Flow chart of patients recruited to the study.

<p>¹Referral based on cough >2weeks, FTT, history of contact with a TB case and a TST ≥10 mm at study closure ²Abnormal CXR; MTB positive by the Hain MTB test or Roche test. ³Abnormal CXR; culture negative for MTB. ⁴Normal CXR; culture positive for NTM and ⁵Normal CXR; culture negative for MTB and NTM. Abbreviations: FTT – failure to thrive; CVW- case verification ward; CXR – chest X-ray; TST - tuberculin skin test; QFTGIT – QuantiFERON Gold In-tube test; dcRT-MLPA – dual colour reverse transcriptase – multiplex ligation dependent probe amplification; MTB – <i>Mycobacterium tuberculosis</i>; NTM – non-tuberculous mycobacteria.</p

Peripheral blood gene expression as a function of PPD-IFN-γ-ELISPOT response in the clinical groups.

<p>(A) <i>TNFR1</i>, (B) <i>TNFR2</i>, (C) <i>FLIPs</i>, (D) <i>FLICE</i>. ELISPOT positivity was defined as described in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061154#s2" target="_blank">Materials and Methods</a>. The data shown are the median and ranges of mRNA levels normalized and expressed as the number of copies per 10⁵ copies of mRNA for the housekeeping gene, <i>HuPO</i>. Significant differences in gene expression between clinical groups are indicated.</p

Comparison of peripheral blood gene expression in the contacts and controls after 3 months of follow-up.

<p>Expression on inclusion in the study (M0) and after 3 months of follow-up (M3) for (A) <i>TNFR1</i>, (B) <i>TNFR2</i>, (C) <i>FLIPs</i> and (D) FLICE. The data shown are the median and ranges for mRNA levels normalized and expressed as the number of copies per 10⁵ copies of the mRNA for the housekeeping gene, <i>HuPO</i>. Mann-Whitney U tests were used for the pairwise comparison of groups. Significant differences between the testing periods are shown. HC: household contact, CC: community control.</p

Peripheral blood gene expression as a function of ESAT-6 ELISPOT response in the clinical groups.

<p>(A) <i>TNFR1</i>, (B) <i>TNFR2</i>, (C) <i>FLIPs</i>, (D) <i>FLICE</i>. The data shown are the median and ranges of mRNA levels normalized and expressed as a number of copies per 10⁵ copies of mRNA for the housekeeping gene, <i>HuPO</i>. Significant differences in gene expression between clinical groups are indicated.</p

Intergroup comparisons of the major clinical parameters.

a<p>Median (25th-75th interquartiles);</p>b<p>numbers (percentages);</p>*<p>out of 6 subjects instead of 7;</p>**<p>no interquartile available as the number of subjects in group C was too small.</p

Baseline characteristics of 210 children.

<p>Abbreviations: CXR-Chest X-ray; TST- tuberculin skin test; QFTGIT- QuantiFERON In-tube TB Gold test; IS-Induced sputum; GA-gastric aspirates; MTB- <i>Mycobacterium tuberculosis</i>; NTM-non-tuberculous mycobacteria.</p><p>Baseline characteristics of 210 children.</p

Dot-plot graph depicting genes and proteins that are differentially expressed between the three clinical groups: TB disease, NTM present and controls.

<p>(A) The median with inter quartile range relative gene expression (log 2 transformed) of genes from peripheral blood. (B) The median concentration (pg/mL) of cytokines in the QFTGIT supernatants of whole blood without stimulation. (C) The median concentration (pg/mL) of cytokines in the QFTGIT supernatants after stimulation of whole blood with <i>M. tuberculosis</i> antigens. p-value<0.05 (*), <0.01 (**), <0.001 (***) were considered to be significant; NS - not significant.</p

Dot-plot graph depicting genes and proteins that are differentially expressed between the three clinical groups: TB disease, NTM present and controls (defined as MTB, NTM uninfected children and negative for TST and QFTGIT).

<p>(A) The median with inter quartile range relative gene expression (log 2 transformed) of genes from peripheral blood. (B) The median concentration (pg/mL) of cytokines in the QFTGIT supernatants after stimulation of whole blood with <i>M. tuberculosis</i> antigens. p-value<0.05 (*), <0.01 (**), <0.001 (***) were considered to be significant.</p

Blood expression of apoptotic genes as a function of TST response in the clinical groups.

<p>(A) <i>TNFR1</i>, (B) <i>TNFR2</i>, (C) <i>FLIPs</i>, (D) <i>FLICE</i>. TST positivity was defined as an induration >5 mm in diameter. Neg, TST induration <5 mm, Pos, TST induration ≥5 mm in diameter. The data shown are the median and ranges of mRNA levels normalized and expressed as a number of copies per 10⁵ copies of mRNA for the housekeeping gene, <i>HuPO</i>. Significant differences in gene expression between clinical groups are shown.</p

Peripheral blood cell proportions as a function of clinical status group.

<p>(A) Monocytes, (B) neutrophils and (C) lymphocytes. The data shown are the mean+SD of cell percentage. NI-CC = Non infected community control (CC with TST induration<5 mm), i-hHC = infected household contact (TST induration ≥14 mm), sHC = household contact that developed TB symptoms, IC = index TB case. Significant differences in gene expression between clinical groups are indicated.</p