Characterization of isoniazid resistance and genetic mutations in isoniazid-resistant and rifampicin-susceptible Mycobacterium tuberculosis in China

• We described the genotypic characterization of isoniazid-resistant and rifampicin-susceptible TB. • China had a modest prevalence of isoniazid-resistant and rifampicin-susceptible TB. • Our study found the low resistance rates for pyrazinamide, ethambutol, and fluoroquinolones in isoniazid-resistant and rifampicin-susceptible TB. 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 the katG 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 the fabG1 -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.