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Background    Mycobacterium tuberculosis  is the principal etiologic agent of human tuberculosis. It has no environmental reservoir and is believed to have co-evolved with its host over millennia. This is supported by skeletal evidence of the disease in early humans, and inferred from  M. tuberculosis  genomic analysis. Direct examination of ancient human remains for  M. tuberculosis  biomarkers should aid our understanding of the nature of prehistoric tuberculosis and the host/pathogen relationship.    Methodology/Principal Findings  We used conventional PCR to examine bone samples with typical tuberculosis lesions from a woman and infant, who were buried together in the now submerged site of Atlit-Yam in the Eastern Mediterranean, dating from 9250-8160 years ago. Rigorous precautions were taken to prevent contamination, and independent centers were used to confirm authenticity of findings. DNA from five  M tuberculosis  genetic loci was detected and had characteristics consistent with extant genetic lineages. High performance liquid chromatography was used as an independent method of verification and it directly detected mycolic acid lipid biomarkers, specific for the  M. tuberculosis  complex.    Conclusions/Significance  Human tuberculosis was confirmed by morphological and molecular methods in a population living in one of the first villages with evidence of agriculture and animal domestication. The widespread use of animals was not a source of infection but may have supported a denser human population that facilitated transmission of the tubercle bacillus. The similarity of the  M. tuberculosis  genetic signature with those of today gives support to the theory of a long-term co-existence of host and pathogen.

Detection and Molecular Characterization of 9000-Year-Old Mycobacterium tuberculosis from a Neolithic Settlement in the Eastern Mediterranean