Is genotyping of single isolates sufficient for population structure analysis of Pseudomonas aeruginosa in cystic fibrosis airways?

Autores
Sommer, Lea M.; Marvig, Rasmus L.; Lujan, Adela Maria; Koza, Anna; Pressler, Tacjana; Molin, Soeren; Johansen, Helle K
Año de publicación
2016
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The primary cause of morbidity and mortality in cystic fibrosis (CF) patients is lung infection by Pseudomonas aeruginosa. Therefore much work has been done to understand the adaptation and evolution of P. aeruginosa in the CF lung. However, many of these studies have focused on longitudinally collected single isolates, and only few have included cross-sectional analyses of entire P. aeruginosa populations in sputum samples. To date only few studies have used the approach of metagenomic analysis for the purpose of investigating P. aeruginosa populations in CF airways. Results: We analysed five metagenomes together with longitudinally collected single isolates from four recently chronically infected CF patients. With this approach we were able to link the clone type and the majority of SNP profiles of the single isolates to that of the metagenome(s) for each individual patient. Conclusion: Based on our analysis we find that when having access to comprehensive collections of longitudinal single isolates it is possible to rediscover the genotypes of the single isolates in the metagenomic samples. This suggests that information gained from genome sequencing of comprehensive collections of single isolates is satisfactory for many investigations of adaptation and evolution of P. aeruginosa to the CF airways.
Fil: Sommer, Lea M.. Technical University of Denmark; Dinamarca. Rigshospitalet. Department of Clinical Microbiology; Dinamarca
Fil: Marvig, Rasmus L.. Rigshospitalet. Department of Clinical Microbiology; Dinamarca
Fil: Lujan, Adela Maria. University of Exeter; Reino Unido. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigaciones en Química Biológica de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Centro de Investigaciones en Química Biológica de Córdoba; Argentina
Fil: Koza, Anna. Technical University of Denmark; Dinamarca
Fil: Pressler, Tacjana. Rigshospitalet. Department of Clinical Microbiology; Dinamarca
Fil: Molin, Soeren. Rigshospitalet. Department of Clinical Microbiology; Dinamarca
Fil: Johansen, Helle K. Rigshospitalet. Department of Clinical Microbiology; Dinamarca
Materia
CYSTIC FIBROSIS
LONGITUDINAL ISOLATES
METAGENOMICS
PSEUDOMONAS AERUGINOSA
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/50850
Acceder
id CONICETDig_91df8be3b3197a444077761366ff2788
oai_identifier_str oai:ri.conicet.gov.ar:11336/50850
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Is genotyping of single isolates sufficient for population structure analysis of Pseudomonas aeruginosa in cystic fibrosis airways?Sommer, Lea M.Marvig, Rasmus L.Lujan, Adela MariaKoza, AnnaPressler, TacjanaMolin, SoerenJohansen, Helle KCYSTIC FIBROSISLONGITUDINAL ISOLATESMETAGENOMICSPSEUDOMONAS AERUGINOSAhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1The primary cause of morbidity and mortality in cystic fibrosis (CF) patients is lung infection by Pseudomonas aeruginosa. Therefore much work has been done to understand the adaptation and evolution of P. aeruginosa in the CF lung. However, many of these studies have focused on longitudinally collected single isolates, and only few have included cross-sectional analyses of entire P. aeruginosa populations in sputum samples. To date only few studies have used the approach of metagenomic analysis for the purpose of investigating P. aeruginosa populations in CF airways. Results: We analysed five metagenomes together with longitudinally collected single isolates from four recently chronically infected CF patients. With this approach we were able to link the clone type and the majority of SNP profiles of the single isolates to that of the metagenome(s) for each individual patient. Conclusion: Based on our analysis we find that when having access to comprehensive collections of longitudinal single isolates it is possible to rediscover the genotypes of the single isolates in the metagenomic samples. This suggests that information gained from genome sequencing of comprehensive collections of single isolates is satisfactory for many investigations of adaptation and evolution of P. aeruginosa to the CF airways.Fil: Sommer, Lea M.. Technical University of Denmark; Dinamarca. Rigshospitalet. Department of Clinical Microbiology; DinamarcaFil: Marvig, Rasmus L.. Rigshospitalet. Department of Clinical Microbiology; DinamarcaFil: Lujan, Adela Maria. University of Exeter; Reino Unido. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigaciones en Química Biológica de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Centro de Investigaciones en Química Biológica de Córdoba; ArgentinaFil: Koza, Anna. Technical University of Denmark; DinamarcaFil: Pressler, Tacjana. Rigshospitalet. Department of Clinical Microbiology; DinamarcaFil: Molin, Soeren. Rigshospitalet. Department of Clinical Microbiology; DinamarcaFil: Johansen, Helle K. Rigshospitalet. Department of Clinical Microbiology; DinamarcaBioMed Central2016-08info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/50850Sommer, Lea M. ; Marvig, Rasmus L. ; Lujan, Adela Maria; Koza, Anna ; Pressler, Tacjana ; et al.; Is genotyping of single isolates sufficient for population structure analysis of Pseudomonas aeruginosa in cystic fibrosis airways?; BioMed Central; BMC Genomics; 17; 1; 8-20161471-2164CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1186/s12864-016-2873-1info:eu-repo/semantics/altIdentifier/url/https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2873-1info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:36:08Zoai:ri.conicet.gov.ar:11336/50850instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 09:36:08.705CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Is genotyping of single isolates sufficient for population structure analysis of Pseudomonas aeruginosa in cystic fibrosis airways?
title Is genotyping of single isolates sufficient for population structure analysis of Pseudomonas aeruginosa in cystic fibrosis airways?
spellingShingle Is genotyping of single isolates sufficient for population structure analysis of Pseudomonas aeruginosa in cystic fibrosis airways?
Sommer, Lea M.
CYSTIC FIBROSIS
LONGITUDINAL ISOLATES
METAGENOMICS
PSEUDOMONAS AERUGINOSA
title_short Is genotyping of single isolates sufficient for population structure analysis of Pseudomonas aeruginosa in cystic fibrosis airways?
title_full Is genotyping of single isolates sufficient for population structure analysis of Pseudomonas aeruginosa in cystic fibrosis airways?
title_fullStr Is genotyping of single isolates sufficient for population structure analysis of Pseudomonas aeruginosa in cystic fibrosis airways?
title_full_unstemmed Is genotyping of single isolates sufficient for population structure analysis of Pseudomonas aeruginosa in cystic fibrosis airways?
title_sort Is genotyping of single isolates sufficient for population structure analysis of Pseudomonas aeruginosa in cystic fibrosis airways?
dc.creator.none.fl_str_mv Sommer, Lea M.
Marvig, Rasmus L.
Lujan, Adela Maria
Koza, Anna
Pressler, Tacjana
Molin, Soeren
Johansen, Helle K
author Sommer, Lea M.
author_facet Sommer, Lea M.
Marvig, Rasmus L.
Lujan, Adela Maria
Koza, Anna
Pressler, Tacjana
Molin, Soeren
Johansen, Helle K
author_role author
author2 Marvig, Rasmus L.
Lujan, Adela Maria
Koza, Anna
Pressler, Tacjana
Molin, Soeren
Johansen, Helle K
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv CYSTIC FIBROSIS
LONGITUDINAL ISOLATES
METAGENOMICS
PSEUDOMONAS AERUGINOSA
topic CYSTIC FIBROSIS
LONGITUDINAL ISOLATES
METAGENOMICS
PSEUDOMONAS AERUGINOSA
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv The primary cause of morbidity and mortality in cystic fibrosis (CF) patients is lung infection by Pseudomonas aeruginosa. Therefore much work has been done to understand the adaptation and evolution of P. aeruginosa in the CF lung. However, many of these studies have focused on longitudinally collected single isolates, and only few have included cross-sectional analyses of entire P. aeruginosa populations in sputum samples. To date only few studies have used the approach of metagenomic analysis for the purpose of investigating P. aeruginosa populations in CF airways. Results: We analysed five metagenomes together with longitudinally collected single isolates from four recently chronically infected CF patients. With this approach we were able to link the clone type and the majority of SNP profiles of the single isolates to that of the metagenome(s) for each individual patient. Conclusion: Based on our analysis we find that when having access to comprehensive collections of longitudinal single isolates it is possible to rediscover the genotypes of the single isolates in the metagenomic samples. This suggests that information gained from genome sequencing of comprehensive collections of single isolates is satisfactory for many investigations of adaptation and evolution of P. aeruginosa to the CF airways.
Fil: Sommer, Lea M.. Technical University of Denmark; Dinamarca. Rigshospitalet. Department of Clinical Microbiology; Dinamarca
Fil: Marvig, Rasmus L.. Rigshospitalet. Department of Clinical Microbiology; Dinamarca
Fil: Lujan, Adela Maria. University of Exeter; Reino Unido. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigaciones en Química Biológica de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Centro de Investigaciones en Química Biológica de Córdoba; Argentina
Fil: Koza, Anna. Technical University of Denmark; Dinamarca
Fil: Pressler, Tacjana. Rigshospitalet. Department of Clinical Microbiology; Dinamarca
Fil: Molin, Soeren. Rigshospitalet. Department of Clinical Microbiology; Dinamarca
Fil: Johansen, Helle K. Rigshospitalet. Department of Clinical Microbiology; Dinamarca
description The primary cause of morbidity and mortality in cystic fibrosis (CF) patients is lung infection by Pseudomonas aeruginosa. Therefore much work has been done to understand the adaptation and evolution of P. aeruginosa in the CF lung. However, many of these studies have focused on longitudinally collected single isolates, and only few have included cross-sectional analyses of entire P. aeruginosa populations in sputum samples. To date only few studies have used the approach of metagenomic analysis for the purpose of investigating P. aeruginosa populations in CF airways. Results: We analysed five metagenomes together with longitudinally collected single isolates from four recently chronically infected CF patients. With this approach we were able to link the clone type and the majority of SNP profiles of the single isolates to that of the metagenome(s) for each individual patient. Conclusion: Based on our analysis we find that when having access to comprehensive collections of longitudinal single isolates it is possible to rediscover the genotypes of the single isolates in the metagenomic samples. This suggests that information gained from genome sequencing of comprehensive collections of single isolates is satisfactory for many investigations of adaptation and evolution of P. aeruginosa to the CF airways.
publishDate 2016
dc.date.none.fl_str_mv 2016-08
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/50850
Sommer, Lea M. ; Marvig, Rasmus L. ; Lujan, Adela Maria; Koza, Anna ; Pressler, Tacjana ; et al.; Is genotyping of single isolates sufficient for population structure analysis of Pseudomonas aeruginosa in cystic fibrosis airways?; BioMed Central; BMC Genomics; 17; 1; 8-2016
1471-2164
CONICET Digital
CONICET
url http://hdl.handle.net/11336/50850
identifier_str_mv Sommer, Lea M. ; Marvig, Rasmus L. ; Lujan, Adela Maria; Koza, Anna ; Pressler, Tacjana ; et al.; Is genotyping of single isolates sufficient for population structure analysis of Pseudomonas aeruginosa in cystic fibrosis airways?; BioMed Central; BMC Genomics; 17; 1; 8-2016
1471-2164
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1186/s12864-016-2873-1
info:eu-repo/semantics/altIdentifier/url/https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2873-1
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.070432

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