FIG 1 .

Genetic and genomic comparisons of the African B. pseudomallei isolates with global B. pseudomallei reference strains. (A) Maximum-parsimony phylogeny of 144 B. pseudomallei genomes. This tree was drawn by using 202,245 core genome, orthologous, bi-allelic SNPs identified by the SPANDx pipeline (75) and rooted by using MSHR0668. Isolates are color coded by origin as follows: Australia, red; Papua New Guinea, green; Asia, blue; Africa (including Madagascar), pink; South America, gold. African and South American isolates form their own clade that falls within the more ancestral Asian clade, which is separate from Australasian B. pseudomallei. Bootstrap values were generated on the basis of 200 replicates. The consistency index is 0.19. (B) Distribution of ITS types by geographic region. Similarly to earlier studies, isolates from Africa and the Americas show an overrepresentation of ITS type G in comparison to strains from Australasia and Asia; however, African isolates also possess ITS types CE and C, alleles that are commonly identified in isolates from regions of Asia and Australasia where B. pseudomallei is hyperendemic.