Genomic characterization of an endemic Mycobacterium tuberculosis strain: evolutionary and epidemiologic implications

Abstract

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.

FIG. 1.

PCR-based identification of deleted regions in study isolates. The solid line represents genomic DNA present in all isolates, and the dashed line represents the genomic region present in HR37Rv but deleted in the strain under study here.

FIG. 2.

Dendrogram of IS6110 RFLP of the 143 isolates in the DS6^Quebec(−) family. Isolates belonging to the deletion-defined group 2 are identified by two dots, those in group 3 are identified by three dots, and those in group 4 are identified by four dots. The UPGMA-based dendrogram of IS6110 RFLP partly segregates the deletion-defined groups but does not define a clear and comparable phylogeny.

FIG. 3.

Deletion-based evolutionary scenario of the Quebec strain. Group 1, no regions deleted; group 2, DS6^Quebec region deleted but no pncA deletion; group 3, DS6^Quebec region and pncA deletion but no DRv0961 deletion; group 4, DS6^Quebec region, pncA and DRv0961 deletion. ✽, The DS6^Quebec region was deleted in 143 of 298 isolates; ✽✽, the pncA deletion was present in 76 of 298 isolates; ✽✽✽, the DRv0961 region was deleted in 15 of 298 isolates.