Discrepant results for standard loci across two centres.

<p>Discrepant results for standard loci across two centres.</p

Agreement of SLD testing in different laboratories in phase I and phase II of the “Baltic-Nordic TB-Laboratory Network” study.

<p>PAS, p-amino salicylic acid.</p

Sizes of PCR fragments determined by the QiaXcel system.

<p>A–Standard loci. B–Hypervariable loci.</p

Combined agreement rates between QiaXcel and reference methods.

<p>Combined agreement rates between QiaXcel and reference methods.</p

Intra-host diversity.

<p>(a) Graph illustrating SNP distance between pairs of patient isolates. (b) MST of 27 individual colonies isolated from a single sputum specimen.</p

Outbreak diversity.

<p>(a) MST of 344 isolates from individual patients. Colour coding of nodes indicates the year of isolation. Each isolate is represented by a separate segment, except for the central major clone, where the number of isolates from each time period is given. (b) Histogram illustrating pairwise SNP distances between isolates. (c) Graph showing date of specimen collection against its SNP distance from the major clone.</p

Drug resistance and compensatory mutations in poly-resistant isolates^a.

<p>Drug resistance and compensatory mutations in poly-resistant isolates<a href="http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.1002137#t001fn001" target="_blank">^a</a>.</p

Interlaboratory agreement rates.

<p>Hypervariable loci shown in red colour. In cases where results from both laboratories were incorrect, these values were not included in discrepancies.</p

Discrepant results for hypervariable loci.

<p>Discrepant results for hypervariable loci.</p

Allele heterogeneity associated with clustered MDR cases.

<p>Maximum likelihood tree of the phylogenetic clade containing isolates with the RpoB V170F substitution. The isolate from P052 in 2001 belongs to the major clone. Isolates from the same patient are highlighted, and those with a rifampicin-resistant phenotype are in red font. For each of the five SNPs that are shared by isolates in the clade, histograms illustrate the proportion of reads that match the mutated allele (dark coloured). Additional mutations within RpoABC are also shown on tree branches.</p