Epidemiology of Mycobacterium tuberculosis strains in San Francisco that do not contain IS6110

IS6110 is commonly used as the basis for molecular epidemiologic and diagnostic studies of Mycobacterium tuberculosis. However, strains that do not contain IS6110 have been reported. If common, such strains would pose a limitation for molecular studies of M. tuberculosis. Analysis of a population-based sample from San Francisco of 1569 specimens submitted for fingerprinting demonstrated that the proportion of strains that lack IS6110 is less than 1%. While this low percentage permits IS6110 fingerprinting in San Francisco, it may be problematic in other settings.