Comprehensive analysis of mutations associated with rifampicin- and isoniazid-resistant tuberculosis in a high-burden setting.

Background: In this study, we aimed to describe the mutations associated with first-line drug resistance in Mycobacterium tuberculosis complex (MTBC) isolates from São Paulo, Brazil, between 2019 and 2021.

Methods: Mutations in the coding regions of rpoB and katG genes and in the promoter region of the inhA gene in MTBC clinical isolates were detected using the GenoType MTBDRplus assay (LPA). All mutations inferred by LPA were sequenced.

Results: Of the 13,489 MTBC isolates with valid LPA results, 657 (4.9%) harbored mutations. The overall prevalence rates of rifampicin-resistant (RIF-R) tuberculosis (TB), isoniazid-resistant (INH-R) TB, and multidrug-resistant (MDR) TB were 1.5, 2.0, and 1.2%, respectively. A significant proportion of RIF-R isolates presented inferred rpoB mutations (89.1%), most of which were the borderline H445N mutation. The inhA promoter C-15T mutation was predominant among the INH-R isolates (52.8%). Most MDR isolates presented rpoB S450L + katG S315T1 mutations. Gene sequencing identified mutations not included in the catalogue of mutations published by the World Health Organization. Phenotypic drug susceptibility testing on isolates with inferred rpoB mutations revealed that the 0.5 µg/mL critical concentration of RIF failed to detect most borderline mutations when using the BACTEC MGIT 960 system.

Conclusions: These findings emphasize the need for continuous surveillance and the integration of molecular and phenotypic methods to ensure an accurate detection and management of drug-resistant TB in high-burden settings.