Characterization of Philippine drug-susceptible and multi-drug resistant mycobacterium tuberculosis isolates through combined 15-locus MIRU-VNTR genotyping and mutation analysis of drug resistance genes

• Main Authors: Pastor, Crist John M., Tan-Liu, Nelia S., Barzaga, Maria Teresa A., Defensor, Dario D., Romano, Christopher T., Dela Cruz, Elsie Marie B., Chung, Francisco S., Jr., Caoili, Salvador Eugenio C., Heralde, Francisco M., III
• Format: text
• Published: Animo Repository 2022
• Subjects: Drug resistance in microorganisms—Genetic aspects; Multidrug-resistant tuberculosis; Mycobacterium tuberculosis; Chemistry; Medicinal-Pharmaceutical Chemistry
• Online Access: https://animorepository.dlsu.edu.ph/faculty_research/6094
• Institution: De La Salle University

Molecular genotyping, an important strategy to characterize bacterial strains infecting patients, allows identification of M. tuberculosis (MTb) complex members with varying responses to anti-mycobacterial therapy. M. tuberculosis Interspersed Repeating Units – Variable Number of Tandem Repeats (MIRU-VNTR) is a fast, reproducible and cost-effective PCR-based method capable of differentiating MTb strains. This study focused on evaluating the utility of MIRU-VNTRs to differentiate 54 MTB isolates from the Lung Center of the Philippines (LCP) through amplification of twelve MIRU-VNTRs and three Exact Tandem Repeats (ETRs). Digital codes were determined per isolate through calculation of VNTR repeats and analyzed using the MIRU-VNTRplus program (http://www.miruvntrplus.org/MIRU/index.faces). Values of the Hunter-Gaston discriminatory index (HGDI) suggest that five of fifteen (33.33%) MIRU-VNTRs are highly discriminating (>0.75). All MIRU-VNTRs and ETRs except ETRC had HGDI values indicative of good resolving power (≥0.5). Among the LCP isolates, four Mtb clusters closely related to the East AfricanIndian strain family were identified on the basis of MIRU-VNTR profiles and mutation data on rpoB, katG and gyrA genes obtained through gene sequencing, which is consistent with previous reports regarding the existence of a distinct Manila family of MTb strains. The said four clusters have been designated as EAI-M1 through EAI-M4, in order of increasing propensity to develop drug resistance. Among these clusters, rpoB, katG and gyrA mutations were observed that are highly similar to those already reported in literature. Our results demonstrate that a 15-locus MIRU-VNTR genotyping strategy in combination with mutation profiling of drug resistance-related genes could serve as a molecular-epidemiology tool for characterizing and monitoring drug-susceptible and multi-drug resistant MTb strains in the Philippines.