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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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-08-01
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| Series: | Frontiers in Public Health |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpubh.2021.710985/full |
| _version_ | 1818729866933043200 |
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| author | Guilherme Marcelino Viana de Siqueira Felipe Marcelo Pereira-dos-Santos Rafael Silva-Rocha María-Eugenia Guazzaroni |
| author_facet | Guilherme Marcelino Viana de Siqueira Felipe Marcelo Pereira-dos-Santos Rafael Silva-Rocha María-Eugenia Guazzaroni |
| author_sort | Guilherme Marcelino Viana de Siqueira |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-17T22:52:42Z |
| format | Article |
| id | doaj.art-7ad845bb3f2d4c23a0cf2627a46489f6 |
| institution | Directory Open Access Journal |
| issn | 2296-2565 |
| language | English |
| last_indexed | 2024-12-17T22:52:42Z |
| publishDate | 2021-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Public Health |
| spelling | doaj.art-7ad845bb3f2d4c23a0cf2627a46489f62022-12-21T21:29:38ZengFrontiers Media S.A.Frontiers in Public Health2296-25652021-08-01910.3389/fpubh.2021.710985710985Nanopore Sequencing Provides Rapid and Reliable Insight Into Microbial Profiles of Intensive Care UnitsGuilherme Marcelino Viana de Siqueira0Felipe Marcelo Pereira-dos-Santos1Rafael Silva-Rocha2María-Eugenia Guazzaroni3Departamento de Biologia, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto (FFCLRP-USP), Ribeirão Preto, BrazilDepartamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto (FMRP-USP), Ribeirão Preto, BrazilDepartamento de Biologia, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto (FFCLRP-USP), Ribeirão Preto, BrazilDepartamento de Biologia, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto (FFCLRP-USP), Ribeirão Preto, BrazilFast 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.https://www.frontiersin.org/articles/10.3389/fpubh.2021.710985/fullnanopore sequencingillumina sequencing16S rRNAenvironmental monitoringintensive care unitshealthcare-associated infections |
| spellingShingle | Guilherme Marcelino Viana de Siqueira Felipe Marcelo Pereira-dos-Santos Rafael Silva-Rocha María-Eugenia Guazzaroni Nanopore Sequencing Provides Rapid and Reliable Insight Into Microbial Profiles of Intensive Care Units Frontiers in Public Health nanopore sequencing illumina sequencing 16S rRNA environmental monitoring intensive care units healthcare-associated infections |
| 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 | nanopore sequencing illumina sequencing 16S rRNA environmental monitoring intensive care units healthcare-associated infections |
| url | https://www.frontiersin.org/articles/10.3389/fpubh.2021.710985/full |
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