ArticleInfection2026
Assessing fluoroquinolone resistance in Mycobacterium tuberculosis using nanopore sequencing: concordance with established diagnostic methods.
Article in Infection, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
introductionFluoroquinolones (FQs) are key components of World Health Organization (WHO)-recommended regimens for multidrug-resistant tuberculosis (MDR-TB). Accurate detection of FQ resistance is essential for optimizing treatment. This study evaluated the concordance between the Second-Line Line Probe Assay (SL-LPA) and Liquid Culture Drug Susceptibility Testing (LC-DST) for detecting FQ resistance in Mycobacterium tuberculosis isolates.
methodsIn this retrospective study, 1402 non-duplicate clinical isolates of MDR TB were tested using SL-LPA and LC-DST at a reference laboratory. Genotypic resistance was identified through mutations in the gyrA and gyrB genes identified by SL-LPA, while phenotypic resistance was determined using MGIT-based LC-DST at critical concentrations for fluoroquinolones. Targeted nanopore sequencing was performed on a subset of isolates with discordant molecular and phenotypic results to investigate resistance-associated mutations.
resultsSL-LPA detected FQ resistance in 907 (64.7%) isolates, whereas LC-DST identified resistance in 852 (60.8%) isolates. Using LC-DST as the reference standard, SL-LPA showed a sensitivity of 93.2%, specificity of 98.6%, positive predictive value of 99.2%, and negative predictive value of 88.7%. Overall concordance between the two methods was observed in 1292 (92.2%) isolates. Discordant results occurred in 110 (7.8%) isolates, mainly involving low-level resistance mutations or inferred resistance due to missing wild-type bands on SL-LPA. Nanopore sequencing of 15 discordant isolates identified high-confidence mutations (Asp94Tyr, Asp94Gly, Asp94Asn) and interim or low-confidence mutations (Ala90Val, Ser91Pro, Asp94Ala, gyrB Asn499Asp, Asp461Asn).
conclusionSL-LPA demonstrates excellent specificity and positive predictive value for detecting FQ resistance; however, discordance associated with low-confidence mutations and heteroresistance highlights the importance of integrating molecular assays with phenotypic DST and sequencing to improve MDR-TB resistance detection and guide treatment decisions.
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