Global ocean resistome revealed: exploring Antibiotic Resistance Genes (ARGs) abundance and distribution on TARA oceans samples through machine learning tools

Detalhes bibliográficos
Autor(a) principal: Cuadrat, Rafael R. C.
Data de Publicação: 2019
Outros Autores: Sorokina, Maria, Andrade, Bruno G., Goris, Tobias, D´Ávila, Alberto M. R.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/41450
Resumo: Molecular Epidemiology Department. German Institute of Human Nutrition Postdam-Rehbruecke - DIE. Germany.
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spelling Cuadrat, Rafael R. C.Sorokina, MariaAndrade, Bruno G.Goris, TobiasD´Ávila, Alberto M. R.2020-05-29T14:44:19Z2020-05-29T14:44:19Z2019CUADRAT, Rafael R. C. et al. Global ocean resistome revealed: exploring Antibiotic Resistance Genes (ARGs) abundance and distribution on TARA oceans samples through machine learning tools. bioRxiv, p. 1-22, Dec. 2019.https://www.arca.fiocruz.br/handle/icict/4145010.1101/765446engBeta-lactamaseMetagenômica marinhaColistinaAprendizado profundoResistência a multidrogasBeta-lactamaseNDM-1Marine metagenomicsColistinDeep learningOLSMultidrug resistanceGlobal ocean resistome revealed: exploring Antibiotic Resistance Genes (ARGs) abundance and distribution on TARA oceans samples through machine learning toolsinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleMolecular Epidemiology Department. German Institute of Human Nutrition Postdam-Rehbruecke - DIE. Germany.Friedrich-Schiller University. Jena, Germany.Embrapa Southeast Livestock.Department of Molecular Toxicology. Research Group Instestinal Microbiology. German Institute of Human Nutrition Postdam-Rehbruecke - DIE. Germany.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e de Sistemas. Rio de Janeiro, RJ, Brasil.The rise of antibiotic resistance (AR) in clinical settings is one of the biggest modern global public health concerns. Therefore, the understanding of AR mechanisms, evolution and global distribution is a priority due to its impact on the treatment course and patient survivability. Besides all efforts in the elucidation of AR mechanisms in clinical strains, little is known about its prevalence and evolution in environmental uncultivable microorganisms. In this study, 293 metagenomic from the TARA Oceans project were used to detect and quantify environmental antibiotic resistance genes (ARGs) using machine learning tools. After extensive manual curation, we show the global ocean ARG abundance, distribution, taxonomy, phylogeny and their potential to be horizontally transferred by plasmids or viruses and their correlation with environmental and geographical parameters. A total of 99,205 environmental ORFs were identified as potential ARGs. These ORFs belong to 560 ARG families that confer resistance to 26 antibiotic classes. 24,567 ORFs were found in contigs classified as plasmidial sequences, suggesting the importance of mobile genetic elements in the dynamics of ARGs transmission. Moreover, 4,804 contigs with more than 2 ARGs were found, including 2 plasmid-like contigs with 5 different ARGs, highlighting the potential presence of multi-resistant microorganisms in the natural ocean environment. This also raises the possibility of horizontal gene transfer (HGT) between clinical and natural environments. The abundance of ARGs showed different patterns of distribution, with some classes being significantly more abundant in coastal biomes. Finally, we identified ARGs conferring resistance to some of the most relevant clinical antibiotics, revealing the presence of 15 ARGs from the recently discovered MCR-1 family with high abundance on Polar Biomes. Of these, 5 were assigned to the genus Psychrobacter, an opportunistic pathogen that can cause fatal infections in humans. Our results are available on Zenodo in MySQL database dump format and all the code used for the analyses, including a Jupyter notebook can be accessed on GitHub (https://github.com/rcuadrat/ocean_resistome).info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/41450/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALAlbertoDÀvila_etal_IOC_2019.pdfAlbertoDÀvila_etal_IOC_2019.pdfapplication/pdf399391https://www.arca.fiocruz.br/bitstream/icict/41450/2/AlbertoD%c3%80vila_etal_IOC_2019.pdf13383d1bc270738ef6c0bb3ae6a1f84cMD52TEXTAlbertoDÀvila_etal_IOC_2019.pdf.txtAlbertoDÀvila_etal_IOC_2019.pdf.txtExtracted texttext/plain59419https://www.arca.fiocruz.br/bitstream/icict/41450/3/AlbertoD%c3%80vila_etal_IOC_2019.pdf.txt986ce3fd9e0e7f68300135848eeade18MD53icict/414502020-05-30 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dc.title.pt_BR.fl_str_mv Global ocean resistome revealed: exploring Antibiotic Resistance Genes (ARGs) abundance and distribution on TARA oceans samples through machine learning tools
title Global ocean resistome revealed: exploring Antibiotic Resistance Genes (ARGs) abundance and distribution on TARA oceans samples through machine learning tools
spellingShingle Global ocean resistome revealed: exploring Antibiotic Resistance Genes (ARGs) abundance and distribution on TARA oceans samples through machine learning tools
Cuadrat, Rafael R. C.
Beta-lactamase
Metagenômica marinha
Colistina
Aprendizado profundo
Resistência a multidrogas
Beta-lactamase
NDM-1
Marine metagenomics
Colistin
Deep learning
OLS
Multidrug resistance
title_short Global ocean resistome revealed: exploring Antibiotic Resistance Genes (ARGs) abundance and distribution on TARA oceans samples through machine learning tools
title_full Global ocean resistome revealed: exploring Antibiotic Resistance Genes (ARGs) abundance and distribution on TARA oceans samples through machine learning tools
title_fullStr Global ocean resistome revealed: exploring Antibiotic Resistance Genes (ARGs) abundance and distribution on TARA oceans samples through machine learning tools
title_full_unstemmed Global ocean resistome revealed: exploring Antibiotic Resistance Genes (ARGs) abundance and distribution on TARA oceans samples through machine learning tools
title_sort Global ocean resistome revealed: exploring Antibiotic Resistance Genes (ARGs) abundance and distribution on TARA oceans samples through machine learning tools
author Cuadrat, Rafael R. C.
author_facet Cuadrat, Rafael R. C.
Sorokina, Maria
Andrade, Bruno G.
Goris, Tobias
D´Ávila, Alberto M. R.
author_role author
author2 Sorokina, Maria
Andrade, Bruno G.
Goris, Tobias
D´Ávila, Alberto M. R.
author2_role author
author
author
author
dc.contributor.author.fl_str_mv Cuadrat, Rafael R. C.
Sorokina, Maria
Andrade, Bruno G.
Goris, Tobias
D´Ávila, Alberto M. R.
dc.subject.other.pt_BR.fl_str_mv Beta-lactamase
Metagenômica marinha
Colistina
Aprendizado profundo
Resistência a multidrogas
topic Beta-lactamase
Metagenômica marinha
Colistina
Aprendizado profundo
Resistência a multidrogas
Beta-lactamase
NDM-1
Marine metagenomics
Colistin
Deep learning
OLS
Multidrug resistance
dc.subject.en.pt_BR.fl_str_mv Beta-lactamase
NDM-1
Marine metagenomics
Colistin
Deep learning
OLS
Multidrug resistance
description Molecular Epidemiology Department. German Institute of Human Nutrition Postdam-Rehbruecke - DIE. Germany.
publishDate 2019
dc.date.issued.fl_str_mv 2019
dc.date.accessioned.fl_str_mv 2020-05-29T14:44:19Z
dc.date.available.fl_str_mv 2020-05-29T14:44:19Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv CUADRAT, Rafael R. C. et al. Global ocean resistome revealed: exploring Antibiotic Resistance Genes (ARGs) abundance and distribution on TARA oceans samples through machine learning tools. bioRxiv, p. 1-22, Dec. 2019.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/41450
dc.identifier.doi.pt_BR.fl_str_mv 10.1101/765446
identifier_str_mv CUADRAT, Rafael R. C. et al. Global ocean resistome revealed: exploring Antibiotic Resistance Genes (ARGs) abundance and distribution on TARA oceans samples through machine learning tools. bioRxiv, p. 1-22, Dec. 2019.
10.1101/765446
url https://www.arca.fiocruz.br/handle/icict/41450
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/41450/1/license.txt
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