The genus Serratia revisited by genomics

David J. Williams; Patrick A. D. Grimont; Adrián Cazares; Francine Grimont; Elisabeth Ageron; Kerry A. Pettigrew; Daniel Cazares; Elisabeth Njamkepo; François-Xavier Weill; Eva Heinz; Matthew T. G. Holden; Nicholas R. Thomson; Sarah J. Coulthurst

doi:10.1038/s41467-022-32929-2

The genus Serratia revisited by genomics

David J. Williams, Patrick A. D. Grimont, Adrián Cazares, Francine Grimont, Elisabeth Ageron, Kerry A. Pettigrew, Daniel Cazares, Elisabeth Njamkepo, François-Xavier Weill, Eva Heinz, Matthew T. G. Holden, Nicholas R. Thomson^*, Sarah J. Coulthurst^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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Abstract

The genus Serratia has been studied for over a century and includes clinically-important and diverse environmental members. Despite this, there is a paucity of genomic information across the genus and a robust whole genome-based phylogenetic framework is lacking. Here, we have assembled and analysed a representative set of 664 genomes from across the genus, including 215 historic isolates originally used in defining the genus. Phylogenomic analysis of the genus reveals a clearly-defined population structure which displays deep divisions and aligns with ecological niche, as well as striking congruence between historical biochemical phenotyping data and contemporary genomics data. We highlight the genomic, phenotypic and plasmid diversity of Serratia, and provide evidence of different patterns of gene flow across the genus. Our work provides a framework for understanding the emergence of clinical and other lineages of Serratia.

Original language	English
Article number	5195
Number of pages	18
Journal	Nature Communications
Volume	13
DOIs	https://doi.org/10.1038/s41467-022-32929-2
Publication status	Published - 3 Sept 2022

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title = "The genus Serratia revisited by genomics",

abstract = "The genus Serratia has been studied for over a century and includes clinically-important and diverse environmental members. Despite this, there is a paucity of genomic information across the genus and a robust whole genome-based phylogenetic framework is lacking. Here, we have assembled and analysed a representative set of 664 genomes from across the genus, including 215 historic isolates originally used in defining the genus. Phylogenomic analysis of the genus reveals a clearly-defined population structure which displays deep divisions and aligns with ecological niche, as well as striking congruence between historical biochemical phenotyping data and contemporary genomics data. We highlight the genomic, phenotypic and plasmid diversity of Serratia, and provide evidence of different patterns of gene flow across the genus. Our work provides a framework for understanding the emergence of clinical and other lineages of Serratia.",

author = "Williams, {David J.} and Grimont, {Patrick A. D.} and Adri{\'a}n Cazares and Francine Grimont and Elisabeth Ageron and Pettigrew, {Kerry A.} and Daniel Cazares and Elisabeth Njamkepo and Fran{\c c}ois-Xavier Weill and Eva Heinz and Holden, {Matthew T. G.} and Thomson, {Nicholas R.} and Coulthurst, {Sarah J.}",

note = "This work was supported by Wellcome (grant numbers: 104556, Senior Research Fellowship S.J.C.; 220321, Senior Research Fellowship Renewal S.J.C.; 109118, Ph.D. studentship; 206194, N.R.T.), the NIHR (NIHR200639, AMR Capital Award to University of Dundee), and Institut Pasteur and INSERM (P.A.D.G. and F.X.W.). ",

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doi = "10.1038/s41467-022-32929-2",

language = "English",

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T1 - The genus Serratia revisited by genomics

AU - Williams, David J.

AU - Grimont, Patrick A. D.

AU - Cazares, Adrián

AU - Grimont, Francine

AU - Ageron, Elisabeth

AU - Pettigrew, Kerry A.

AU - Cazares, Daniel

AU - Njamkepo, Elisabeth

AU - Weill, François-Xavier

AU - Heinz, Eva

AU - Holden, Matthew T. G.

AU - Thomson, Nicholas R.

AU - Coulthurst, Sarah J.

N1 - This work was supported by Wellcome (grant numbers: 104556, Senior Research Fellowship S.J.C.; 220321, Senior Research Fellowship Renewal S.J.C.; 109118, Ph.D. studentship; 206194, N.R.T.), the NIHR (NIHR200639, AMR Capital Award to University of Dundee), and Institut Pasteur and INSERM (P.A.D.G. and F.X.W.).

PY - 2022/9/3

Y1 - 2022/9/3

N2 - The genus Serratia has been studied for over a century and includes clinically-important and diverse environmental members. Despite this, there is a paucity of genomic information across the genus and a robust whole genome-based phylogenetic framework is lacking. Here, we have assembled and analysed a representative set of 664 genomes from across the genus, including 215 historic isolates originally used in defining the genus. Phylogenomic analysis of the genus reveals a clearly-defined population structure which displays deep divisions and aligns with ecological niche, as well as striking congruence between historical biochemical phenotyping data and contemporary genomics data. We highlight the genomic, phenotypic and plasmid diversity of Serratia, and provide evidence of different patterns of gene flow across the genus. Our work provides a framework for understanding the emergence of clinical and other lineages of Serratia.

AB - The genus Serratia has been studied for over a century and includes clinically-important and diverse environmental members. Despite this, there is a paucity of genomic information across the genus and a robust whole genome-based phylogenetic framework is lacking. Here, we have assembled and analysed a representative set of 664 genomes from across the genus, including 215 historic isolates originally used in defining the genus. Phylogenomic analysis of the genus reveals a clearly-defined population structure which displays deep divisions and aligns with ecological niche, as well as striking congruence between historical biochemical phenotyping data and contemporary genomics data. We highlight the genomic, phenotypic and plasmid diversity of Serratia, and provide evidence of different patterns of gene flow across the genus. Our work provides a framework for understanding the emergence of clinical and other lineages of Serratia.

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DO - 10.1038/s41467-022-32929-2

M3 - Article

SN - 2041-1723

VL - 13

JO - Nature Communications

JF - Nature Communications

M1 - 5195

ER -

The genus Serratia revisited by genomics

Abstract

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