Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics

Abstract The isolation and sequencing of new strains of Pseudomonas aeruginosa created an extensive dataset of closed genomes. Many of the publicly available genomes are only used in their original publication while additional in silico information, based on comparison to previously published genome...

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Autores principales:	Carola Berger, Christian Rückert, Jochen Blom, Korneel Rabaey, Jörn Kalinowski, Miriam A. Rosenbaum
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/5921e5e543b94ca9ad1bab87534f1ca6
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spelling	oai:doaj.org-article:5921e5e543b94ca9ad1bab87534f1ca62021-12-02T15:23:04ZEstimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics10.1038/s41598-020-80592-82045-2322https://doaj.org/article/5921e5e543b94ca9ad1bab87534f1ca62021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-80592-8https://doaj.org/toc/2045-2322Abstract The isolation and sequencing of new strains of Pseudomonas aeruginosa created an extensive dataset of closed genomes. Many of the publicly available genomes are only used in their original publication while additional in silico information, based on comparison to previously published genomes, is not being explored. In this study, we defined and investigated the genome of the environmental isolate P. aeruginosa KRP1 and compared it to more than 100 publicly available closed P. aeruginosa genomes. By using different genomic island prediction programs, we could identify a total of 17 genomic islands and 8 genomic islets, marking the majority of the accessory genome that covers ~ 12% of the total genome. Based on intra-strain comparisons, we are able to predict the pathogenic potential of this environmental isolate. It shares a substantial amount of genomic information with the highly virulent PSE9 and LESB58 strains. For both of these, the increased virulence has been directly linked to their accessory genome before. Hence, the integrated use of previously published data can help to minimize expensive and time consuming wetlab work to determine the pathogenetic potential.Carola BergerChristian RückertJochen BlomKorneel RabaeyJörn KalinowskiMiriam A. RosenbaumNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Carola Berger Christian Rückert Jochen Blom Korneel Rabaey Jörn Kalinowski Miriam A. Rosenbaum Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics
description	Abstract The isolation and sequencing of new strains of Pseudomonas aeruginosa created an extensive dataset of closed genomes. Many of the publicly available genomes are only used in their original publication while additional in silico information, based on comparison to previously published genomes, is not being explored. In this study, we defined and investigated the genome of the environmental isolate P. aeruginosa KRP1 and compared it to more than 100 publicly available closed P. aeruginosa genomes. By using different genomic island prediction programs, we could identify a total of 17 genomic islands and 8 genomic islets, marking the majority of the accessory genome that covers ~ 12% of the total genome. Based on intra-strain comparisons, we are able to predict the pathogenic potential of this environmental isolate. It shares a substantial amount of genomic information with the highly virulent PSE9 and LESB58 strains. For both of these, the increased virulence has been directly linked to their accessory genome before. Hence, the integrated use of previously published data can help to minimize expensive and time consuming wetlab work to determine the pathogenetic potential.
format	article
author	Carola Berger Christian Rückert Jochen Blom Korneel Rabaey Jörn Kalinowski Miriam A. Rosenbaum
author_facet	Carola Berger Christian Rückert Jochen Blom Korneel Rabaey Jörn Kalinowski Miriam A. Rosenbaum
author_sort	Carola Berger
title	Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics
title_short	Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics
title_full	Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics
title_fullStr	Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics
title_full_unstemmed	Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics
title_sort	estimation of pathogenic potential of an environmental pseudomonas aeruginosa isolate using comparative genomics
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/5921e5e543b94ca9ad1bab87534f1ca6
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_version_	1718387325402087424

Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics

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