IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-38902-x.html
   My bibliography  Save this article

A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia

Author

Listed:
  • Wim L. Cuypers

    (University of Antwerp
    Institute of Tropical Medicine)

  • Pieter Meysman

    (University of Antwerp)

  • François-Xavier Weill

    (Université Paris Cité, Unité des bactéries pathogènes entériques)

  • Rene S. Hendriksen

    (Technical University of Denmark, National Food Institute (DTU-Food), Research Group of Global Capacity Building, Kgs.)

  • Getenet Beyene

    (Jimma University)

  • John Wain

    (Norwich Research Park
    University of East Anglia)

  • Satheesh Nair

    (United Kingdom Health Security Agency, Colindale)

  • Marie A. Chattaway

    (United Kingdom Health Security Agency, Colindale)

  • Blanca M. Perez-Sepulveda

    (University of Liverpool)

  • Pieter-Jan Ceyssens

    (Division of Human Bacterial Diseases, Sciensano)

  • Tessa Block

    (Institute of Tropical Medicine)

  • Winnie W. Y. Lee

    (United Kingdom Health Security Agency, Colindale
    Imperial College London)

  • Maria Pardos de la Gandara

    (Université Paris Cité, Unité des bactéries pathogènes entériques)

  • Christian Kornschober

    (Institute for Medical Microbiology and Hygiene)

  • Jacob Moran-Gilad

    (Ben Gurion University of the Negev)

  • Kees T. Veldman

    (Wageningen Bioveterinary Research)

  • Martin Cormican

    (University of Galway)

  • Mia Torpdahl

    (Statens Serum Institut)

  • Patricia I. Fields

    (Centers for Disease Control and Prevention)

  • Tomáš Černý

    (State Veterinary Institute Prague)

  • Liselotte Hardy

    (Institute of Tropical Medicine)

  • Bieke Tack

    (Institute of Tropical Medicine
    KU Leuven)

  • Kate C. Mellor

    (London School of Hygiene and Tropical Medicine, Bloomsbury
    Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Nicholas Thomson

    (London School of Hygiene and Tropical Medicine, Bloomsbury
    Wellcome Trust Sanger Institute, Genome Campus, Hinxton)

  • Gordon Dougan

    (University of Cambridge)

  • Stijn Deborggraeve

    (Institute of Tropical Medicine)

  • Jan Jacobs

    (Institute of Tropical Medicine
    KU Leuven)

  • Kris Laukens

    (University of Antwerp)

  • Sandra Puyvelde

    (Wellcome Trust Sanger Institute, Genome Campus, Hinxton
    University of Cambridge
    University of Antwerp)

Abstract

Antimicrobial resistant Salmonella enterica serovar Concord (S. Concord) is known to cause severe gastrointestinal and bloodstream infections in patients from Ethiopia and Ethiopian adoptees, and occasional records exist of S. Concord linked to other countries. The evolution and geographical distribution of S. Concord remained unclear. Here, we provide a genomic overview of the population structure and antimicrobial resistance (AMR) of S. Concord by analysing genomes from 284 historical and contemporary isolates obtained between 1944 and 2022 across the globe. We demonstrate that S. Concord is a polyphyletic serovar distributed among three Salmonella super-lineages. Super-lineage A is composed of eight S. Concord lineages, of which four are associated with multiple countries and low levels of AMR. Other lineages are restricted to Ethiopia and horizontally acquired resistance to most antimicrobials used for treating invasive Salmonella infections in low- and middle-income countries. By reconstructing complete genomes for 10 representative strains, we demonstrate the presence of AMR markers integrated in structurally diverse IncHI2 and IncA/C2 plasmids, and/or the chromosome. Molecular surveillance of pathogens such as S. Concord supports the understanding of AMR and the multi-sector response to the global AMR threat. This study provides a comprehensive baseline data set essential for future molecular surveillance.

Suggested Citation

  • Wim L. Cuypers & Pieter Meysman & François-Xavier Weill & Rene S. Hendriksen & Getenet Beyene & John Wain & Satheesh Nair & Marie A. Chattaway & Blanca M. Perez-Sepulveda & Pieter-Jan Ceyssens & Tessa, 2023. "A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-38902-x
    DOI: 10.1038/s41467-023-38902-x
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-38902-x
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-38902-x?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Sandra Van Puyvelde & Derek Pickard & Koen Vandelannoote & Eva Heinz & Barbara Barbé & Tessa de Block & Simon Clare & Eve L. Coomber & Katherine Harcourt & Sushmita Sridhar & Emily A. Lees & Nicole E., 2019. "An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Tuan-Anh Tran & Sushmita Sridhar & Stephen T. Reece & Octavie Lunguya & Jan Jacobs & Sandra Puyvelde & Florian Marks & Gordon Dougan & Nicholas R. Thomson & Binh T. Nguyen & Pham The Bao & Stephen Bak, 2024. "Combining machine learning with high-content imaging to infer ciprofloxacin susceptibility in isolates of Salmonella Typhimurium," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    2. Ying Xiang & Kunpeng Zhu & Kaiyuan Min & Yaowen Zhang & Jiangfeng Liu & Kangkang Liu & Yiran Han & Xinge Li & Xinying Du & Xin Wang & Ying Huang & Xinping Li & Yuqian Peng & Chaojie Yang & Hongbo Liu , 2024. "Characterization of a Salmonella enterica serovar Typhimurium lineage with rough colony morphology and multidrug resistance," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-38902-x. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.