Mycobacterium tuberculosis in Ontario, Canada: Insights from IS6110 restriction fragment length polymorphism and mycobacterial interspersed repetitive-unit-variable-number tandem-repeat genotyping

Abstract

A collection of 1,308 clinical Mycobacterium tuberculosis isolates from Ontario, Canada, was genotyped by IS6110 restriction fragment length polymorphism (RFLP) and mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) analysis. RFLP or >12 MIRU-VNTR loci were necessary for resolution of Indo-Oceanic strains. The low clustering rate and high strain diversity indicate that, in Ontario, most tuberculosis results from reactivation of latent infections.

FIG. 1.

Improved typing of the Indo-Oceanic pseudocluster. Whereas all strains (n = 80) shared the same, original 12-loci pattern (254326223432), typing at 12 additional loci produced 47 distinct patterns, including 35 unique profiles. The remaining strains formed 12 clusters (6× n = 2; 3× n = 3; 1× n = 4; 2× n = 10), most of which could be further resolved by RFLP. However, one pair (cluster A) was identical by both methods, and two (clusters D and G) exhibited single band shifts. Conversely, one RFLP-defined pair (cluster M) exhibited differences at two loci upon extended MIRU-VNTR typing. For each strain, IS6110 RFLP profiles and repeat values at the extended MIRU-VNTR loci are shown. Relationships between strains are indicated by the phylogenetic (unweighted-pair group method with arithmetic mean) tree, and strains in MIRU-VNTR-defined clusters are labeled (clusters A to L).

FIG. 2.

Minimum spanning tree of 77 strain clusters. Each circle represents a cluster of strains (2 to 12 isolates) identical by 12-loci MIRU-VNTR typing. Circle sizes are proportional to the number of isolates. Divisions within circles represent sets of clusters that have identical MIRU-VNTR patterns but different IS6110 RFLP profiles. Connected clusters differ at one (thick line), two (thin line), three (dotted line), or four (dashed line) MIRU-VNTR loci. Lineage names were assigned by comparison of MIRU-VNTR patterns to the MIRU-VNTRplus reference strain database (1). The Toronto cluster is endemic to our population.