Files in this Data Supplement:

• Supplemental file 1 - Tables S1 (Primers used in this study), S2 (Sensitivity of the MTC PCR typing panel using culture thermolysates of different mycobacteria), S3 (Description of genes flanking or altered or deleted at the RD^RioM. tuberculosis s strain, organized by patient and segregated by RD^RioRio M. tuberculosis isolates from Rio de Janiero), S6 (MIRU-VNTR patterns for WT and RD^Rio M. tuberculosis isolates from Rio de Janiero), S7 (Allelic diversity of each MIRU-VNTR locus in Rio de Janiero LAM M. tuberculosis strains), S8A (Comparative review of mycobacteriological records), S8B (Comparative retrospective review of patient records), and S8C (Patient characteristics segregated by pulmonary TB caused by WT and RD^Rio M. tuberculosis strains, analyzed by multiple logistic regression) and Fig. S1A (Alignment of the coding regions of the Rv3346c and Rv3355c genes with the Rv3346/55c chimeric fusion gene that is present at the site of deletion in the RD^Rio locus), S1B (Alignment of the amino acid sequences of the hypothetical Rv3346c and Rv3355c proteins with the proposed translation product of the Rv3346/55c chimeric fusion gene), S1C (Illustration of homologous recombination between Rv3346c and Rv3355c, the proposed mechanism of deletion that derived the RD^Rio LSP), and S2 (Map showing residence locations of TB cases, segregated by WT and RD^Rio genotypes in the city of Rio de Janiero and outlying areas)
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