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Article: Rapid and economical drug resistance profiling with Nanopore MinION for clinical specimens with low bacillary burden of Mycobacterium tuberculosis

TitleRapid and economical drug resistance profiling with Nanopore MinION for clinical specimens with low bacillary burden of Mycobacterium tuberculosis
Authors
KeywordsAntibiotic resistance
Illumina MiSeq
MDR-TB
Nanopore MinION
NGS
Issue Date2020
PublisherBioMed 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?
AbstractObjective: 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 Identifierhttp://hdl.handle.net/10722/291051
ISSN
2015 SCImago Journal Rankings: 0.702
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorChan, WS-
dc.contributor.authorAu, CH-
dc.contributor.authorChung, Y-
dc.contributor.authorLeung, HCM-
dc.contributor.authorHo, DN-
dc.contributor.authorWong, EYL-
dc.contributor.authorLam, TW-
dc.contributor.authorChan, TL-
dc.contributor.authorMa, ESK-
dc.contributor.authorTang, BSF-
dc.date.accessioned2020-11-02T05:50:52Z-
dc.date.available2020-11-02T05:50:52Z-
dc.date.issued2020-
dc.identifier.citationBMC Research Notes, 2020, v. 13 n. 1, p. article no. 444-
dc.identifier.issn1756-0500-
dc.identifier.urihttp://hdl.handle.net/10722/291051-
dc.description.abstractObjective: 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.languageeng-
dc.publisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcresnotes/-
dc.relation.ispartofBMC Research Notes-
dc.rightsBMC Research Notes. Copyright © BioMed Central Ltd.-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.subjectAntibiotic resistance-
dc.subjectIllumina MiSeq-
dc.subjectMDR-TB-
dc.subjectNanopore MinION-
dc.subjectNGS-
dc.titleRapid and economical drug resistance profiling with Nanopore MinION for clinical specimens with low bacillary burden of Mycobacterium tuberculosis-
dc.typeArticle-
dc.identifier.emailLeung, HCM: cmleung3@hku.hk-
dc.identifier.emailLam, TW: twlam@cs.hku.hk-
dc.identifier.authorityLeung, HCM=rp00144-
dc.identifier.authorityLam, TW=rp00135-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1186/s13104-020-05287-9-
dc.identifier.pmid32948225-
dc.identifier.pmcidPMC7501614-
dc.identifier.scopuseid_2-s2.0-85091324252-
dc.identifier.hkuros318148-
dc.identifier.volume13-
dc.identifier.issue1-
dc.identifier.spagearticle no. 444-
dc.identifier.epagearticle no. 444-
dc.identifier.isiWOS:000573627500004-
dc.publisher.placeUnited Kingdom-
dc.identifier.issnl1756-0500-

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