ArticleInfection2025
Targeted sputum sequencing for rapid and broad drug resistance of Mycobacterium tuberculosis.
Article in Infection, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- The transformative impact of ultra-rapid nanopore sequencing in precision medicine.Frontiers in immunology · 2026Review
- Drug resistance mechanisms inFrontiers in pharmacology · 2026Review
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Authors and funding
6 authors.
Funding
Abstract
purposeRapid detection of drug resistance in Mycobacterium tuberculosis (Mtb) from clinical samples facilitates the timely provision of optimal treatment regimens for tuberculosis (TB) patients.
methodsIn November, 2023, the WHO released its second catalogue of resistance-conferring mutations in Mtb. Utilizing this information, we developed a single 17-plex PCR assay covering 16 key resistance genes and modified thermo-protection buffer to amplify 30 kbp DNA directly from sputum samples for nanopore sequencing. We implemented our protocol using rapid barcoding for sequencing with both a Flongle and a MinION flow cell.
resultsThe single multiplex PCR assay was successfully validated on clinical sputum samples using the thermo-protection buffer. The protocol was applied to both Flongle and MinION flow cells, analyzing 12 and 40 samples, respectively. Data analysis suggested that optimal performance could be achieved by processing 6 and 12 samples with similar microscope staining scores on these two platforms. This approach facilitated rapid antimicrobial resistance (AMR) predictions directly from sputum on the day of collection or the following day, with a cost of less than $35 per sample. Compared to AMR predictions based on whole-genome sequencing (WGS) using Mykrobe and TBProfiler, our amplicon-based analysis tool, ARapidTb, demonstrated superior resistance detection capabilities. When analyzing publicly available nanopore WGS datasets for 442 isolates, ARapidTb achieved agreement rates of 95.8% and 98.0%, outperforming Mykrobe (89.4% and 98.3%) and TBProfiler (75.6% and 89.8%).
conclusionsOur study significantly reduces the time required for drug resistance detection, enabling quicker initiation of appropriate treatments and potentially improving patient outcomes and TB management.
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