Genetic scheme for mtrA gene replacements in M. tuberculosis. (A) Mycobacterial suicide plasmid pTZ113 was integrated into the chromosome of M. tuberculosis H37Rv via legitimate single-crossover homologous recombination. (B and C) In the presence of plasmid pTZ178 (mtrA+), the merodiploid strain can be resolved upon selection on sucrose to either side of the Kmr cassette to leave the mtrA::Kmr disruption in the chromosome (B) or leave wild-type mtrA+ in the chromosome (C). In the absence of pTZ178 (no plasmid), only strains retaining wild-type mtrA+ are recovered (C). (D) Southern blot analysis of four independent strains with mtrA::Kmr allelic replacements on the chromosome obtained in the presence of pTZ178 (scheme B). EcoRI fragments: I, 3.4 kb; II, 4.6 kb; III, 7.1 kb. WT, wild type.