Spoligotype-based population structure and isoniazid-resistance gene mutation of Mycobacterium tuberculosis isolates from Thailand

• In Thailand, the predominant MTB lineages were East Asian and Indo-Oceanic. • EA and IO spoligotypes revealed a high association with anti-TB drug resistance. • Beijing genotype was significantly associated with isoniazid (INH) monoresistance. • Two mutations, katG Ser315Thr and –15C→T in inhA promotor region, accounted for 68% of INH resistance. The present study aims to investigate the population structure of Thai Mycobacterium tuberculosis (MTB) isolates and anti-tuberculosis (TB) drug resistance and to determine the most frequent genetic mutations conferring isoniazid (INH) resistance. Genomic DNA from 287 MTB clinical isolates were extracted and used for spoligotyping, amplification and sequencing analysis of the region of different (RD) 105, and of the INH resistance (IR) associated genes, inhA, katG and oxyR - ahpC genes. Eighty-one clinical isolates were resistant to at least one first-line drug; 53 of these were resistant to INH. All strains were classified into three lineages based on their spoligotypes: East Asia (EA)/Beijing, Indo-Oceanic (IO), and Euro-American (EuA). EA and IO lineages revealed a strong association with anti-TB drug resistance ( P = 0.005 and 0.013, respectively). A total of 33 mutations were found among IR isolates, which for 28 (84.8%), 3 (9.1%), and 2 (6.1%) occurred in katG, inhA , and oxyR - ahpC genes, respectively. Moreover, the most common mutations found were 54.7% of IR presented Ser315Thr at katG (54.7%) and C-15T at inhA (15.1%) presented. This result suggests the involvement of other genetic markers or other mechanisms of resistance. This study provides information about strains diversity, drug resistance profiles, and their possible association. EA and IO lineages were predominant in Thailand, and they were highly associated with anti-TB drug resistance. Testing two mutations including katG Ser315Thr and inhA –15C→T could detect 68% of the IR strains.