Large Sequence Polymorphisms Classify Mycobacterium tuberculosis Strains with Ancestral Spoligotyping Patterns ▿ Laura Flores 1 , Tran Van 2 , Sujatha Narayanan 3 , Kathryn DeRiemer 4 , Midori Kato-Maeda 1 and Sebastien Gagneux 2 , 5 , * 1 Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital and the University of California, San Francisco, California 2 Division of Infectious Diseases and Geographic Medicine, Stanford University Medical Center, Stanford, California 3 Tuberculosis Research Center, Chennai, India 4 School of Medicine, University of California, Davis, California 5 Institute for Systems Biology, Seattle, Washington ABSTRACT Genomic deletion analysis revealed that strains of Mycobacterium tuberculosis exhibiting spoligotyping patterns with almost all spacers present belong either to a strain lineage that includes the W-Beijing strain family or to the ancestral strain lineage of M. tuberculosis .