Representative spoligotyping patterns of ST 01, 02 and 04, and their associated clades. Dark squares indicate the presence of the spacer, and white squares indicate its absence (loss of spacers by a deletion mechanism). Unless they show some similarities (common absence of spacers 1–24) the three genotypes ST 01, 02 and 04 are from different families, i.e. Haarlem (absence of spacer 31 and spacers 33–36), LAM (absence of spacers 21–24 and spacers 33–36) and Beijing clades (absence of spacers 1–34) respectively. This illustrates that computation of distances on some types (for Minimum Spanning Tree construction) may be misleading.