Rapid profiling of drug-resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer

Spread of drug-resistant bacteria is a serious problem worldwide. We thus designed a new sequence-based protocol that can quickly identify bacterial compositions of clinical samples and their drug-resistance profiles simultaneously. Here we utilized propidium monoazide (PMA) that prohibits DNA ampli...

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Autores principales: Ohno, Ayumu, Umezawa, Kazuo, Asai, Satomi, Kryukov, Kirill, Nakagawa, So, Miyachi, Hayato, Imanishi, Tadashi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7873225/
https://www.ncbi.nlm.nih.gov/pubmed/33564026
http://dx.doi.org/10.1038/s41598-021-82903-z
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author Ohno, Ayumu
Umezawa, Kazuo
Asai, Satomi
Kryukov, Kirill
Nakagawa, So
Miyachi, Hayato
Imanishi, Tadashi
author_facet Ohno, Ayumu
Umezawa, Kazuo
Asai, Satomi
Kryukov, Kirill
Nakagawa, So
Miyachi, Hayato
Imanishi, Tadashi
author_sort Ohno, Ayumu
collection PubMed
description Spread of drug-resistant bacteria is a serious problem worldwide. We thus designed a new sequence-based protocol that can quickly identify bacterial compositions of clinical samples and their drug-resistance profiles simultaneously. Here we utilized propidium monoazide (PMA) that prohibits DNA amplifications from dead bacteria, and subjected the original and antibiotics-treated samples to 16S rRNA metagenome sequencing. We tested our protocol on bacterial mixtures, and observed that sequencing reads derived from drug-resistant bacteria were significantly increased compared with those from drug-sensitive bacteria when samples were treated by antibiotics. Our protocol is scalable and will be useful for quickly profiling drug-resistant bacteria.
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spelling pubmed-78732252021-02-11 Rapid profiling of drug-resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer Ohno, Ayumu Umezawa, Kazuo Asai, Satomi Kryukov, Kirill Nakagawa, So Miyachi, Hayato Imanishi, Tadashi Sci Rep Article Spread of drug-resistant bacteria is a serious problem worldwide. We thus designed a new sequence-based protocol that can quickly identify bacterial compositions of clinical samples and their drug-resistance profiles simultaneously. Here we utilized propidium monoazide (PMA) that prohibits DNA amplifications from dead bacteria, and subjected the original and antibiotics-treated samples to 16S rRNA metagenome sequencing. We tested our protocol on bacterial mixtures, and observed that sequencing reads derived from drug-resistant bacteria were significantly increased compared with those from drug-sensitive bacteria when samples were treated by antibiotics. Our protocol is scalable and will be useful for quickly profiling drug-resistant bacteria. Nature Publishing Group UK 2021-02-09 /pmc/articles/PMC7873225/ /pubmed/33564026 http://dx.doi.org/10.1038/s41598-021-82903-z Text en © The Author(s) 2021 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Ohno, Ayumu
Umezawa, Kazuo
Asai, Satomi
Kryukov, Kirill
Nakagawa, So
Miyachi, Hayato
Imanishi, Tadashi
Rapid profiling of drug-resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer
title Rapid profiling of drug-resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer
title_full Rapid profiling of drug-resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer
title_fullStr Rapid profiling of drug-resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer
title_full_unstemmed Rapid profiling of drug-resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer
title_short Rapid profiling of drug-resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer
title_sort rapid profiling of drug-resistant bacteria using dna-binding dyes and a nanopore-based dna sequencer
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7873225/
https://www.ncbi.nlm.nih.gov/pubmed/33564026
http://dx.doi.org/10.1038/s41598-021-82903-z
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