Molecular and microscopy results for the 11 isolates with MTBC and other organisms.

<p>Molecular and microscopy results for the 11 isolates with MTBC and other organisms.</p

Timeline (months) and characteristics of the patients involved in the outbreak.

<p>The epidemiological links are shown with arrows. *Chest radiograph showing cavitation. †Positive sputum smear examination. ‡Laryngeal tuberculosis.</p

SNP-based network.

<p>The letters inside the circles correspond to the patients; SNP correspond to the number of the SNP observed in the <i>M. tuberculosis</i> isolate and described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058235#pone-0058235-t001" target="_blank">Table 1</a>; lines represent links based on the SNPs and arrows show the sequential SNP acquisition. WT refers to the genotype of A1. *Mutations predicted to affect the protein according to SIFT. †Culture negative or not performed.</p

Characteristics of the SNPs observed among the nine <i>M. tuberculosis</i> isolates.

*<p>By Himar1-based transposon mutagenesis in H37Rv strain culture in vitro <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058235#pone.0058235-Sassetti1" target="_blank">[27]</a>.</p>†<p>The first value is based on the SIFT prediction using the 13 non-<i>M. tuberculosis</i> complex genomes and the second value is based on the SWISS-PROT & TrEMBL sequence database.</p

Fournier-Leveletal_DataSEM

Input file and R scripts used to perform the SEM analysis

Fournier-Leveletal_DataQTLMapping

Input for the QTL mapping performed using the MCQTL software (Jourjon et al.,2006