Shared-type and lineage/sub-lineage distribution of 65 <i>M. tuberculosis</i> isolates from New Delhi, India.

<p>Shared-type and lineage/sub-lineage distribution of 65 <i>M. tuberculosis</i> isolates from New Delhi, India.</p

Primers used for the analysis of single nucleotide polymorphisms in 65 <i>M. tuberculosis</i> isolates from New Delhi, India.

<p>Primers used for the analysis of single nucleotide polymorphisms in 65 <i>M. tuberculosis</i> isolates from New Delhi, India.</p

Diversity of 65 <i>M. tuberculosis</i> isolates from New Delhi, India deduced from MIRU-VNTR, spoligotyping and single nucleotide polymorphism analyses.

<p>MIRU-VNTR clusters that could be discriminated by spoligotyping are highlighted in blue and clusters that could be discriminated based on mutations in the <i>katG</i>, <i>rpoB</i> and/or <i>embB</i> genes are highlighted in yellow. Clusters that could not be discriminated using a combination of all markers are highlighted in green. The dendrogram was produced following Pearson correlation and unweighted pair group method with arithmetic average analysis.</p

Number of single nucleotide polymorphisms observed for the 6 regions of interest in 65 <i>M. tuberculosis</i> isolates from New Delhi, India.

<p>Number of single nucleotide polymorphisms observed for the 6 regions of interest in 65 <i>M. tuberculosis</i> isolates from New Delhi, India.</p

Flowchart depicting conduct of baseline and two-step tuberculin testing.

<p>Flowchart depicting conduct of baseline and two-step tuberculin testing.</p

Regions chosen for PCR verification based on the CGH array analysis.

<p>The dendogram based on CGH array analysis of 22 <i>M. tuberculosis</i> isolates from Myanmar (11 Beijing, 4 ST42, 2 ST89 and 5 previously unreported [UR] shared-types [ST]) was produced by weighted pair group method (WPGMA) clustering using a Pearson correlation based distance measure defined on regional z-score values, corresponding to P-values between 1e-3 and 1e-16. The green color indicates extra regions that are present in the clinical isolates, but not in the reference strain <i>M. tuberculosis</i> H37Rv, whereas the red color depicts deletions in the clinical isolates compared to the reference strain <i>M. tuberculosis</i> H37Rv.</p

Gene graph of the <i>M.tuberculosis</i> H37Rv <i>1754c-1765c, Mb1785-1787</i>, <i>MT1808</i> and <i>MT1812-1813</i> regions.

<p>The graph is based on region z-scores, with each line representing one isolate analyzed by CGH. Region z-scores of more than ±4.42 (absolute value) occurring in one or more samples, corresponding to a standard normal P-value of 0.00001 (1e-5) indicate deletions (above the 0-line) or extra regions (below 0-line). Red lines represent isolates of the Beijing lineage, green lines; ST42 lineage and blue lines; non-Beijing isolates other than ST42.</p

The relationship between the cytokine-producing CD4+CD45RO+ T cells and the QuantiFERON Gold In-Tube (QFT) response at baseline.

<p>The relationship between the absolute frequencies of (<b>A</b>) all IFNγ-producing and (<b>B</b>) polyfunctional (IFNγ, IL2 and TNFα) PPD-specific CD4+CD45RO+ T cells and the magnitude of the QFT response are shown. The relationship between the absolute frequencies of cytokine-producing T-cells in response to SEB is shown for comparison (<b>C and D</b>). Statistical analyses were performed by Spearman’s correlation coefficient (rho).</p

Primers used for the PCR verification of deleted and extra regions as observed by CGH analysis.

*<p>:<a href="http://xrl.us/6cg3" target="_blank">http://xrl.us/6cg3</a></p><p>The annealing temperature for each primer set and the expected PCR product size based on the published sequences of <i>M. tuberculosis</i> H37Rv, <i>M. bovis</i> AF22197 or <i>M. tuberculosis</i> CDC1551 are also provided.</p

Genetic diversity among 22 <i>Mycobacterium tuberculosis</i> isolates tested by CGH.

<p>The dendogram was produced by weighted pair group method (WPGMA) clustering using a Pearson correlation based distance measure defined on regional z-score values. The red color indicates deletions in the clinical isolates compared to the reference strain <i>M. tuberculosis</i> H37Rv, whereas the green color shows extra regions in the clinical isolates not present in the reference strain <i>M. tuberculosis</i> H37Rv.</p