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- Publisher Website: 10.1186/s13104-020-05287-9
- Scopus: eid_2-s2.0-85091324252
- PMID: 32948225
- WOS: WOS:000573627500004
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Article: Rapid and economical drug resistance profiling with Nanopore MinION for clinical specimens with low bacillary burden of Mycobacterium tuberculosis
Title | Rapid and economical drug resistance profiling with Nanopore MinION for clinical specimens with low bacillary burden of Mycobacterium tuberculosis |
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Authors | |
Keywords | Antibiotic resistance Illumina MiSeq MDR-TB Nanopore MinION NGS |
Issue Date | 2020 |
Publisher | BioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcresnotes/ |
Citation | BMC Research Notes, 2020, v. 13 n. 1, p. article no. 444 How to Cite? |
Abstract | Objective:
We designed and tested a Nanopore sequencing panel for direct tuberculosis drug resistance profiling. The panel targeted 10 resistance-associated loci. We assessed the feasibility of amplifying and sequencing these loci from 23 clinical specimens with low bacillary burden.
Results:
At least 8 loci were successfully amplified from the majority for predicting first- and second-line drug resistance (14/23, 60.87%), and the 12 specimens yielding all 10 targets were sequenced with Nanopore MinION and Illumina MiSeq. MinION sequencing data was corrected by Nanopolish and recurrent variants were filtered. A total of 67,082 bases across all consensus sequences were analyzed, with 67,019 bases called by both MinION and MiSeq as wildtype. For the 41 single nucleotide variants (SNVs) called by MiSeq with 100% variant allelic frequency (VAF), 39 (95.1%) were called by MinION. For the 22 mixed bases called by MiSeq, a SNV with the highest VAF (70%) was called by MinION. With short assay time, reasonable reagent cost as well as continuously improving sequencing chemistry and signal correction pipelines, this Nanopore method can be a viable option for direct tuberculosis drug resistance profiling in the near future. |
Persistent Identifier | http://hdl.handle.net/10722/291051 |
ISSN | 2023 Impact Factor: 1.6 2023 SCImago Journal Rankings: 0.486 |
PubMed Central ID | |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Chan, WS | - |
dc.contributor.author | Au, CH | - |
dc.contributor.author | Chung, Y | - |
dc.contributor.author | Leung, HCM | - |
dc.contributor.author | Ho, DN | - |
dc.contributor.author | Wong, EYL | - |
dc.contributor.author | Lam, TW | - |
dc.contributor.author | Chan, TL | - |
dc.contributor.author | Ma, ESK | - |
dc.contributor.author | Tang, BSF | - |
dc.date.accessioned | 2020-11-02T05:50:52Z | - |
dc.date.available | 2020-11-02T05:50:52Z | - |
dc.date.issued | 2020 | - |
dc.identifier.citation | BMC Research Notes, 2020, v. 13 n. 1, p. article no. 444 | - |
dc.identifier.issn | 1756-0500 | - |
dc.identifier.uri | http://hdl.handle.net/10722/291051 | - |
dc.description.abstract | Objective: We designed and tested a Nanopore sequencing panel for direct tuberculosis drug resistance profiling. The panel targeted 10 resistance-associated loci. We assessed the feasibility of amplifying and sequencing these loci from 23 clinical specimens with low bacillary burden. Results: At least 8 loci were successfully amplified from the majority for predicting first- and second-line drug resistance (14/23, 60.87%), and the 12 specimens yielding all 10 targets were sequenced with Nanopore MinION and Illumina MiSeq. MinION sequencing data was corrected by Nanopolish and recurrent variants were filtered. A total of 67,082 bases across all consensus sequences were analyzed, with 67,019 bases called by both MinION and MiSeq as wildtype. For the 41 single nucleotide variants (SNVs) called by MiSeq with 100% variant allelic frequency (VAF), 39 (95.1%) were called by MinION. For the 22 mixed bases called by MiSeq, a SNV with the highest VAF (70%) was called by MinION. With short assay time, reasonable reagent cost as well as continuously improving sequencing chemistry and signal correction pipelines, this Nanopore method can be a viable option for direct tuberculosis drug resistance profiling in the near future. | - |
dc.language | eng | - |
dc.publisher | BioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcresnotes/ | - |
dc.relation.ispartof | BMC Research Notes | - |
dc.rights | BMC Research Notes. Copyright © BioMed Central Ltd. | - |
dc.rights | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | - |
dc.subject | Antibiotic resistance | - |
dc.subject | Illumina MiSeq | - |
dc.subject | MDR-TB | - |
dc.subject | Nanopore MinION | - |
dc.subject | NGS | - |
dc.title | Rapid and economical drug resistance profiling with Nanopore MinION for clinical specimens with low bacillary burden of Mycobacterium tuberculosis | - |
dc.type | Article | - |
dc.identifier.email | Leung, HCM: cmleung3@hku.hk | - |
dc.identifier.email | Lam, TW: twlam@cs.hku.hk | - |
dc.identifier.authority | Leung, HCM=rp00144 | - |
dc.identifier.authority | Lam, TW=rp00135 | - |
dc.description.nature | published_or_final_version | - |
dc.identifier.doi | 10.1186/s13104-020-05287-9 | - |
dc.identifier.pmid | 32948225 | - |
dc.identifier.pmcid | PMC7501614 | - |
dc.identifier.scopus | eid_2-s2.0-85091324252 | - |
dc.identifier.hkuros | 318148 | - |
dc.identifier.volume | 13 | - |
dc.identifier.issue | 1 | - |
dc.identifier.spage | article no. 444 | - |
dc.identifier.epage | article no. 444 | - |
dc.identifier.isi | WOS:000573627500004 | - |
dc.publisher.place | United Kingdom | - |
dc.identifier.issnl | 1756-0500 | - |