Rapid Identification of Drug-Resistant Tuberculosis Genes Using Direct PCR Amplification and Oxford Nanopore Technology Sequencing

Mycobacterium tuberculosis antimicrobial resistance has been continually reported and is a major public health issue worldwide. Rapid prediction of drug resistance is important for selecting appropriate antibiotic treatments, which significantly increases cure rates. Gene sequencing technology has p...

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Autores principales: Zhao, Kaishun, Tu, Chunlin, Chen, Wei, Liang, Haiying, Zhang, Wenjing, Wang, Yilei, Jin, Ye, Hu, Jianrong, Sun, Yameng, Xu, Jun, Yu, Yanfang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8979720/
https://www.ncbi.nlm.nih.gov/pubmed/35386470
http://dx.doi.org/10.1155/2022/7588033
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author Zhao, Kaishun
Tu, Chunlin
Chen, Wei
Liang, Haiying
Zhang, Wenjing
Wang, Yilei
Jin, Ye
Hu, Jianrong
Sun, Yameng
Xu, Jun
Yu, Yanfang
author_facet Zhao, Kaishun
Tu, Chunlin
Chen, Wei
Liang, Haiying
Zhang, Wenjing
Wang, Yilei
Jin, Ye
Hu, Jianrong
Sun, Yameng
Xu, Jun
Yu, Yanfang
author_sort Zhao, Kaishun
collection PubMed
description Mycobacterium tuberculosis antimicrobial resistance has been continually reported and is a major public health issue worldwide. Rapid prediction of drug resistance is important for selecting appropriate antibiotic treatments, which significantly increases cure rates. Gene sequencing technology has proven to be a powerful strategy for identifying relevant drug resistance information. This study established a sequencing method and bioinformatics pipeline for resistance gene analysis using an Oxford Nanopore Technologies sequencer. The pipeline was validated by Sanger sequencing and exhibited 100% concordance with the identified variants. Turnaround time for the nanopore sequencing workflow was approximately 12 h, facilitating drug resistance prediction several weeks earlier than that of traditional phenotype drug susceptibility testing. This study produced a customized gene panel assay for rapid bacterial identification via nanopore sequencing, which improves the timeliness of tuberculosis diagnoses and provides a reliable method that may have clinical application.
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spelling pubmed-89797202022-04-05 Rapid Identification of Drug-Resistant Tuberculosis Genes Using Direct PCR Amplification and Oxford Nanopore Technology Sequencing Zhao, Kaishun Tu, Chunlin Chen, Wei Liang, Haiying Zhang, Wenjing Wang, Yilei Jin, Ye Hu, Jianrong Sun, Yameng Xu, Jun Yu, Yanfang Can J Infect Dis Med Microbiol Research Article Mycobacterium tuberculosis antimicrobial resistance has been continually reported and is a major public health issue worldwide. Rapid prediction of drug resistance is important for selecting appropriate antibiotic treatments, which significantly increases cure rates. Gene sequencing technology has proven to be a powerful strategy for identifying relevant drug resistance information. This study established a sequencing method and bioinformatics pipeline for resistance gene analysis using an Oxford Nanopore Technologies sequencer. The pipeline was validated by Sanger sequencing and exhibited 100% concordance with the identified variants. Turnaround time for the nanopore sequencing workflow was approximately 12 h, facilitating drug resistance prediction several weeks earlier than that of traditional phenotype drug susceptibility testing. This study produced a customized gene panel assay for rapid bacterial identification via nanopore sequencing, which improves the timeliness of tuberculosis diagnoses and provides a reliable method that may have clinical application. Hindawi 2022-03-28 /pmc/articles/PMC8979720/ /pubmed/35386470 http://dx.doi.org/10.1155/2022/7588033 Text en Copyright © 2022 Kaishun Zhao et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Zhao, Kaishun
Tu, Chunlin
Chen, Wei
Liang, Haiying
Zhang, Wenjing
Wang, Yilei
Jin, Ye
Hu, Jianrong
Sun, Yameng
Xu, Jun
Yu, Yanfang
Rapid Identification of Drug-Resistant Tuberculosis Genes Using Direct PCR Amplification and Oxford Nanopore Technology Sequencing
title Rapid Identification of Drug-Resistant Tuberculosis Genes Using Direct PCR Amplification and Oxford Nanopore Technology Sequencing
title_full Rapid Identification of Drug-Resistant Tuberculosis Genes Using Direct PCR Amplification and Oxford Nanopore Technology Sequencing
title_fullStr Rapid Identification of Drug-Resistant Tuberculosis Genes Using Direct PCR Amplification and Oxford Nanopore Technology Sequencing
title_full_unstemmed Rapid Identification of Drug-Resistant Tuberculosis Genes Using Direct PCR Amplification and Oxford Nanopore Technology Sequencing
title_short Rapid Identification of Drug-Resistant Tuberculosis Genes Using Direct PCR Amplification and Oxford Nanopore Technology Sequencing
title_sort rapid identification of drug-resistant tuberculosis genes using direct pcr amplification and oxford nanopore technology sequencing
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8979720/
https://www.ncbi.nlm.nih.gov/pubmed/35386470
http://dx.doi.org/10.1155/2022/7588033
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