Clinical application of targeted next generation sequencing in detecting rifampicin and rifabutin resistance in tuberculosis patients

Abstract

To evaluate the clinical value of targeted next generation sequencing (tNGS) in diagnosing rifampicin and rifabutin resistance in tuberculosis patients. In this retrospective cohort study, 119 culture-positive Mycobacterium tuberculosis (MTB) strains from tuberculosis patients in Shenzhen Third People's Hospital from 2020 to 2023 were collected, then tNGS was performed to detect mutations of rpoB gene. Fourteen different types of rpoB gene mutation were detected in 46 mutation MTB strains, including 43 resistance related mutations and 3 synonymous mutations at codon 529. Using the phenotypic drug susceptibility results of rifampicin and rifabutin as the reference standard, the sensitivities of tNGS for detecting resistance to rifampicin and rifabutin were 100%, and the specificities were 96.2% and 89.4% respectively, therefore, tNGS showed good diagnostic performance. Mutations at positions 531 and 526 of rpoB were highly associated with resistance to rifampicin and rifabutin. Moreover, the results of tNGS from the clinical specimens were consistent with those from the corresponding culture strains. tNGS analysis was performed on 83 MTB strains from 18 patients with multiple positive cultures. The results showed that 2 patients with no mutations in the initial MTB strains were subsequently detected with rpoB gene mutation and their phenotypic drug susceptibilities changed from sensitive to resistant. In summary, using tNGS to detect rpoB mutations can reduce false positive results caused by synonymous mutations, and have satisfactory performance for the diagnosis of rifampicin and rifabutin resistance. tNGS can directly detect clinical sputum samples, and also can be used to dynamically monitor the molecular resistance profiles of MTB, therefore it has extremely broad clinical application prospects.