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An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation

Author

Listed:
  • Sandra Van Puyvelde

    (Institute of Tropical Medicine
    Wellcome Genome Campus, Hinxton
    University of Antwerp)

  • Derek Pickard

    (Wellcome Genome Campus, Hinxton
    Addenbrooke’s Hospital, University of Cambridge)

  • Koen Vandelannoote

    (Institute of Tropical Medicine)

  • Eva Heinz

    (Wellcome Genome Campus, Hinxton
    Liverpool School of Tropical Medicine)

  • Barbara Barbé

    (Institute of Tropical Medicine)

  • Tessa de Block

    (Institute of Tropical Medicine)

  • Simon Clare

    (Wellcome Genome Campus, Hinxton)

  • Eve L. Coomber

    (Wellcome Genome Campus, Hinxton)

  • Katherine Harcourt

    (Wellcome Genome Campus, Hinxton)

  • Sushmita Sridhar

    (Wellcome Genome Campus, Hinxton
    Addenbrooke’s Hospital, University of Cambridge)

  • Emily A. Lees

    (Wellcome Genome Campus, Hinxton
    Addenbrooke’s Hospital, University of Cambridge)

  • Nicole E. Wheeler

    (Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton)

  • Elizabeth J. Klemm

    (Wellcome Genome Campus, Hinxton)

  • Laura Kuijpers

    (Institute of Tropical Medicine
    KU Leuven, Herestraat 49—box 1030)

  • Lisette Mbuyi Kalonji

    (National Institute for Biomedical Research
    University Hospital of Kinshasa)

  • Marie-France Phoba

    (National Institute for Biomedical Research
    University Hospital of Kinshasa)

  • Dadi Falay

    (University Hospital of Kisangani)

  • Dauly Ngbonda

    (University Hospital of Kisangani)

  • Octavie Lunguya

    (National Institute for Biomedical Research
    University Hospital of Kinshasa)

  • Jan Jacobs

    (Institute of Tropical Medicine
    KU Leuven, Herestraat 49—box 1030)

  • Gordon Dougan

    (Wellcome Genome Campus, Hinxton
    Addenbrooke’s Hospital, University of Cambridge)

  • Stijn Deborggraeve

    (Institute of Tropical Medicine)

Abstract

Bloodstream infections by Salmonella enterica serovar Typhimurium constitute a major health burden in sub-Saharan Africa (SSA). These invasive non-typhoidal (iNTS) infections are dominated by isolates of the antibiotic resistance-associated sequence type (ST) 313. Here, we report emergence of ST313 sublineage II.1 in the Democratic Republic of the Congo. Sublineage II.1 exhibits extensive drug resistance, involving a combination of multidrug resistance, extended spectrum β-lactamase production and azithromycin resistance. ST313 lineage II.1 isolates harbour an IncHI2 plasmid we name pSTm-ST313-II.1, with one isolate also exhibiting decreased ciprofloxacin susceptibility. Whole genome sequencing reveals that ST313 II.1 isolates have accumulated genetic signatures potentially associated with altered pathogenicity and host adaptation, related to changes observed in biofilm formation and metabolic capacity. Sublineage II.1 emerged at the beginning of the 21st century and is involved in on-going outbreaks. Our data provide evidence of further evolution within the ST313 clade associated with iNTS in SSA.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-11844-z
    DOI: 10.1038/s41467-019-11844-z
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    Cited by:

    1. 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.

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