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Setting: The basis for Mycobacterium tuberculosis virulence is not completely understood. Analysis of the genomic structure of clinical isolates will give information that can be related to biological activities involved in virulence., Objective: To determine the extension of the deletion in the plcA-plcB-plcC locus of selected M. tuberculosis isolates, as well as other changes in the chromosome., Design: In the present work we characterized a group of M. tuberculosis isolates devoid of the plcA-plcB-plcC locus by PCR, sequencing and microarrays., Results: PCR amplification of this region demonstrated a complete lack of plcA and plcB ORF's in all of the isolates. The plcC gene was completely deleted in one of the strains (DR-689) and the other three isolates still conserved part of this ORF. The loss of lateral DNA sequences ranged from 3723 to 7646bp. An IS6110 element was present in all tested strains cases, and some isolates presented the insertion of ORF's coding for proteins homologous to the ESAT-6 and QILSS families. Genomic DNA of all the strains was extracted and analyzed with an in-house microarray system to observe loss of other genes possibly implicated in attenuated virulence. Two of the strains presented novel deletions; the rest of the isolates showed deletions already reported for other M. tuberculosis strains. DR-689, a Beijing type M. tuberculosis strain isolated in Canada, showed an IS6110 RFLP and a genomic deletion pattern similar to a San Francisco family of strains, although completely unrelated epidemiologically., Conclusion: Genomic changes in M. tuberculosis seem to occur in a controlled manner and they are possibly related to changes in its pathogenic properties.