COMPARISON OF NANOPORE SEQUENCING VERSUS CONVENTIONAL PCR FOR RAPID DETECTION OF DRUG-RESISTANT TUBERCULOSIS IN CLINICAL PRACTICE

Abstract

Background: Drug-resistant tuberculosis (DR-TB) remains a critical global health challenge, particularly in regions with high disease burden. Rapid and accurate detection of resistance is essential for initiating effective therapy and curbing transmission. Objective: This study aimed to compare nanopore sequencing with conventional PCR in detecting drug-resistant tuberculosis in clinical practice. Methods: This cross-sectional analytical study was conducted at Tertiary Care Hospital, Lahore from November 2024 to April 2025. It included 153 patients with confirmed pulmonary TB. Sputum samples were analyzed using both conventional PCR and nanopore sequencing, with phenotypic drug susceptibility testing (DST) taken as the gold standard. Diagnostic accuracy parameters, turnaround times, and feasibility were assessed. Results: The mean age of patients was 41.6 ± 13.2 years; 61.4% were male. PCR detected rifampicin resistance in 42 (27.5%) and isoniazid resistance in 39 (25.4%) cases, while nanopore sequencing detected rifampicin resistance in 49 (32.0%) and isoniazid resistance in 45 (29.4%) cases. Compared to phenotypic DST, PCR showed a sensitivity of 84.0% and overall accuracy of 88.2%, whereas nanopore sequencing achieved a sensitivity of 96.0% and overall accuracy of 96.7%. Nanopore sequencing also identified rare rpoB, gyrA, and rrs mutations missed by PCR. Conclusion: Nanopore sequencing demonstrated superior accuracy, broader mutation coverage, and faster turnaround compared to conventional PCR, making it a promising tool for routine detection of drug-resistant TB