Figure 1.
Population structure using SNP and small indel data with tabulated larger deletions.
Clustering dendrogram constructed using R statistical software, based on a pair-wise identity. On average there are 860 SNP alleles and 64 small indels differences between any two isolates. Large deletions were identified using a consensus from paired end mapping distance or split read approaches followed by an assembly-validated strategy using Velvet software[37]. Only deletions considered informative are shown. SIT numbers were assigned in accordance in the international database SITVITWEB[41].
Figure 2.
Radial phylogram constructed using SNPs and showing clustered samples.
The best-scoring maximum likelihood phylogenetic tree was constructed using the set of 6,847 SNP sites. Support values computed from 100 bootstrap replicates provide assessment of confidence for each clade and are shown at the nodes of the tree. SNP variations within the clusters are summarised in Table 3.
Figure 3.
Episodes of tuberculosis for clustered patients.
D = Date of diagnosis of initial TB episode as self reported by patient; S = date collection of sequenced sample; Black shading = Microbiologically proven TB; Grey shading = Duration of symptoms prior to diagnosis for episode when the sequenced sample was collected, as reported by patient; Bold = strain implicated in transmission of MDR.