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

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 Block, Winnie W. Y. Lee, Maria Pardos de la Gandara, Christian Kornschober, Jacob Moran-Gilad, Kees T. Veldman, Martin Cormican, Mia Torpdahl, Patricia I. Fields, Tomáš Černý, Liselotte Hardy, Bieke Tack, Kate C. Mellor, Nicholas Thomson, Gordon Dougan, Stijn Deborggraeve, Jan Jacobs, Kris Laukens and Sandra Puyvelde ()
Additional contact information
Wim L. Cuypers: University of Antwerp
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
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
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
Kate C. Mellor: London School of Hygiene and Tropical Medicine, Bloomsbury
Nicholas Thomson: London School of Hygiene and Tropical Medicine, Bloomsbury
Gordon Dougan: University of Cambridge
Stijn Deborggraeve: Institute of Tropical Medicine
Jan Jacobs: Institute of Tropical Medicine
Kris Laukens: University of Antwerp
Sandra Puyvelde: Wellcome Trust Sanger Institute, Genome Campus, Hinxton

Nature Communications, 2023, vol. 14, issue 1, 1-12

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-023-38902-x

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