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The genus Serratia revisited by genomics

Author

Listed:
  • David J. Williams

    (University of Dundee
    Wellcome Genome Campus)

  • Patrick A. D. Grimont

    (Unité Biodiversité des Bactéries Pathogènes Emergentes, INSERM Unité 389, Institut Pasteur)

  • Adrián Cazares

    (Wellcome Genome Campus
    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
    Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades)

  • 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
    Liverpool School of Tropical Medicine)

  • Matthew T. G. Holden

    (University of St Andrews)

  • Nicholas R. Thomson

    (Wellcome Genome Campus
    London School of Hygiene and Tropical Medicine)

  • Sarah J. Coulthurst

    (University of Dundee)

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.

Suggested Citation

  • 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 & Matthe, 2022. "The genus Serratia revisited by genomics," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-32929-2
    DOI: 10.1038/s41467-022-32929-2
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    References listed on IDEAS

    as
    1. Maria Luisa Cristina & Marina Sartini & Anna Maria Spagnolo, 2019. "Serratia marcescens Infections in Neonatal Intensive Care Units (NICUs)," IJERPH, MDPI, vol. 16(4), pages 1-10, February.
    2. Chirag Jain & Luis M. Rodriguez-R & Adam M. Phillippy & Konstantinos T. Konstantinidis & Srinivas Aluru, 2018. "High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries," Nature Communications, Nature, vol. 9(1), pages 1-8, December.
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    Cited by:

    1. Martin Hagan & Genady Pankov & Ramses Gallegos-Monterrosa & David J. Williams & Christopher Earl & Grant Buchanan & William N. Hunter & Sarah J. Coulthurst, 2023. "Rhs NADase effectors and their immunity proteins are exchangeable mediators of inter-bacterial competition in Serratia," Nature Communications, Nature, vol. 14(1), pages 1-16, December.

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