Recent transmission among immigrants and transmission permeability between the immigrant and autochthonous populations were found. Epidemiologic strategies that combine universal genotyping and refined surveys of the clustered patients are needed to investigate transmission patterns in complex scenarios.

When discrepant cases showing subtle genotypic differences were tolerated, the discrepancies fell from 14.6% to 8.6%. Epidemiological links were found for 83.8% of the cases clustered by both RFLP and MIRU-15 analyses, whereas for the cases clustered by RFLP or MIRU-VNTR analysis alone, links were identified for only 30.8% or 38.9% of the cases, respectively. The latter group of cases mainly comprised isolates that could also have been clustered, if subtle genotypic differences had been tolerated. MIRU-15 genotyping seems to be a good alternative to RFLP genotyping for real-time interventional schemes. The correlation between MIRU-15 and IS6110 RFLP findings was reasonable, although some uncertainties as to the assignation of clusters by MIRU-15 analysis were identified.Molecular tools have been widely used to characterize Mycobacterium tuberculosis isolates, with the aim of better understanding the epidemiology of tuberculosis (TB) (1,6,8,18,23). This has enabled us to document suspected outbreaks (4, 28, 34), identify risk factors associated with TB transmission (13,20,36), and evaluate the efficiency of control programs by observing the dynamics of clustered cases (9,12,17,22,24).Restriction fragment length polymorphism (RFLP) analysis based on the IS6110 sequence is the reference genotyping method for M. tuberculosis (35). However, its limitations (mainly response times) make its adaptation unsuitable for real-time intervention epidemiological schemes. New genotyping techniques based on PCR have recently been developed and are more suitable for these purposes.One of the most promising PCR-based methods is mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) genotyping (21,(30)(31)(32). A novel format based on 15 loci has improved upon the initial 12-loci version. Its discriminatory power has been found to be equivalent to that of the standard approach on the basis of reference method, and its response time could be competitive. However, very few long-term analyses apply this technique universally in parallel to the reference method to identify advantages and pitfalls (1,25,27,33).In order to compare both techniques, we selected the province of Almería, in southeast Spain, because of the complexity of its socioepidemiological population profile, which challenges us to develop new and more-efficient methods of surveying TB transmission. In Almería, around 60% of the cases