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 | |
| Publication status | Published - 3 Sept 2022 |
| Externally published | Yes |
Bibliographical note
Funding Information: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.). Firstly, we would like to acknowledge the contribution of, and thank, all those colleagues who contributed over many years to the collection of the Serratia isolates forming the Institut Pasteur collection of Patrick Grimont. We also thank Alistair Leanord, Teresa Inkster, James Chalmers, Gillian Orange and Nigel Smith for providing recent isolates of Serratia marcescens from UK hospitals, and Hazel Auken and George Salmond for sharing isolates reported previously. We thank Sally Kay, Liz McMinn and Florence Juglas for logistical support, the Wellcome Sanger Institute (WSI) sequencing teams for processing these samples, and Christoph Puethe and the WSI Pathogen Informatics team for help with data management. We thank Gal Horesh, Mat Beale and Matt Dorman for expert technical advice and valuable discussions. For the purpose of Open Access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.
Funding Information:
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.). Firstly, we would like to acknowledge the contribution of, and thank, all those colleagues who contributed over many years to the collection of the Serratia isolates forming the Institut Pasteur collection of Patrick Grimont. We also thank Alistair Leanord, Teresa Inkster, James Chalmers, Gillian Orange and Nigel Smith for providing recent isolates of Serratia marcescens from UK hospitals, and Hazel Auken and George Salmond for sharing isolates reported previously. We thank Sally Kay, Liz McMinn and Florence Juglas for logistical support, the Wellcome Sanger Institute (WSI) sequencing teams for processing these samples, and Christoph Puethe and the WSI Pathogen Informatics team for help with data management. We thank Gal Horesh, Mat Beale and Matt Dorman for expert technical advice and valuable discussions. For the purpose of Open Access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.
Publisher Copyright:
© 2022, The Author(s).
© 2022. The Author(s).