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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Bibliographic Details
Published inScientific reports Vol. 11; no. 1; p. 3436
Main Authors Ohno, Ayumu, Umezawa, Kazuo, Asai, Satomi, Kryukov, Kirill, Nakagawa, So, Miyachi, Hayato, Imanishi, Tadashi
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 09.02.2021
Nature Publishing Group
Nature Portfolio
Subjects
631/1647/2217
631/1647/2234
631/1647/514
631/208/212
631/208/2489
631/208/325
692/4017
Antibiotics
Bacteria
Deoxyribonucleic acid
DNA
Drug resistance
Humanities and Social Sciences
multidisciplinary
Nucleotide sequence
rRNA 16S
Science
Science (multidisciplinary)
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Summary: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.
Bibliography:ObjectType-Article-1
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ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-021-82903-z