Genome sequencing of clinical isolates of TbD1-intact or -deleted Mycobacterium tuberculosis strains. MTBSEQ

We performed whole-genome sequencing of the three following strains: (1) Mycobacterium tuberculosis 79112 with an intact TbD1 region that was isolated from a patient of Indian origin by the team of Dr Denis Mitchison; (2) Mycobacterium tuberculosis 79499 with a deleted TbD1 region that was isolated from a patient of Indian origin by the team of Dr Denis Mitchison; and (3) Mycobacterium tuberculosis Tb36 with an intact TbD1 region that was isolated from a patient of Indian origin and obtained from the collection of Dr Dick van Soolingen. Genome sequencing of Mycobacterium tuberculosis 79112 was performed by the Genoscope (CEA, Evry, France). Sanger reads from 10-kb fragment shotgun libraries were assembled with contigs obtained from Newbler assemblies of 454/Roche reads using Arachne. Scaffolds were validated using the Mekano interface (Genoscope). Primer walking, PCR and in vitro transposition were used for finishing purposes. The assembled consensus sequences were validated using Illumina reads. Genome sequencing of Mycobacterium tuberculosis 79499 and Tb36 was performed by the Genopole (Institut Pasteur, Paris, France). Illumina reads were assembled using Velvet and generated contigs were ordered according to similarity with the reference genome of Mycobacterium tuberculosis H37Rv.