Discordance between Mycobacterial Interspersed Repetitive-Unit-Variable-Number Tandem-Repeat Typing and IS 6110 Restriction Fragment Length Polymorphism Genotyping for Analysis of Mycobacterium tuberculosis Beijing Strains in a Setting of High Incidence of Tuberculosis

Abstract

IS6110 restriction fragment length polymorphism (RFLP) genotyping is the most widely used genotyping method to study the epidemiology of Mycobacterium tuberculosis. However, due to the complexity of the IS6110 RFLP genotyping technique, and the interpretation of RFLP data, mycobacterial interspersed repetitive-unitvariable-number tandem-repeat (MIRU-VNTR) genotyping has been proposed as the new genotyping standard. This study aimed to determine the discriminatory power of different MIRU-VNTR locus combinations relative to IS6110 RFLP genotyping, using a collection of Beijing genotype M. tuberculosis strains with a well-established phylogenetic history. Clustering, diversity index, clustering concordance, concordance among unique genotypes, and divergent and convergent evolution were calculated for seven combinations of 27 different MIRU-VNTR loci and compared to IS6110 RFLP results. Our results confirmed previous findings that MIRU-VNTR genotyping can be used to estimate the extent of recent or ongoing transmission. However, molecular epidemiological linking of cases varied significantly depending on the genotyping method used. We conclude that IS6110 RFLP and MIRU-VNTR loci evolve independently and at different rates, which leads to discordance between transmission chains predicted by the respective genotyping methods. Concordance between the two genotyping methods could be improved by the inclusion of genetic distance (GD) into the clustering formulae for some of the MIRU-VNTR loci combinations. In summary, our findings differ from previous reports, which may be explained by the fact that in settings of low tuberculosis incidence, the genetic distance between epidemiologically unrelated isolates was sufficient to define a strain using either marker, whereas in settings of high incidence, continuous evolution and persistence of strains revealed the weaknesses inherent to these markers.Over the past 2 decades, molecular genotyping methods have enhanced our understanding of the epidemiology of tuberculosis (TB) in numerous geographical settings. These methods have enabled geo-temporal tracking of Mycobacterium tuberculosis strains with the view to identifying source cases responsible for TB outbreaks (3), tracking of recent and ongoing disease transmission (31), distinguishing between reinfection and relapse (28), evaluating the effectiveness of direct observed therapy short-course-based TB control programs (5, 16), and identifying global genetic lineages (7). Ideally, molecular genotyping tools should be inexpensive, highly discriminative, deliver rapid results, be straightforward to perform, and produce easily interpretable results that allow for accurate interlaboratory comparisons (universally comparable databases).Three genotyping methods are currently widely used in molecular epidemiological studies of TB: IS6110 restriction fragment length polymorphism (RFLP) genotyping (27), spoligotyping (14), and mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) genotyping (21,22). Cu...

Evaluation of Mycobacterium tuberculosis Typing Methods in a 4-Year Study in Schleswig-Holstein, Northern Germany

“…It has already been shown that 12-loci MIRU-VNTR typing was not sufficient to discriminate Beijing family strains (6,9). Similarly, Hanekom and colleagues reported that even 15-and 24-loci MIRU-VNTR typing has a reduced discriminatory power compared to IS6110 typing for strains of the Beijing lineage in Cape Town, South Africa, and that the inclusion of more variable loci might be necessary to reach the same level as that with IS6110 RFLP typing (7). As an exception, Shamputa et al found a similar discriminatory power of 24-loci MIRU-VNTR and IS6110 RFLP typing on Korean Beijing strains and suggested that 24-loci-based MIRU-VNTR typing is a likely suitable alternative to RFLP to differentiate clinical isolates in their setting dominated by Beijing strains (15).…”

“…In comparative populationbased evaluations, we and others found a similar if not slightly better performance of 15-or 24-loci MIRU-VNTR typing compared to IS6110 RFLP typing for discrimination of clinical isolates and detection of transmission chains in TB patient populations (13). Few subsequent studies compared MIRU-VNTR typing with the "gold standard" IS6110 RFLP typing, because the latter is rather laborious and more difficult to perform (6,7,15). The majority of the studies confirmed the initial finding that 24-loci MIRU typing can be used for MTBC genotyping with a similar performance as IS6110 typing, but some studies suggested a lower discriminatory power of 24-loci MIRU-VNTR typing in settings where Beijing strains are dominant (7,15).…”

“…Few subsequent studies compared MIRU-VNTR typing with the "gold standard" IS6110 RFLP typing, because the latter is rather laborious and more difficult to perform (6,7,15). The majority of the studies confirmed the initial finding that 24-loci MIRU typing can be used for MTBC genotyping with a similar performance as IS6110 typing, but some studies suggested a lower discriminatory power of 24-loci MIRU-VNTR typing in settings where Beijing strains are dominant (7,15). However, for the latter comparative evaluations, no in-depth contact tracing information was available to further evaluate the capability of a particular genotyping method to detect recent transmission chains correctly but distinguish unrelated strains with sufficient discrimination.…”

Genetic profile of Mycobacterium tuberculosis and treatment outcomes in human pulmonary tuberculosis in Tanzania

“…Similar trends have been observed in other African countries where local genotypes tend to form a greater proportion of the circulating strains (Kallenius et al, 1999;Niobe-Eyangoh et al, 2004;Easterbrook et al, 2004;Chihota et al, 2007). In recent findings, a study showed that different strains of M. tuberculosis have adapted to specific human populations and such strains have a higher probability of transmission than others (Gagneux et al, 2006;Gagneux & Small, 2007;Hanekom et al 2008).…”

“…Recent findings indicate that different strains of M. tuberculosis have adapted to specific human populations and such strains have a higher probability of transmission in these communities than others (Gagneux et al, 2006;Gagneux & Small, 2007;Hanekom et al, 2008). The Beijing family is thought to be hyper-virulent and to have high probability for developing drug resistance .…”