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A retrospective and regional approach assessing the genomic diversity of Salmonella Dublin

From a historically rare serotype, Salmonella enterica subsp. enterica Dublin slowly became one of the most prevalent Salmonella in cattle and raw milk cheese in some regions of France. We present a retrospective genomic analysis of 480 S. Dublin isolates to address the context, evolutionary dynamic...

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Autores principales: De Sousa Violante, Madeleine, Podeur, Gaëtan, Michel, Valérie, Guillier, Laurent, Radomski, Nicolas, Lailler, Renaud, Le Hello, Simon, Weill, François-Xavier, Mistou, Michel-Yves, Mallet, Ludovic
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9270687/
https://www.ncbi.nlm.nih.gov/pubmed/35821882
http://dx.doi.org/10.1093/nargab/lqac047
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author De Sousa Violante, Madeleine
Podeur, Gaëtan
Michel, Valérie
Guillier, Laurent
Radomski, Nicolas
Lailler, Renaud
Le Hello, Simon
Weill, François-Xavier
Mistou, Michel-Yves
Mallet, Ludovic
author_facet De Sousa Violante, Madeleine
Podeur, Gaëtan
Michel, Valérie
Guillier, Laurent
Radomski, Nicolas
Lailler, Renaud
Le Hello, Simon
Weill, François-Xavier
Mistou, Michel-Yves
Mallet, Ludovic
author_sort De Sousa Violante, Madeleine
collection PubMed
description From a historically rare serotype, Salmonella enterica subsp. enterica Dublin slowly became one of the most prevalent Salmonella in cattle and raw milk cheese in some regions of France. We present a retrospective genomic analysis of 480 S. Dublin isolates to address the context, evolutionary dynamics, local diversity and the genesis processes of regional S. Dublin outbreaks events between 2015 and 2017. Samples were clustered and assessed for correlation against metadata including isolation date, isolation matrices, geographical origin and epidemiological hypotheses. Significant findings can be drawn from this work. We found that the geographical distance was a major factor explaining genetic groups in the early stages of the cheese production processes (animals, farms) while down-the-line transformation steps were more likely to host genomic diversity. This supports the hypothesis of a generalised local persistence of strains from animal to finished products, with occasional migration. We also observed that the bacterial surveillance is representative of diversity, while targeted investigations without genomics evidence often included unrelated isolates. Combining both approaches in phylogeography methods allows a better representation of the dynamics, of outbreaks.
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spelling pubmed-92706872022-07-11 A retrospective and regional approach assessing the genomic diversity of Salmonella Dublin De Sousa Violante, Madeleine Podeur, Gaëtan Michel, Valérie Guillier, Laurent Radomski, Nicolas Lailler, Renaud Le Hello, Simon Weill, François-Xavier Mistou, Michel-Yves Mallet, Ludovic NAR Genom Bioinform Standard Article From a historically rare serotype, Salmonella enterica subsp. enterica Dublin slowly became one of the most prevalent Salmonella in cattle and raw milk cheese in some regions of France. We present a retrospective genomic analysis of 480 S. Dublin isolates to address the context, evolutionary dynamics, local diversity and the genesis processes of regional S. Dublin outbreaks events between 2015 and 2017. Samples were clustered and assessed for correlation against metadata including isolation date, isolation matrices, geographical origin and epidemiological hypotheses. Significant findings can be drawn from this work. We found that the geographical distance was a major factor explaining genetic groups in the early stages of the cheese production processes (animals, farms) while down-the-line transformation steps were more likely to host genomic diversity. This supports the hypothesis of a generalised local persistence of strains from animal to finished products, with occasional migration. We also observed that the bacterial surveillance is representative of diversity, while targeted investigations without genomics evidence often included unrelated isolates. Combining both approaches in phylogeography methods allows a better representation of the dynamics, of outbreaks. Oxford University Press 2022-07-09 /pmc/articles/PMC9270687/ /pubmed/35821882 http://dx.doi.org/10.1093/nargab/lqac047 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Standard Article
De Sousa Violante, Madeleine
Podeur, Gaëtan
Michel, Valérie
Guillier, Laurent
Radomski, Nicolas
Lailler, Renaud
Le Hello, Simon
Weill, François-Xavier
Mistou, Michel-Yves
Mallet, Ludovic
A retrospective and regional approach assessing the genomic diversity of Salmonella Dublin
title A retrospective and regional approach assessing the genomic diversity of Salmonella Dublin
title_full A retrospective and regional approach assessing the genomic diversity of Salmonella Dublin
title_fullStr A retrospective and regional approach assessing the genomic diversity of Salmonella Dublin
title_full_unstemmed A retrospective and regional approach assessing the genomic diversity of Salmonella Dublin
title_short A retrospective and regional approach assessing the genomic diversity of Salmonella Dublin
title_sort retrospective and regional approach assessing the genomic diversity of salmonella dublin
topic Standard Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9270687/
https://www.ncbi.nlm.nih.gov/pubmed/35821882
http://dx.doi.org/10.1093/nargab/lqac047
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