Prevalence and resistance spectrum of ahpC mutations in isoniazid-resistant Mycobacterium tuberculosis isolates

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 katG³¹⁵+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.IMPORTANCEAmong 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.