Evaluation of next-generation sequencing for detecting drug-resistant tuberculosis and investigating Mycobacterium tuberculosis lineages at the National Lung Hospital

Abstract

Objectives: To evaluate the performance of next-generation sequencing (NGS) using the Deeplex Myc-TB kit in detecting drug-resistant tuberculosis and investigating Mycobacterium tuberculosis lineages at the National Lung Hospital. Subjects and methods: This study included 79 M. tuberculosis strains retrieved from the strain bank of the Department of Microbiology and the National Tuberculosis Reference Laboratory, National Lung Hospital, which were analysed by NGS using the Deeplex Myc-TB kit on the Illumina platform. Results: NGS demonstrated high concordance with phenotypic drug susceptibility testing (DST), particularly for isoniazid and streptomycin. Lower concordance levels were observed for ethambutol, rifampicin, pyrazinamide, amikacin, and kanamycin. Molecular epidemiological analysis revealed that lineage 2 (Beijing) was predominant (84.8%). Mixed infection accounted for 41.8% of isolates, primarily involving lineage 2 and lineage 2.2.1, reflecting their close phylogenetic relationship and the microevolutionary diversity of M. tuberculosis. Conclusions: NGS showed a high level of agreement with the MGIT liquid phenotypic drug susceptibility testing method. Molecular epidemiological characterisation confirmed the predominance of lineage 2 (Beijing), consistent with the circulating pattern of this lineage in Vietnam. Additionally, the mixed-infection rate reached 41.8%, but most mixed infections involved the closely related lineage 2 and lineage 2.2.1, suggesting microevolutionary diversification rather than infection with two independent strains.