In a study of 302 Mycobacterium tuberculosis clinical isolates from the low-incidence Canadian-born population of Quebec, we characterized a large endemic strain family by using genomic deletions. The DS6 Quebec deleted region (11.4 kb) defined a strain family of 143 isolates encompassing two subgroups: one characterized by pyrazinamide (PZA) susceptibility and the other marked by a PZA-monoresistant phenotype. A second deletion (8 bp) in the pncA gene was shared by all 76 isolates with the PZA resistance phenotype, whereas a third DRv0961 deletion (970 bp) defined a further subset of 15 isolates. From their deletion profiles, we derived a most parsimonious evolutionary scenario and compared multiple standard genotyping modalities (using IS6110 restriction fragment length polymorphism [RFLP], spoligotyping, and mycobacterial interspersed repetitive units [MIRU]) across the deletion-based subgroups. The use of a single genotyping modality yielded an unexpectedly high proportion of clustered isolates for a high IS6110 copy strain (27% by IS6110 RFLP, 61% by MIRU, and 77% by spoligotyping). By combining all three modalities, only 14% were genotypically clustered overall, a result more congruent with the epidemiologic profile of reactivation tuberculosis, as suggested by the older age (mean age, 60 years), rural setting, and low proportion of epidemiologic links. These results provide insight into the evolution of genotypes in endemic strains and the potential for false clustering in molecular epidemiologic studies.In the past decade, population-based molecular epidemiologic studies of tuberculosis (TB) have been performed in a number of geographically and socially diverse populations (4,14,33). Through the use of different genotyping methods (predominantly IS6110-based restriction fragment length polymorphism [RFLP]), various studies have determined the proportion of genotypically clustered isolates and thereby inferred the extent of recent transmission in a population (3). In the process, a number of widespread Mycobacterium tuberculosis strains have been recognized and further characterized in an attempt to better define their global prevalence and epidemiologic impact (5,11,12,23,43).To date, strain families have primarily been recognized by similar patterns by using genetic markers (e.g., IS6110 patterns) (23) with further refinements, including the demonstration of shared IS6110 insertion sites (24) and/or characteristic drug resistance sequence polymorphisms where present (5). More recently, genomic deletions have presented themselves as unidirectional evolutionary polymorphisms useful for deriving phylogenies of the M. tuberculosis complex and M. tuberculosis sensu stricto isolates (22, 27). Since M. tuberculosis has a clonal population structure, and strains studied to date have revealed an average of 2.9 such deletions per clone, it follows that documenting a signature region of DNA lacking only from certain isolates would effectively define the strain and/or family of interest (22).In Quebec, Canada, we h...