title: Whole Genome Sequencing of Mycobacterium tuberculosis: an isolate from January 2011 of MDR strain from long term infection with a unique genomic deletion
design: Smears from samples and TB cultures were stained using Ziehl-Neelsen staining and cultured on Lowenstein-Jensen (LJ) media using standard methods (Kent, P. T.; Kubica, G. P., Public Health Mycobacteriology: A Guide for the Level III Laboratory. 1985), and in addition cultured on BACTECe MGITe 960 (BD, Sparks, MD, USA) system. The species was identified using conventional biochemical methods (Marks, J. A system for the examination of tubercle bacilli and other mycobacteria. Tubercle 1976. 57(3), 207-25 DOI: 10.1016/0041-3879(76)90030-1.  Collins, C. H.; Grange, J. M.; Yates, M. D., Organization and Practice in Tuberculosis Bacteriology. 1985) and a commercially available strip DNA probe test (Hain Lifesciences, Nehren, Germany). Genomic DNA from inactivated bacterial cultures was extracted according to the manufacturers protocol using Maxwell RSC cultured cells DNA kit and Maxwell 16 System (Promega). DNA Paired-end libraries were prepared using the Illumina Nextera XT DNA Library Preparation Kit according to Illumina protocols. For sequencing, we utilized the Illumina MiSeq platform using a MiSeq Reagent Kit v2 (500-cycles) (catalogue MS-102-2003) or a MiSeq Reagent Kit v3 (600-cycle), (catalogue MS-102-3003).