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Visualization of mid IS6110 orientation: blue for wild type (as in reference H37Rv) or for unknown orientation; red for inverse orientation (see Table 1). DR plus flanking sequences were aligned to DR and flanking regions of reference template H37Rv. Sequences were from Mycobacterium tuberculosis NGS read sets generated in this study (patients A, B, and C corrected by manual PCR; and T3_Eth), on-line resources of read sets, mapped on H37Rv NC_000962.3, and on-line resources of complete chromosome sequences. (PPT 481 kb)

MIRU-VNTR loci and octal spoligotypes. Samples: A-B-C&T3_Eth. Controls: 0486â 12 Beijing clinical isolate, ECDCPT 21&25 EAI, reference H37Rv, Pasteur BCGP2. (DOCX 19 kb)

MIRU-VNTR loci and octal spoligotypes. Samples: A-B-C&T3_Eth. Controls: 0486â 12 Beijing clinical isolate, ECDCPT 21&25 EAI, reference H37Rv, Pasteur BCGP2. (DOCX 19 kb)

Mutations of cas1 shared by MTBC T3_Eth strains and by Proto-Beijing strains. (PPTX 2956 kb)

Location of CRISPR-flanking genes and mid-CRISPR IS6110 mobile element used for primer choices and alignments. (DOCX 17 kb)

Visualization of mid IS6110 orientation: blue for wild type (as in reference H37Rv) or for unknown orientation; red for inverse orientation (see Table 1). DR plus flanking sequences were aligned to DR and flanking regions of reference template H37Rv. Sequences were from Mycobacterium tuberculosis NGS read sets generated in this study (patients A, B, and C corrected by manual PCR; and T3_Eth), on-line resources of read sets, mapped on H37Rv NC_000962.3, and on-line resources of complete chromosome sequences. (PPT 481 kb)

Primers employed for PCR verification of deletions of CRISPR/DR and flanking regions. (DOCX 14 kb)

Location of CRISPR-flanking genes and mid-CRISPR IS6110 mobile element used for primer choices and alignments. (DOCX 17 kb)

Primers employed for PCR verification of deletions of CRISPR/DR and flanking regions. (DOCX 14 kb)

List S1. Sources for drug sensitivity data presented in Table 1. (DOCX 15 kb)