Mycobacterium bovis, a member of the Mycobacterium tuberculosis complex, has a particularly wide host range and causes tuberculosis in most mammals, including humans. A signature tag mutagenesis approach, which employed illegitimate recombination and infection of guinea pigs, was applied to M. bovis to discover genes important for virulence and to find potential vaccine candidates. Fifteen attenuated mutants were identified, four of which produced no lesions when inoculated separately into guinea pigs. One of these four mutants had nine deleted genes including mmpL4 and sigK and, in guinea pigs with aerosol challenge, provided protection against tuberculosis at least equal to that of M. bovis BCG. Seven mutants had mutations near the esxA (esat-6) locus, and immunoblot analysis of these confirmed the essential role of other genes at this locus in the secretion of EsxA (ESAT-6) and EsxB (CFP10). Mutations in the eight other attenuated mutants were widely spread through the chromosome and included pks1, which is naturally inactivated in clinical strains of M. tuberculosis. Many genes identified were different from those found by signature tag mutagenesis of M. tuberculosis by use of a mouse infection model and illustrate how the use of different approaches enables identification of a wider range of attenuating mutants.Tuberculosis exacts enormous human suffering and death on a global basis and is also a widespread cause of animal morbidity and mortality. The primary human pathogen is Mycobacterium tuberculosis, although in many regions a significant amount of human disease results from infection with the very closely related organisms Mycobacterium africanum and the major animal pathogen Mycobacterium bovis. Together with a few less important species, these organisms are collectively referred to as the M. tuberculosis complex. The high degree of similarity in the pathogenesis of disease caused by these pathogens and the recent findings from genomic studies that the vast majority of genes within these species are identical or nearly so (16,22) clearly indicate that the majority of their virulence genes are shared in common. There is particular interest in discovering the identity of these genes, so that new strategies including improved vaccines and antibacterials can be developed for combating tuberculosis.Over the last 15 years, there has been continual development of molecular genetic techniques that can be applied to the M. tuberculosis complex (2). This enabled the discovery of individual tuberculosis virulence genes from 1995 onwards (7, 38) and led to the application over the last 5 years of a number of global techniques for identifying large numbers of genes that are essential for virulence or whose expression is altered during different stages of infection and disease. Among these global techniques, signature tag mutagenesis (18) is widely recognized as a powerful tool for investigating pathogenic organisms because of its ability to directly identify mutants that have reduced virulence (24). This identific...