Exploring Discordance: Assessing Linezolid Resistance in Mycobacterium tuberculosis through Phenotypic DST and Genotypic Nanopore Sequencing Methods.

<bold>Introduction:</bold> Phenotypic drug susceptibility testing (DST) for Linezolid (LZD) is the established gold standard, albeit time-consuming. Nanopore sequencing presents an appealing alternative. This study aims to evaluate the agreement between phenotypic and genotypic Linezolid resistance in Mycobacterium tuberculosis isolates. <bold>Methods:</bold> Consecutive drug-resistant M. tuberculosis isolates from pulmonary samples (January to June 2021) underwent liquid culture DST for Linezolid. All resistant isolates and an equal number of consecutively obtained sensitive isolates underwent minimum inhibitory concentration testing for Linezolid (0.3 μg/ml to 4 μg/ml) and targeted sequencing of rrl and rplC genes using Nanopore technology. <bold>Results:</bold> MIC50, MIC90, and Geometric Mean MIC for 28 Linezolid-resistant isolates were 1.0 μg/ml, 4 μg/ml, and 2.82 μg/ml, respectively. For 28 Linezolid-sensitive isolates, these values were 0.25 μg/ml, 0.5 μg/ml, and 0.354 μg/ml, respectively. Sequencing identified a C154R mutation in the rplC gene of only one LZD-resistant isolate, with no mutations found in the rrl gene of any isolate. <bold>Conclusion:</bold> The agreement between sequencing and LC-DST for detecting Linezolid resistance was determined to be none to slight (Cohen’s Kappa value: 0.03571, SD: 0.03537, 95% CI: -0.034 to 0.105). A significant discrepancy currently exists between phenotypic and genotypic resistance detection for Linezolid. This study sheds light on the intricacies of these methods and underscores the need for further exploration to enhance diagnostic accuracy in Linezolid resistance detection in M. tuberculosis isolates.