Description of a Novel Fish Pathogen, Plesiomonas shigelloides subsp. oncorhynchi, Isolated from Rainbow Trout (Oncorhynchus mykiss): First Genome Analysis and Comparative Genomics

Plesiomonas shigelloides is the only species in its genus, and has zoonotic importance due to the serious implications resulting from the consumption of contaminated seafood. This is the first report on the genomic features of the whole-genome sequence (WGS) of P. shigelloides strain V-78, recovered...

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Autores: Duman, Muhammed, García-Valdés, Elena, Ay, Hilal, Altun, Soner, Saticioglu, Izzet Burcin
Formato: artículo
Estado:Versión publicada
Fecha de publicación:2023
País:España
Recursos:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/337985
Acesso em linha:http://hdl.handle.net/10261/337985
https://api.elsevier.com/content/abstract/scopus_id/85156113497
Access Level:acceso abierto
Palavra-chave:Aquaculture
Plesiomonas genus
Plesiomoniasis
Whole-genome sequences
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spelling Description of a Novel Fish Pathogen, Plesiomonas shigelloides subsp. oncorhynchi, Isolated from Rainbow Trout (Oncorhynchus mykiss): First Genome Analysis and Comparative GenomicsDuman, MuhammedGarcía-Valdés, ElenaAy, HilalAltun, SonerSaticioglu, Izzet BurcinAquaculturePlesiomonas genusPlesiomoniasisWhole-genome sequencesPlesiomonas shigelloides is the only species in its genus, and has zoonotic importance due to the serious implications resulting from the consumption of contaminated seafood. This is the first report on the genomic features of the whole-genome sequence (WGS) of P. shigelloides strain V-78, recovered from diseased rainbow trout, Oncorhynchus mykiss. The genome of P. shigelloides V-78 consists of 4,478,098 base pairs (bp), which encode 3730 proteins, and has a G + C content of 51.1%. The bioinformatics analysis of WGS of V-78 confirmed the presence of 121 tRNA genes and 42 rRNA genes (15 genes for 5S rRNA, 13 genes for 16S rRNA, and 14 genes for 23S rRNA). Comprehensive genome analyses revealed that the strain encodes for secondary metabolites, antimicrobial resistance, and virulence genes. The strain V-78 has 31 known antibiotic resistance models, which encode many antimicrobial resistances. In addition, strain V-78 has 42 different virulence genes, such as adhesion, secretion system, and motility. The digital DNA–DNA hybridization value against P. shigelloides NCTC 10360 was 74.2%, while the average nucleotide identity value was 97.1%. Based on the scrutinized analysis of genomic data, strain V-78 should be considered a novel subspecies of P. shigelloides, for which Plesiomonas shigelloides subsp. oncorhynchi is proposed.This research was funded by Bursa Uludag University grant number TGA-2022-1052.Peer reviewedMultidisciplinary Digital Publishing InstituteBursa Uludağ UniversityDuman, Muhammed [0000-0001-7707-2705]García-Valdés, Elena [0000-0001-5829-0002]Ay, Hilal [0000-0002-8735-4703]Saticioglu, Izzet Burcin [0000-0002-2721-3204]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202320232023info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/337985https://api.elsevier.com/content/abstract/scopus_id/85156113497reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)InglésThe underlying dataset has been published as supplementary material of the article in the publisher platform at DOI 10.3390/fishes8040179https://doi.org/10.3390/fishes8040179Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3379852026-05-22T06:33:51Z
dc.title.none.fl_str_mv Description of a Novel Fish Pathogen, Plesiomonas shigelloides subsp. oncorhynchi, Isolated from Rainbow Trout (Oncorhynchus mykiss): First Genome Analysis and Comparative Genomics
title Description of a Novel Fish Pathogen, Plesiomonas shigelloides subsp. oncorhynchi, Isolated from Rainbow Trout (Oncorhynchus mykiss): First Genome Analysis and Comparative Genomics
spellingShingle Description of a Novel Fish Pathogen, Plesiomonas shigelloides subsp. oncorhynchi, Isolated from Rainbow Trout (Oncorhynchus mykiss): First Genome Analysis and Comparative Genomics
Duman, Muhammed
Aquaculture
Plesiomonas genus
Plesiomoniasis
Whole-genome sequences
title_short Description of a Novel Fish Pathogen, Plesiomonas shigelloides subsp. oncorhynchi, Isolated from Rainbow Trout (Oncorhynchus mykiss): First Genome Analysis and Comparative Genomics
title_full Description of a Novel Fish Pathogen, Plesiomonas shigelloides subsp. oncorhynchi, Isolated from Rainbow Trout (Oncorhynchus mykiss): First Genome Analysis and Comparative Genomics
title_fullStr Description of a Novel Fish Pathogen, Plesiomonas shigelloides subsp. oncorhynchi, Isolated from Rainbow Trout (Oncorhynchus mykiss): First Genome Analysis and Comparative Genomics
title_full_unstemmed Description of a Novel Fish Pathogen, Plesiomonas shigelloides subsp. oncorhynchi, Isolated from Rainbow Trout (Oncorhynchus mykiss): First Genome Analysis and Comparative Genomics
title_sort Description of a Novel Fish Pathogen, Plesiomonas shigelloides subsp. oncorhynchi, Isolated from Rainbow Trout (Oncorhynchus mykiss): First Genome Analysis and Comparative Genomics
dc.creator.none.fl_str_mv Duman, Muhammed
García-Valdés, Elena
Ay, Hilal
Altun, Soner
Saticioglu, Izzet Burcin
author Duman, Muhammed
author_facet Duman, Muhammed
García-Valdés, Elena
Ay, Hilal
Altun, Soner
Saticioglu, Izzet Burcin
author_role author
author2 García-Valdés, Elena
Ay, Hilal
Altun, Soner
Saticioglu, Izzet Burcin
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Bursa Uludağ University
Duman, Muhammed [0000-0001-7707-2705]
García-Valdés, Elena [0000-0001-5829-0002]
Ay, Hilal [0000-0002-8735-4703]
Saticioglu, Izzet Burcin [0000-0002-2721-3204]
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Aquaculture
Plesiomonas genus
Plesiomoniasis
Whole-genome sequences
topic Aquaculture
Plesiomonas genus
Plesiomoniasis
Whole-genome sequences
description Plesiomonas shigelloides is the only species in its genus, and has zoonotic importance due to the serious implications resulting from the consumption of contaminated seafood. This is the first report on the genomic features of the whole-genome sequence (WGS) of P. shigelloides strain V-78, recovered from diseased rainbow trout, Oncorhynchus mykiss. The genome of P. shigelloides V-78 consists of 4,478,098 base pairs (bp), which encode 3730 proteins, and has a G + C content of 51.1%. The bioinformatics analysis of WGS of V-78 confirmed the presence of 121 tRNA genes and 42 rRNA genes (15 genes for 5S rRNA, 13 genes for 16S rRNA, and 14 genes for 23S rRNA). Comprehensive genome analyses revealed that the strain encodes for secondary metabolites, antimicrobial resistance, and virulence genes. The strain V-78 has 31 known antibiotic resistance models, which encode many antimicrobial resistances. In addition, strain V-78 has 42 different virulence genes, such as adhesion, secretion system, and motility. The digital DNA–DNA hybridization value against P. shigelloides NCTC 10360 was 74.2%, while the average nucleotide identity value was 97.1%. Based on the scrutinized analysis of genomic data, strain V-78 should be considered a novel subspecies of P. shigelloides, for which Plesiomonas shigelloides subsp. oncorhynchi is proposed.
publishDate 2023
dc.date.none.fl_str_mv 2023
2023
2023
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/337985
https://api.elsevier.com/content/abstract/scopus_id/85156113497
url http://hdl.handle.net/10261/337985
https://api.elsevier.com/content/abstract/scopus_id/85156113497
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv The underlying dataset has been published as supplementary material of the article in the publisher platform at DOI 10.3390/fishes8040179
https://doi.org/10.3390/fishes8040179
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute
publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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