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Original Research
Comparative evaluation of the Xpert MTB/XDR and FluoroType XDR assays for detecting fluoroquinolone resistance in multidrug-resistant tuberculosis clinical isolates
Submitted: 23 January 2026 | Published: 21 September 2026
About the author(s)
Kabelo G. Kaapu, Department of Pathology, School of Medicine, University of Limpopo, Polokwane, South AfricaMmule K. Mathebe, Department of Microbiology, School of Medicine, University of Limpopo, Polokwane, South Africa
Ndivhuho A. Makhado, Basic and Translational Science, Africa Health Research Institute, Durban, South Africa; and Department of Microbiological Pathology, Tuberculosis Research Unit, Sefako Makgatho Health Sciences University, Pretoria, South Africa
Molebogeng R. Lekalakala-Mokaba, Department of Pathology, School of Medicine, University of Limpopo, Polokwane, South Africa; and Department of Microbiology, National Health Laboratory Services, Polokwane, South Africa
Ivy Rukasha, Department of Pathology, School of Medicine, University of Limpopo, Polokwane, South Africa; and Department of Microbiology, National Health Laboratory Services, Polokwane, South Africa
Abstract
Background: Accurate detection of fluoroquinolone (FLQ) resistance in multidrug-resistant tuberculosis (MDR-TB) is essential for effective treatment.
Aim: To compare Xpert MTB/XDR and FluoroType XDR for detecting FLQ resistance in MDR-TB.
Setting: National Health Laboratory Service diagnostic laboratory, Polokwane, South Africa.
Methods: Seventy-eight MDR-TB isolates collected from January 2024 to July 2024 were tested using Xpert MTB/XDR, FluoroType XDR and GenoType MTBDRsl line probe assay (LPA) as the reference standard. Whole-genome sequencing (WGS) data from 35 isolates were used to resolve discordant results. Diagnostic accuracy and agreement were assessed using sensitivity, specificity and Cohen’s kappa.
Results: Xpert MTB/XDR showed 97.7% sensitivity (95% confidence interval [CI]: 87.9–99.8) and 100.0% specificity (95% CI: 89.7–100.0). FluoroType XDR showed 100.0% sensitivity (95% CI: 90.6–100.0) and 97.2% specificity (95% CI: 85.5–99.9), with five indeterminate results. Compared directly with Xpert, FluoroType showed 94.9% sensitivity and 100.0% specificity. Agreement was strong (κ = 0.95; 95% CI: 0.88–1.00). WGS resolved two discordant cases: one resistant isolate with a *gyrA* Asp94Gly mutation and one susceptible isolate without resistance-associated mutations.
Conclusion: Both assays performed well for FLQ resistance detection. FluoroType XDR showed higher sensitivity but more indeterminate results. Strong assay agreement and WGS resolution of discordances support their use in MDR-TB diagnostics.
Contribution: This study demonstrates strong concordance between Xpert MTB/XDR and FluoroType XDR for FLQ resistance detection and highlights the value of WGS in resolving discordant results.
Keywords
Sustainable Development Goal
Metrics
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