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Article: Targeted-Sequencing Workflows for Comprehensive Drug Resistance Profiling of Mycobacterium tuberculosis Cultures Using Two Commercial Sequencing Platforms: Comparison of Analytical and Diagnostic Performance, Turnaround Time, and Cost

TitleTargeted-Sequencing Workflows for Comprehensive Drug Resistance Profiling of Mycobacterium tuberculosis Cultures Using Two Commercial Sequencing Platforms: Comparison of Analytical and Diagnostic Performance, Turnaround Time, and Cost
Authors
KeywordsMycobacterium tuberculosis
next-generation sequencing
drug-resistant TB
Illumina MiSeq
Nanopore MinION
Issue Date2020
PublisherOxford University Press. The Journal's web site is located at http://www.clinchem.org
Citation
Clinical Chemistry, 2020, v. 66, p. 809-820 How to Cite?
AbstractBackground: The emergence of Mycobacterium tuberculosis with complex drug resistance profiles necessitates a rapid and comprehensive drug susceptibility test for guidance of patient treatment. We developed two targeted-sequencing workflows based on Illumina MiSeq and Nanopore MinION for the prediction of drug resistance in M. tuberculosis toward 12 antibiotics. Methods: A total of 163 M. tuberculosis isolates collected from Hong Kong and Ethiopia were subjected to a multiplex PCR for simultaneous amplification of 19 drug resistance-associated genetic regions. The amplicons were then barcoded and sequenced in parallel on MiSeq and MinION in respective batch sizes of 24 and 12 samples. A web-based bioinformatics pipeline, BacterioChek-TB, was developed to translate the raw datasets into clinician-friendly reports. Results: Both platforms successfully sequenced all samples with mean read depths of 1,127× and 1,649×, respectively. The variant calling by MiSeq and MinION could achieve 100% agreement if variants with an allele frequency of <40% reported by MinION were excluded. Both workflows achieved a mean clinical sensitivity of 94.8% and clinical specificity of 98.0% when compared with phenotypic drug susceptibility test (pDST). Turnaround times for the MiSeq and MinION workflows were 38 and 15 h, facilitating the delivery of treatment guidance at least 17–18 days earlier than pDST, respectively. The higher cost per sample on the MinION platform ($71.56) versus the MiSeq platform ($67.83) was attributed to differences in batching capabilities. Conclusion: Our study demonstrates the interchangeability of MiSeq and MinION platforms for generation of accurate and actionable results for the treatment of tuberculosis.
Persistent Identifierhttp://hdl.handle.net/10722/285448
ISSN
2019 Impact Factor: 7.292
2015 SCImago Journal Rankings: 2.472

 

DC FieldValueLanguage
dc.contributor.authorKetema, T-
dc.contributor.authorNG, TTL-
dc.contributor.authorLAO, HY-
dc.contributor.authorLeung, KSS-
dc.contributor.authorTam, KKG-
dc.contributor.authorRAJWANI, R-
dc.contributor.authorTAM, STY-
dc.contributor.authorHO, LPK-
dc.contributor.authorCHU, CMK-
dc.contributor.authorGONZALEZ, D-
dc.contributor.authorSAYADA, C-
dc.contributor.authorMA, OCK-
dc.contributor.authorNEGA, BH-
dc.contributor.authorANENI, G-
dc.contributor.authorYam, WC-
dc.contributor.authorSIU, GKH-
dc.date.accessioned2020-08-18T03:53:30Z-
dc.date.available2020-08-18T03:53:30Z-
dc.date.issued2020-
dc.identifier.citationClinical Chemistry, 2020, v. 66, p. 809-820-
dc.identifier.issn0009-9147-
dc.identifier.urihttp://hdl.handle.net/10722/285448-
dc.description.abstractBackground: The emergence of Mycobacterium tuberculosis with complex drug resistance profiles necessitates a rapid and comprehensive drug susceptibility test for guidance of patient treatment. We developed two targeted-sequencing workflows based on Illumina MiSeq and Nanopore MinION for the prediction of drug resistance in M. tuberculosis toward 12 antibiotics. Methods: A total of 163 M. tuberculosis isolates collected from Hong Kong and Ethiopia were subjected to a multiplex PCR for simultaneous amplification of 19 drug resistance-associated genetic regions. The amplicons were then barcoded and sequenced in parallel on MiSeq and MinION in respective batch sizes of 24 and 12 samples. A web-based bioinformatics pipeline, BacterioChek-TB, was developed to translate the raw datasets into clinician-friendly reports. Results: Both platforms successfully sequenced all samples with mean read depths of 1,127× and 1,649×, respectively. The variant calling by MiSeq and MinION could achieve 100% agreement if variants with an allele frequency of <40% reported by MinION were excluded. Both workflows achieved a mean clinical sensitivity of 94.8% and clinical specificity of 98.0% when compared with phenotypic drug susceptibility test (pDST). Turnaround times for the MiSeq and MinION workflows were 38 and 15 h, facilitating the delivery of treatment guidance at least 17–18 days earlier than pDST, respectively. The higher cost per sample on the MinION platform ($71.56) versus the MiSeq platform ($67.83) was attributed to differences in batching capabilities. Conclusion: Our study demonstrates the interchangeability of MiSeq and MinION platforms for generation of accurate and actionable results for the treatment of tuberculosis.-
dc.languageeng-
dc.publisherOxford University Press. The Journal's web site is located at http://www.clinchem.org-
dc.relation.ispartofClinical Chemistry-
dc.rightsPre-print: Journal Title] ©: [year] [owner as specified on the article] Published by Oxford University Press [on behalf of xxxxxx]. All rights reserved. Pre-print (Once an article is published, preprint notice should be amended to): This is an electronic version of an article published in [include the complete citation information for the final version of the Article as published in the print edition of the Journal.] Post-print: This is a pre-copy-editing, author-produced PDF of an article accepted for publication in [insert journal title] following peer review. The definitive publisher-authenticated version [insert complete citation information here] is available online at: xxxxxxx [insert URL that the author will receive upon publication here].-
dc.subjectMycobacterium tuberculosis-
dc.subjectnext-generation sequencing-
dc.subjectdrug-resistant TB-
dc.subjectIllumina MiSeq-
dc.subjectNanopore MinION-
dc.titleTargeted-Sequencing Workflows for Comprehensive Drug Resistance Profiling of Mycobacterium tuberculosis Cultures Using Two Commercial Sequencing Platforms: Comparison of Analytical and Diagnostic Performance, Turnaround Time, and Cost-
dc.typeArticle-
dc.identifier.emailLeung, KSS: kssleung@hku.hk-
dc.identifier.emailTam, KKG: kingstkg@hku.hk-
dc.identifier.emailYam, WC: wcyam@hku.hk-
dc.identifier.authorityYam, WC=rp00313-
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1093/clinchem/hvaa092-
dc.identifier.pmid32402055-
dc.identifier.scopuseid_2-s2.0-85085905530-
dc.identifier.hkuros312825-
dc.identifier.volume66-
dc.identifier.spage809-
dc.identifier.epage820-
dc.publisher.placeUnited States-

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