Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Nanopore sequencing provides rapid and reliable insight into microbial profiles of Intensive Care Units

Guilherme Marcelino Viana de Siqueira, Felipe Marcelo Pereira-dos-Santos, Rafael Silva-Rocha, View ORCID ProfileMaría-Eugenia Guazzaroni
doi: https://doi.org/10.1101/2021.05.14.444165
Guilherme Marcelino Viana de Siqueira
1Faculdade de Filosofia Ciências e Letras de Ribeirão Preto (FFCLRP-USP), Ribeirão Preto, SP, Brasil. 14040-901
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Felipe Marcelo Pereira-dos-Santos
2Faculdade de Medicina de Ribeirão Preto (FMRP-USP), Ribeirão Preto, SP, Brasil. 14049-900
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Rafael Silva-Rocha
2Faculdade de Medicina de Ribeirão Preto (FMRP-USP), Ribeirão Preto, SP, Brasil. 14049-900
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
María-Eugenia Guazzaroni
1Faculdade de Filosofia Ciências e Letras de Ribeirão Preto (FFCLRP-USP), Ribeirão Preto, SP, Brasil. 14040-901
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for María-Eugenia Guazzaroni
  • For correspondence: meguazzaroni@ffclrp.usp.br
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Data/Code
  • Preview PDF
Loading

Abstract

Fast and accurate identification of pathogens is an essential task in healthcare settings. Next 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 from a hospital in Brazil. While our results point 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.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵† These authors share last authorship

  • https://github.com/GuazzaroniLab/nanopore_ICU_profiling

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted May 14, 2021.
Download PDF

Supplementary Material

Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Nanopore sequencing provides rapid and reliable insight into microbial profiles of Intensive Care Units
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Nanopore sequencing provides rapid and reliable insight into microbial profiles of Intensive Care Units
Guilherme Marcelino Viana de Siqueira, Felipe Marcelo Pereira-dos-Santos, Rafael Silva-Rocha, María-Eugenia Guazzaroni
bioRxiv 2021.05.14.444165; doi: https://doi.org/10.1101/2021.05.14.444165
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Nanopore sequencing provides rapid and reliable insight into microbial profiles of Intensive Care Units
Guilherme Marcelino Viana de Siqueira, Felipe Marcelo Pereira-dos-Santos, Rafael Silva-Rocha, María-Eugenia Guazzaroni
bioRxiv 2021.05.14.444165; doi: https://doi.org/10.1101/2021.05.14.444165

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Microbiology
Subject Areas
All Articles
  • Animal Behavior and Cognition (4658)
  • Biochemistry (10313)
  • Bioengineering (7636)
  • Bioinformatics (26241)
  • Biophysics (13481)
  • Cancer Biology (10648)
  • Cell Biology (15361)
  • Clinical Trials (138)
  • Developmental Biology (8463)
  • Ecology (12776)
  • Epidemiology (2067)
  • Evolutionary Biology (16794)
  • Genetics (11372)
  • Genomics (15431)
  • Immunology (10580)
  • Microbiology (25087)
  • Molecular Biology (10172)
  • Neuroscience (54233)
  • Paleontology (398)
  • Pathology (1660)
  • Pharmacology and Toxicology (2883)
  • Physiology (4326)
  • Plant Biology (9213)
  • Scientific Communication and Education (1582)
  • Synthetic Biology (2545)
  • Systems Biology (6761)
  • Zoology (1458)