In recent years, the application of molecular tools has shown us that clonal complexity in infection byMycobacterium tuberculosis is not anecdotal. Exogenous reinfections, mixed infections, compartmentalization, and microevolution are different aspects of this issue. The detection and characterization of clonal variants of M. tuberculosis by standard genotyping methods is laborious and frequently requires expertise. Our aim was to evaluate a new genotyping PCR-based method for M. tuberculosis, mycobacterial interspersed repetitive unitvariable-number tandem repeat typing (MIRU-VNTR), as a potential tool to simplify and optimize the clonal analysis of tuberculosis. MIRU-VNTR was able to detect mixed clonal variants in vitro, even for clones at low ratios (1:99). This technique was prospectively applied to search for cases infected by more than one clone. Clonal variants within the same host were detected in 3 out of 115 cases (2.6%), including cases with clones which were indistinguishable by restriction fragment length polymorphism or spoligotyping. In one case, coinfecting clonal variants differed in antibiotic susceptibilities. MIRU-VNTR was applied to cases with proven polyclonal infection, and it succeeded in detecting the coinfecting strains and proved useful in confirming cases of compartmentalized infection. MIRU-VNTR is a simple, rapid, and sensitive method which could facilitate and optimize the identification and characterization of clonal complexity in M. tuberculosis infection.In recent years, clonal analysis of Mycobacterium tuberculosis infection has shown us that, in certain circumstances, tuberculosis is a much more complex situation than the schematic vision of one strain infecting one host. The complex situations found in tuberculosis include recurrences caused by exogenous reinfections (2,4,5,7,19); simultaneous coinfections by more than one M. tuberculosis strain (3,5,8,13,20); compartmentalization of the infection; with different strains infecting different tissues (3, 9, 12); and microevolution phenomena leading to the appearance of clonal variants within a host (6, 10). Unfortunately, the methodological approach to a search for clonal heterogenity or polyclonality is complex and/or laborious because it requires (i) a refined analysis of genotypic patterns to prove the existence of different clones or (ii) the analysis of multiple independent colonies from each specimen in order to detect the presence of clonal variants. These methodological exigencies have been responsible for the small number of reports examining this issue. Mycobacterial interspersed repetitive unit-variable-number tandem repeat typing (MIRU-VNTR) (17) is a novel PCR-based typing method for M. tuberculosis which is based on the amplification of 12 independent loci and the assignation of the number of tandem repeats found in each locus. The purpose of this study is to test the usefulness of this novel method for simplifying and optimizing the exploration and characterization of clonal complexity in tuberculosis.
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