Genetic diversity of drug-resistant Mycobacterium tuberculosis clinical isolates from Khuzestan province, Iran

The emergence of drug-resistant strains of the Mycobacterium tuberculosis (MTB) has challenged tuberculosis control programs. So far, few studies using the 24-locus mycobacterial interspersed repetitive unit variable number tandem repeats (MIRU-VNTR) have investigated the genetic diversity of MTB in Iran. This study aimed to determine the genetic diversity of MTB isolates resistant to first-line anti-tuberculosis drugs using 24-locus MIRU-VNTR in southwestern Iran. Out of 6620 MTB clinical isolates, 29 resistant isolates to one or more isoniazid, rifampin, and ethambutol were detected using drug susceptibility testing by the proportional method. The manual 24-locus MIRU-VNTR was used to determine the MTB resistant isolates’ phylogenetic relationship. MIRU-VNTRplus web application tools were applied to analyze the associated data. Using 24-locus MIRU-VNTR, 13.8% of isolates (n = 4) were distributed in two clusters, and the remaining 86.2% (n = 25) showed a unique pattern. Four clonal complexes were observed in the minimum spanning tree based on the double-locus variant. Most isolates belonged to Delhi/CAS (34.5%, 10/29) and NEW-1 (24.1%, 7/29) sub-lineages, followed by EAI and LAM with a frequency of 6.9% (2/29) and 3.5% (1/29), respectively. Eight isolates (27.6%) did not match any genotype in the database. The 24-locus MIRU-VNTR showed a high discriminatory power; however, the 15-locus and 12-locus set analyses were more discriminative. Our study revealed a high degree of genetic diversity among drug-resistant MTB isolates, which could be interpreted as the low rate of person-to-person transmission in this region. The 15-locus MIRU-VNTR would be recommended for preliminary genotyping of drug-resistant MTB.