B. cereus group Multi-Datatype MLST+AFLP Supercluster Reconstruction

Here is a brief description about the strategy used for reconstructing multi-gene and multi-datatype superclusters of B. cereus group isolates.

Data from the five MLST schemes and three AFLP typing studies were used to construct superclusters of genetically closely related strains. Genotyping profiles from MLEE have not been included in the computation of the superclusters because MLEE, which is based on protein profiles, has a much lower resolution power than MLST and AFLP. Isolates were grouped if they shared identical sequences at all loci of a given MLST scheme (i.e., belong to the same sequence type (ST) using 6 or 7 loci, depending on the scheme) or shared an identical AFLP profile. The grouping was done in a recursive manner. That is, if strain A had identical data to strain B based on typing method 1, and was identical to strain C based on method 2, then strains A, B, and C were grouped. All strains sharing typing data with B and all strains sharing data with C were subsequently added to the supercluster, then all strains identical to the latter strains were added, and so on until no further isolate sharing an identical MLST and AFLP profile with the strains currently in the group could be found. As a result of this procedure, every isolate of a given supercluster shares identical typing data to at least one other isolate in the group. Note also that all superclusters that were built by this procedure are mutually exclusive, i.e., a given isolate belongs to one and only one group. Although MLST and AFLP are based on different amounts of genetic information, in this analysis no weighting scheme was applied, as strains were simply treated as "identical" or "non-identical" to each other. The algorithm described above corresponds to solving connected graphs in mathematics.

Below is an example of a reconstructed multi-datatype "MLST+AFLP" supercluster. Strains sharing identical typing profiles are connected by lines colored by typing method. While strains B.cg_AH585 and B.t_HD489 share an identical AFLP profile with strain B.c_ATCC14579, each from different AFLP studies (AFLP1 and AFLP2, red lines), all other strains are identical to B.c_ATCC14579 and among them based on different MLST schemes and genes (blue lines).

Multi-Datatype Supercluster reconstruction summary picture

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