Assessment of an optimized mycobacterial interspersed repetitive- unit-variable-number tandem-repeat typing system combined with spoligotyping for population-based molecular epidemiology studies of tuberculosis

Abstract

An optimized set of 24 mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) loci, including a discriminatory subset of 15 loci, has recently been defined for the typing of Mycobacterium tuberculosis. Here, we evaluated the performances of this MIRU-VNTR typing system in combination with spoligotyping for the detection of transmission chains in a population-based study comprising 91% of culture-confirmed tuberculosis patients reported in 2003 in Hamburg, Germany. Of the 154 isolates investigated, more than 90% had high IS6110 copy numbers (>/=6). IS6110 restriction fragment length polymorphism (RFLP) typing resulted in 13 clusters, 5 of which had a confirmed epidemiological link. All five, as well as six of the eight IS6110 clusters with no identified epidemiological link, were perfectly matched by MIRU-VNTR typing with the 24 loci. Two IS6110 clusters were split by differences into 6 to 12 MIRU-VNTR loci, clearly supporting the absence of a link, as judged by contact tracing data. In contrast, only one MIRU-VNTR cluster, grouping what were probably epidemiologically unlinked isolates, was split by IS6110 RFLP. However, these isolates were also distinguished by spoligotyping. Both the optimized 24-locus and 15-locus sets thus showed a comparable to slightly better predictive value, especially when combined with spoligotyping, than the current gold standard IS6110 RFLP for the study of tuberculosis transmission in Hamburg. Because the epidemiological characteristics of this setting are similar to those of many developed countries, these results support the wide applicability of this real-time genotyping approach for population-based studies of M. tuberculosis transmission.

FIG. 1.

IS6110 DNA fingerprint patterns, spoligotype patterns, and MIRU-VNTR copy numbers of the 39 strains grouped in 13 IS6110 clusters. In addition, the genotypes of the three strains additionally clustered by identical MIRU patterns but differentiated by spoligotyping (cluster 9b) are shown. Isolates of IS6110 clusters 1 and 12 without epidemiological link (see the text) are clearly distinguished by differences in their MIRU-VNTR profiles (boxed).

FIG. 2.

MIRU-VNTR SLVs. Isolates differing by a single MIRU-VNTR locus (boxed) out of the 24 loci are shown, along with the corresponding IS6110 RFLP and spoligotyping profiles. Isolate 10041/03 displayed SLVs (shown by a single box or two separate connected boxes) with three different isolates. Similarly, the isolates in MIRU-VNTR cluster 9+9b (see the text) displayed SLVs (shown by a single box or two separate connected boxes) with two different isolates.