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

Abstract 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...

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Autores principales:	Ayumu Ohno, Kazuo Umezawa, Satomi Asai, Kirill Kryukov, So Nakagawa, Hayato Miyachi, Tadashi Imanishi
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/a6218a78c05244d4b18b99ef1f80ac2e
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spelling	oai:doaj.org-article:a6218a78c05244d4b18b99ef1f80ac2e2021-12-02T14:11:31ZRapid profiling of drug-resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer10.1038/s41598-021-82903-z2045-2322https://doaj.org/article/a6218a78c05244d4b18b99ef1f80ac2e2021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-82903-zhttps://doaj.org/toc/2045-2322Abstract 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.Ayumu OhnoKazuo UmezawaSatomi AsaiKirill KryukovSo NakagawaHayato MiyachiTadashi ImanishiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-7 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ayumu Ohno Kazuo Umezawa Satomi Asai Kirill Kryukov So Nakagawa Hayato Miyachi Tadashi Imanishi Rapid profiling of drug-resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer
description	Abstract 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.
format	article
author	Ayumu Ohno Kazuo Umezawa Satomi Asai Kirill Kryukov So Nakagawa Hayato Miyachi Tadashi Imanishi
author_facet	Ayumu Ohno Kazuo Umezawa Satomi Asai Kirill Kryukov So Nakagawa Hayato Miyachi Tadashi Imanishi
author_sort	Ayumu Ohno
title	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_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_sort	rapid profiling of drug-resistant bacteria using dna-binding dyes and a nanopore-based dna sequencer
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/a6218a78c05244d4b18b99ef1f80ac2e
work_keys_str_mv	AT ayumuohno rapidprofilingofdrugresistantbacteriausingdnabindingdyesandananoporebaseddnasequencer AT kazuoumezawa rapidprofilingofdrugresistantbacteriausingdnabindingdyesandananoporebaseddnasequencer AT satomiasai rapidprofilingofdrugresistantbacteriausingdnabindingdyesandananoporebaseddnasequencer AT kirillkryukov rapidprofilingofdrugresistantbacteriausingdnabindingdyesandananoporebaseddnasequencer AT sonakagawa rapidprofilingofdrugresistantbacteriausingdnabindingdyesandananoporebaseddnasequencer AT hayatomiyachi rapidprofilingofdrugresistantbacteriausingdnabindingdyesandananoporebaseddnasequencer AT tadashiimanishi rapidprofilingofdrugresistantbacteriausingdnabindingdyesandananoporebaseddnasequencer
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Rapid profiling of drug-resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer

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