Patients with tuberculosis resistant to isoniazid but susceptible to rifampicin (H^r-R^s TB) remain a neglected demographic, despite a high disease burden and poor outcomes of these patients. The aim of this study was to investigate the characteristics of isoniazid-resistance-related mutations in Mycobacterium tuberculosis and resistance rates to drugs included in WHO-recommended regimens for H^r-R^s patients.

Mycobacterium tuberculosis isolates (n = 4922) obtained from national tuberculosis drug-resistance surveillance were subjected to whole-genome sequencing to identify H^r-R^s strains. The minimal inhibitory concentrations (MICs) were established for the H^r-R^s strains to determine the isoniazid resistance levels. We also identified drug-resistance-associated mutations for five drugs (fluoroquinolones, ethambutol, pyrazinamide, streptomycin, and amikacin) in the H^r-R^s strains.

Of the 4922 strains, 384 (7.8 %) were H^r-R^s. The subculture of seven strains failed, so 377 (98.2 %) strains underwent phenotypic MIC testing. Among the 384 genotypic H^r-R^s strains, 242 (63.0 %) contained thekatG Ser315Thr substitution; 115 (29.9 %) contained the -15C>T in the promoter region of the fabG1 gene; and 16 (4.2 %) contained Ser315Asn in the katG gene. Of the 239 strains with the Ser315Thr substitution, 229 (95.8 %) had MIC ≥ 2 μg/mL, and of the 114 strains with the -15C>T mutation, 103 (90.4 %) had 0.25 μg/mL ≤ MIC ≤ 1 μg/mL. The genotypic resistance rates were 0.8 % (3/384) for pyrazinamide, 2.3 % (9/384) for ethambutol and fluoroquinolones; 39.6 % (152/384) of the strains were resistant to streptomycin, but only 0.5 % (2/384) of the strains were resistant to amikacin.

Ser315Thr in katG was the predominant mutation conferring the H^r-R^s phenotype, followed by thefabG1 -15C>T mutation. The combination of rifampicin, pyrazinamide, ethambutol, and levofloxacin should be effective in the treatment of patients with H^r-R^s tuberculosis because the resistance rates for these drugs in China are low.