Comparative performance evaluation of two rapid molecular assays for detecting drug-resistant tuberculosis in clinical isolates

ABSTRACT To evaluate and compare the diagnostic performances of two rapid molecular assays (MeltPro and iFIND) for detecting Mycobacterium tuberculosis (MTB) resistance to first- (isoniazid, rifampicin) and second-line (fluoroquinolones) anti-tuberculosis drugs in clinical isolates, clinical isolates of MTB were obtained from patients at the First Affiliated Hospital, Zhejiang University School of Medicine (2017 to 2024). All isolates underwent parallel testing using MeltPro, iFIND, and phenotypic drug susceptibility testing (pDST). Sensitivity, specificity, and area under the ROC curve (AUC) were calculated to evaluate the diagnostic performance, with pDST serving as the gold reference standard for comparative assessment. The pDST analysis of 102 individual TB isolates from unique patients showed rifampicin, isoniazid, and fluoroquinolone resistance in 17 (16.7%), 22 (21.6%), and 13 (12.8%) isolates, respectively. In detecting rifampicin resistance, the MeltPro assay achieved 94.12% sensitivity and 98.82% specificity compared with 88.24 and 98.82%, respectively, for the iFIND assay. For isoniazid, the MeltPro assay achieved 95.45% sensitivity and 98.75% specificity compared with 90.91 and 98.75%, respectively, for the iFIND assay. Both rapid assays detected 100% of fluoroquinolone-resistant strains, with overall accuracies of 97.06 of 97.0 pDST (Kappa ≥0.89). AUCs for rifampicin and isoniazid resistance exceeded 0.90 in both assays, with no statistically significant differences between the two methods (all P > 0.05). The MeltPro and iFIND assays offer rapid, accurate detection of resistance to rifampicin, isoniazid, and fluoroquinolones in MTB isolates. With rapid turnaround and high throughput, these platforms hold particular promise for densely populated settings with high sample volumes. IMPORTANCE This study highlights the efficiency of MeltPro and iFIND assays for detecting multidrug-resistant tuberculosis (MDR-TB)-including resistance to rifampicin, isoniazid, and fluoroquinolones-in clinical isolates. Timely diagnosis is critical for disease control, yet conventional phenotypic drug susceptibility testing (pDST) is limited by prolonged turnaround times. Despite advances in molecular tools, such as Xpert MTB/RIF, faster, more efficient, fully automated platforms for comprehensive TB/MDR-TB detection remain urgently needed. This comparative evaluation demonstrates that MeltPro and iFIND offer expanded detection capabilities with rapid, automated workflows and relatively low cost, making them ideal for high-throughput settings with efficient sample referral.