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Nanopore Sequencing Provides Rapid and Reliable Insight Into Microbial Profiles of Intensive Care Units

Fast and accurate identification of pathogens is an essential task in healthcare settings. Second-generation sequencing platforms such as Illumina have greatly expanded the capacity with which different organisms can be detected in hospital samples, and third-generation nanopore-driven sequencing de...

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Autores principales: de Siqueira, Guilherme Marcelino Viana, Pereira-dos-Santos, Felipe Marcelo, Silva-Rocha, Rafael, Guazzaroni, María-Eugenia
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8429932/
https://www.ncbi.nlm.nih.gov/pubmed/34513786
http://dx.doi.org/10.3389/fpubh.2021.710985
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author de Siqueira, Guilherme Marcelino Viana
Pereira-dos-Santos, Felipe Marcelo
Silva-Rocha, Rafael
Guazzaroni, María-Eugenia
author_facet de Siqueira, Guilherme Marcelino Viana
Pereira-dos-Santos, Felipe Marcelo
Silva-Rocha, Rafael
Guazzaroni, María-Eugenia
author_sort de Siqueira, Guilherme Marcelino Viana
collection PubMed
description Fast and accurate identification of pathogens is an essential task in healthcare settings. Second-generation sequencing platforms such as Illumina have greatly expanded the capacity with which different organisms can be detected in hospital samples, and third-generation nanopore-driven sequencing devices such as Oxford Nanopore's minION have recently emerged as ideal sequencing platforms for routine healthcare surveillance due to their long-read capacity and high portability. Despite its great potential, protocols and analysis pipelines for nanopore sequencing are still being extensively validated. In this work, we assess the ability of nanopore sequencing to provide reliable community profiles based on 16S rRNA sequencing in comparison to traditional Illumina platforms using samples collected from Intensive Care Units of a hospital in Brazil. While our results demonstrate that lower throughputs may be a shortcoming of the method in more complex samples, we show that the use of single-use Flongle flowcells in nanopore sequencing runs can provide insightful information on the community composition in healthcare settings.
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spelling pubmed-84299322021-09-11 Nanopore Sequencing Provides Rapid and Reliable Insight Into Microbial Profiles of Intensive Care Units de Siqueira, Guilherme Marcelino Viana Pereira-dos-Santos, Felipe Marcelo Silva-Rocha, Rafael Guazzaroni, María-Eugenia Front Public Health Public Health Fast and accurate identification of pathogens is an essential task in healthcare settings. Second-generation sequencing platforms such as Illumina have greatly expanded the capacity with which different organisms can be detected in hospital samples, and third-generation nanopore-driven sequencing devices such as Oxford Nanopore's minION have recently emerged as ideal sequencing platforms for routine healthcare surveillance due to their long-read capacity and high portability. Despite its great potential, protocols and analysis pipelines for nanopore sequencing are still being extensively validated. In this work, we assess the ability of nanopore sequencing to provide reliable community profiles based on 16S rRNA sequencing in comparison to traditional Illumina platforms using samples collected from Intensive Care Units of a hospital in Brazil. While our results demonstrate that lower throughputs may be a shortcoming of the method in more complex samples, we show that the use of single-use Flongle flowcells in nanopore sequencing runs can provide insightful information on the community composition in healthcare settings. Frontiers Media S.A. 2021-08-27 /pmc/articles/PMC8429932/ /pubmed/34513786 http://dx.doi.org/10.3389/fpubh.2021.710985 Text en Copyright © 2021 de Siqueira, Pereira-dos-Santos, Silva-Rocha and Guazzaroni. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Public Health
de Siqueira, Guilherme Marcelino Viana
Pereira-dos-Santos, Felipe Marcelo
Silva-Rocha, Rafael
Guazzaroni, María-Eugenia
Nanopore Sequencing Provides Rapid and Reliable Insight Into Microbial Profiles of Intensive Care Units
title Nanopore Sequencing Provides Rapid and Reliable Insight Into Microbial Profiles of Intensive Care Units
title_full Nanopore Sequencing Provides Rapid and Reliable Insight Into Microbial Profiles of Intensive Care Units
title_fullStr Nanopore Sequencing Provides Rapid and Reliable Insight Into Microbial Profiles of Intensive Care Units
title_full_unstemmed Nanopore Sequencing Provides Rapid and Reliable Insight Into Microbial Profiles of Intensive Care Units
title_short Nanopore Sequencing Provides Rapid and Reliable Insight Into Microbial Profiles of Intensive Care Units
title_sort nanopore sequencing provides rapid and reliable insight into microbial profiles of intensive care units
topic Public Health
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8429932/
https://www.ncbi.nlm.nih.gov/pubmed/34513786
http://dx.doi.org/10.3389/fpubh.2021.710985
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