Prevalence and resistance spectrum of <i>ahpC</i> mutations in isoniazid-resistant <i>Mycobacterium tuberculosis</i> isolates

ABSTRACT To characterize the mutation profile of the ahpC gene in isoniazid resistance (INH r ) Mycobacterium tuberculosis (MTB) isolates and to evaluate the correlation between specific mutations and resistance levels, a total of 1,337 INH r MTB isolates were collected through the Chinese Drug Resistance Surveillance Program (2013–2020). The minimum inhibitory concentrations (MICs) for INH, rifampicin (RIF), and ethionamide were determined by broth microdilution, followed by whole-genome sequencing analysis. Among 1,337 INH r - MTB isolates, 45.5% (608/1,337) were multidrug-resistant (MDR), and 54.5% (729/1,337) were RIF-sensitive cases, with lineage 2 predominating (1,013/1,337, 75.8%). Resistance mutations were identified in 79.1% (1,058/1,337) of strains, primarily katG Ser315Thr (65.5%, 695/1,058) and inhA C-777T (19.7%, 208/1,058). Notably, 5.3% (56/1,058) isolates harbored standalone ahpC mutations, with 83.3% (5/6) C-81T, 60.0% (9/15) G-48A, 57.1% (4/7) C-54T, 50.0% (3/6) C-57T, and 42.1% (8/19) C-52T mutations showing high-level INH resistance. Accordingly, 91.7% (11/12) dual katG 315 + inhA mutations conferred high-level INH resistance, while ahpC C-57T mutants universally exhibited MDR. The ahpC mutations are associated with high-level INH resistance in variants without concurrent katG or inhA mutations. This finding significantly advances our understanding of tuberculosis resistance profiling, enabling more comprehensive detection of INH r -MTB and optimizing therapeutic strategies. IMPORTANCE Among INH-resistant MTB clinical isolates, mutations in the ahpC promoter region have been considered to occur in combination with other mutations, such as katG and inhA , in a compensatory role. While the ahpC mutations have been incorporated into the World Health Organization (WHO)-recommended rapid diagnostic test, Xpert MTB/extensively drug-resistant tuberculosis (XDR), it has been still ambiguous about the standalone effects on INH resistance spectrum. Our findings demonstrate that the ahpC mutations are associated with high-level INH resistance in variants without concurrent katG or inhA mutations. This finding significantly advances our understanding of TB resistance profiling, enabling a more comprehensive detection of INH r -MTB and optimizing therapeutic strategies.