Evaluation of the 15 and 24-loci MIRU-VNTR genotyping tools with spoligotyping in the identification of Mycobacterium tuberculosis strains and their genetic diversity in molecular epidemiology studies

Abstract

Background: The transmission dynamics of Mycobacterium tuberculosis (Mtb) using various genotyping tools has been studied globally and a particular tool for genotyping Mtb is the mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR). Tuberculosis (TB) remains an important public health problem worldwide and Sri Lanka being a country of tourist destination; because of major development projects undergoing, it has a high proportion of tourists and immigrants from Asia and Europe that are characterized with highest TB incidences and drug-resistant clinical isolates. Hence, in order to address the question of Mtb genetic diversity, we investigated the discriminatory power of both MIRU-VNTR typing of 15 and 24 loci with spoligotyping to differentiate Mtb isolates.Method: Acid-fast bacilli positive sputum samples (n = 150) from first visit patients were collected. Decontamination of sputum and extraction of genomic DNA were carried out using standard techniques. The isolates were characterized by MIRU-VNTR for both the 15 and 24 loci and spoligotyping.Results: In our study population, MIRU-VNTR 15 and 24 loci did not show a significant difference among the identified M. tuberculosis strains. However, MIRU 24 loci yielded an additional strain LAM, which is of T1 origin. 15 loci strain grouping had more clusters of strains grouped together while 24 loci differentiated the same cluster of strains into distinct strain types.Conclusion: We conclude that the use of 15-locus MIRU-VNTR typing is sufficient for a first-line epidemiological study to genotype M. tuberculosis, but the additional discriminatory power of 24 loci MIRU-VNTR has been able to differentiate samples within highly homologous groups.