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 () and Sarah J. Coulthurst ()
Additional contact information
David J. Williams: University of Dundee
Patrick A. D. Grimont: Unité Biodiversité des Bactéries Pathogènes Emergentes, INSERM Unité 389, Institut Pasteur
Adrián Cazares: Wellcome Genome Campus
Francine Grimont: Unité Biodiversité des Bactéries Pathogènes Emergentes, INSERM Unité 389, Institut Pasteur
Elisabeth Ageron: Unité Biodiversité des Bactéries Pathogènes Emergentes, INSERM Unité 389, Institut Pasteur
Kerry A. Pettigrew: University of St Andrews
Daniel Cazares: Wellcome Genome Campus
Elisabeth Njamkepo: Institut Pasteur, Université de Paris, Unité des Bactéries Pathogènes Entériques
François-Xavier Weill: Institut Pasteur, Université de Paris, Unité des Bactéries Pathogènes Entériques
Eva Heinz: Wellcome Genome Campus
Matthew T. G. Holden: University of St Andrews
Nicholas R. Thomson: Wellcome Genome Campus
Sarah J. Coulthurst: University of Dundee

Nature Communications, 2022, vol. 13, issue 1, 1-18

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-022-32929-2

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