames ancestor sequenced genome refseq NC_007530 (chromosome), NC_007322 and NC_007323 (two plasmids, containing the four loci pXO1, pXO2, VNTR16 and VNTR17).

It is important to keep in mind that this copy number is a convention. The "true" repeat copy number at a given locus may be 4.5, 5.5 etc. A convention is a decision on how to round up such values. The convention has no impact on data quality, only the same convention needs to be applied before merging data sets produced by different groups. Also different groups might want to use different primers, for good reasons such as PCR multiplexing. This is likely to change the expected PCR product size, but should not change the corresponding repeat copy number.

The source for each data is indicated in the database in the "publication" column, further inquiries should be sent to the corresponding author of the associated publication ("contact" column).

See online : the former cooperative Bacillus anthracis genotype database