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The first evaluation of targeted nanopore-based sequencing for tuberculosis drug resistance detection

A M Cabibbe(1) K Moghaddasi(1) V Batignani(1) G S K Morgan(1) F Di Marco(1) D M Cirillo(1)

1:San Raffaele Scientific Institute

We investigated the performance of the targeted Next Generation Sequencing (tNGS)-based Oxford Nanopore Diagnostics (OND) AmPORE TB assay, recently approved by the World Health Organization (WHO) for clinical use on tuberculosis (TB)-positive respiratory samples. 

A total of 105 DNA samples from Xpert MT/RIF and smear-positive TB sputum samples were tested with the AmPORE TB kit, using the Genoscreen Deeplex Myc-TB as comparative assay. For AmPORE TB, the samples were divided into five sequencing runs on MinION device. Data analysis was performed using proprietary software. The WHO catalogue of mutations was used for drug resistance interpretation.

The AmPORE TB turnaround time was approximately 5–6 hours from the extracted DNA to the tNGS report for batches of 22 individual samples. The assay achieved a high validity rate of 98% (103/105 samples), homogeneous mean reads coverage across TB-positive samples, and 100% Positive and Negative Agreements for detecting mutations associated with resistance to rifampicin, pyrazinamide, fluoroquinolones, ethambutol and capreomycin, compared to Deeplex MycTB. The main discrepancies for the remaining drugs were attributable to the different assay panel designs.

The AmPORE TB assay drastically reduced the time to tNGS reporting from days to hours and showed a performance largely equivalent to that of the Deeplex Myc-TB kit.


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