BCG vaccines are a family of closely related daughter strains of an attenuated isolate of Mycobacterium bovis derived by in vitro passage from 1908 to 1921. During subsequent laboratory propagation of the vaccine strain until its lyophilization in 1961, BCG Pasteur underwent at least seven further genomic mutations. The impact of these mutations on the properties of the vaccine is currently unknown. One mutation, a glycine-to-aspartic acid substitution in the mmaA3 gene, occurred between 1927 and 1931 and impairs methoxymycolic acid synthesis in BCG strains obtained from the Pasteur Institute after this period. Mycolic acids of the cell wall are classified into three functional groups (alpha-, methoxy-, and ketomycolic acids), and together these lipids form a highly specialized permeability barrier around the bacterium. To explore the impact of methoxymycolic acid production by BCG strains, we complemented the functional gene of mmaA3 into BCG Denmark and tested a number of in vitro and in vivo phenotypes. Surprisingly, restoration of methoxymycolic acids alone had no effect on cell wall permeability, resistance to antibiotics, or growth in cultured macrophages and C57BL/6 mice. Our results demonstrate that the loss of methoxymycolic acid production did not apparently affect the virulence of BCG strains.Bacille Calmette-Guérin (BCG) vaccines are live attenuated strains of Mycobacterium bovis derived by in vitro passage from 1908 to 1921. BCG vaccines are given to millions of infants each year as antituberculosis vaccines, although their capacity to prevent tuberculosis in clinical trials has ranged from 80% protection to no detectable benefit (11). Several hypotheses have been proposed to explain this variable protection, including exposure to environmental mycobacteria (26) and differences between BCG vaccine strains (8).From genomic analyses, it is now known that during in vitro passage, M. bovis lost a genomic region called RD1 (19), which has been shown to contribute to the observed attenuation of virulence of M. bovis BCG strains (16,27). However, complementation of RD1 in the Pasteur strain of BCG did not completely restore pathogenicity in immunocompetent mice (27), suggesting that further mutations contribute to the observed phenotype of BCG strains. Because BCG stocks were propagated for another 40 to 50 years in various vaccine production laboratories, it has been hypothesized that ongoing evolution of BCG in vitro may have resulted in additional attenuation to the detriment of protective efficacy (5). Early reports on BCG suggest a second phase of attenuation in the late 1920s (24), with a decrease in BCG virulence in animal models (15) and reduced persistence of BCG in the mesenteric lymph nodes of vaccinated children (35). These observations are consistent with recent genomic analysis of existing BCG strains that revealed numerous mutations occurring after 1921 (6, 23).Further evidence of evolution of BCG strains followed from studies demonstrating the loss of methoxymycolic acid production in BCG P...