Drug resistance in Mycobacterium tuberculosis complex strains is solely due to chromosomal mutations that could affect bacterial virulence. Molecular epidemiology studies have shown that resistant strains are less likely to be clustered than susceptible strains. However, a few multidrug-resistant (MDR) M. tuberculosis complex strains have been described as causing outbreaks, suggesting that they have restored virulence or increased transmission. One of the biggest MDR tuberculosis outbreaks documented to date was caused by the B strain of M. bovis. Restriction fragment length polymorphism fingerprinting revealed that the B strain contains two copies of IS6110. Here, we mapped and sequenced the regions flanking the two copies of IS6110 in the B strain. Ligation-mediated PCR showed that one of these IS6110 copies is located within the promoter region of phoP, a transcriptional regulator that is essential for M. tuberculosis virulence. We used PCR to screen 219 MDR M. tuberculosis complex strains (90.4% of all MDR isolates) isolated in Spain between 1998 and 2002 and found that the B strain was the only strain that contained a copy of IS6110 in the phoP promoter. To determine whether IS6110 affects phoP promoter activity in the B strain, we individually cloned the phoP gene and its promoter region (including IS6110 from the B strain and the equivalent region from M. tuberculosis without IS6110 as a control) into a mycobacterial replicative plasmid and transformed M. smegmatis with the resulting plasmid. Primer extension analysis showed that phoP transcription was strongly upregulated when the promoter region contained IS6110, as in the case of the B strain.Tuberculosis (TB) is currently one of the leading causes of mortality throughout the world (8,25,27). The human immunodeficiency virus-AIDS pandemic, the deterioration of public health systems in developing countries, and the emergence of multidrug-resistant (MDR) Mycobacterium tuberculosis complex strains have further contributed to the spread of TB. Knowledge of the molecular mechanisms involved in the bacillus-host cell interaction is essential for developing adequate strategies for TB control. Recent advances in the genetic manipulation of mycobacteria (2, 29) combined with the publication of the complete M. tuberculosis genome sequence (6) have made it possible to study the contribution of individual genes to M. tuberculosis virulence (5, 7). However, little is known about the regulatory and expression mechanisms that determine the virulence of clinical isolates of M. tuberculosis.Insertion sequence (IS) 6110 has been extensively used for molecular typing of M. tuberculosis strains. Restriction fragment length polymorphism (RFLP) analysis using IS6110 as a probe is currently the most common molecular method used to type M. tuberculosis complex strains. However, the physiological role and impact of specific IS6110 insertions on the biology of bacilli are not well known. IS6110 fingerprinting studies have demonstrated heterogeneity between virulence and transm...