Genotypic Distribution and a Potential Diagnostic Assay of Multidrug-Resistant Tuberculosis in Northern Thailand

• Published in: Infection and drug resistance 2020-01, Vol.13, p.3375-3382
• Main Authors: Anukool, Usanee, Phunpae, Ponrut, Tharinjaroen, Chayada Sitthidet, Butr-Indr, Bordin, Saikaew, Sukanya, Netirat, Nathiprada, Intorasoot, Sorasak, Suthachai, Vorasak, Tragoolpua, Khajornsak, Chaiprasert, Angkana
• Format: Article
• Language: English
• Subjects: Codons; Deoxyribonucleic acid; Diagnosis; Diagnostic tests; DNA; DNA sequencing; Drug resistance; Genetic aspects; Genomes; genotype; Genotypes; high-resolution melting curve analysis; Isoniazid; Laboratories; Melting curve; Microbial drug resistance; Mortality; Multidrug resistance; Multidrug resistant organisms; multidrug-resistant tuberculosis; Mutation; mycobacterium tuberculosis; Nucleotide sequence; Original Research; Reagents; Rifampin; RNA polymerase; RpoB protein; Sequence analysis; Survival analysis; Tuberculosis
• ISSN: 1178-6973; 1178-6973
• DOI: 10.2147/idr.s263082

Knowledge of the prevalence and distribution of multidrug-resistant tuberculosis (MDR-TB) genotypes in northern Thailand is still limited. An accurate, rapid, and cost-effective diagnostic of MDR-TB is crucial to improve treatment and control of increased MDR-TB. The molecular diagnostic assays named "RIF-RD" and "INH-RD" were designed to detect rifampicin (RIF) and isoniazid (INH) resistance based on real-time PCR and high-resolution melting curve analysis. Applying the ∆T cutoff values, the RIF-RD and INH-RD were evaluated against the standard drug susceptibility testing (DST) using 107 and 103 clinical (Mtb) isolates from northern Thailand. DNA sequence analysis of partial , and promoter of 73 Mtb isolates, which included 30 MDR-TB, was performed to elucidate the mutations involved with RIF and INH resistance. When compared with the phenotypic DST, RIF-RD targeting showed sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of 83.9, 98.6, 96.9, and 92.0%, respectively. The multiplex reaction of the INH-RD targeted both and promoter showed high sensitivity, specificity, PPV, and NPV of 97.1, 94.2, 89.2, and 98.5%, respectively. Six patterns of mutation, predominately at codons 531 (50%) and 526 (40%) along with a rare S522L (3.33%) and D516V (3.33%), were detected. A single pattern of mutation (S315T) (63.3%) and four patterns of promoter mutation, predominately -15 (C>T), were found. Approximately, 17% of MDR-TB strains possessed double mutations within the and promoter. Up to 86.7% and 96.7% of MDR-TB could be accurately detected by RIF-RD and INH-RD, emphasizing its usefulness as a low unit price assay for rapid screening of MDR-TB, with confirmation of INH resistance in low and middle-income countries. The MDR-TB genotypes provided will be beneficial for TB control and the development of drug-resistant TB diagnostic technology in the future.