Targeted Nanopore Sequencing for Molecular Characterization of First-Line Drug Resistance and Treatment Outcomes Among Patients in the Republic of Congo

Tuberculosis (TB) remains a major global public health concern, further complicated by the emergence and transmission of drug-resistant strains. Diversity within the Mycobacterium tuberculosis complex (MTBC) may also influence disease progression and treatment response. We conducted a longitudinal study among 126 Xpert MTB/RIF Ultra-confirmed TB patients enrolled and followed at the Antituberculosis Center of Brazzaville between July 2023 and November 2024. MTBC species were identified using the Genotype MTBC assay, and resistance-associated mutations in rpoB, katG, and embB were characterized by targeted Oxford Nanopore sequencing and interpreted using the WHO mutation catalogue and TB-Profiler. The overall treatment success rate was 81.7% (103/126). Among 109/126 samples successfully typed, M. tuberculosis accounted for 92.7% (101/109), Mycobacterium africanum for 3.7% (4/109), while mixed infection accounted for 0.9% (1/109) and inconclusive profiles for 2.8% (3/109). Resistance-associated mutations were assessed in 65 of the 126 enrolled patients with high-quality sequencing data. Among these 65 isolates, 32.3% (21/65) harbored resistance to at least one of the targeted first-line drugs, including isoniazid (23.1%; 15/65), rifampicin (15.4%; 10/65), and ethambutol (9.2%; 6/65). Multidrug-resistant TB was identified in 12.3% (8/65). The predominant mutations occurred at rpoB codon 435, katG codon 315, and embB codon 306. Treatment success was lower among patients infected with strains carrying a resistance-associated mutation (71.4%). Isoniazid resistance was associated with reduced odds of treatment success in unadjusted analysis (OR = 0.22, 95% CI: 0.05–0.93; p = 0.04). These findings suggest a considerable burden of genotypically predicted first-line drug resistance and support expanding molecular drug-susceptibility testing beyond rifampicin in TB surveillance and patient management in the Republic of Congo.