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Figure 1. Unifying phylogeny for Mycobacterium tuberculosis.
A) Maximum parsimony tree of M. tuberculosis and M. bovis
based on 37 silent single-nucleotide polymorphisms in 225 isolates. Synonymous
sequence types (SST) are marked 1–35. The frequency of each SST is marked
in parentheses. The nodes of the major lineages are highlighted: lineage
I (cyan), lineage II (red), lineage III (blue), lineage IV (yellow), and
M. bovis (green). The colors correspond to those in Figure
2. Note both M. africanum Type I isolates sequenced were SST
1. B) Schematic representation of the genetic groups 1, 2, and 3 defined
by the katG-gyrA scheme. C) Schematic representation of the presence
or absence of the tuberculosis specific region of difference, TbD1. D)
Schematic representation of the strain families Beijing, Haarlem, Africa,
Delhi, East Africa-India (EA-I), and Latin America-Mediterranean (LA-M),
previously described by IS6110 restriction fragment length polymorphism
typing and spoligotyping, demonstrating concordance with the phylogenetic
tree. E) Spoligotyping patterns for representative isolates of each lineage
demonstrating lack of probe hybridization at spacers 1–34 in lineage I,
33–36 in lineage II, 4–7 and 23–24 in lineage III, 29–32 and 34 in lineage
IV, and 39–43 in M. bovis.
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