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Population structure analysis and laboratory monitoring of Shigella by core-genome multilocus sequence typing

Author

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  • Iman Yassine

    (Institut Pasteur, Université de Paris, Unité des bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella
    Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University)

  • Sophie Lefèvre

    (Institut Pasteur, Université de Paris, Unité des bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella)

  • Elisabeth E. Hansen

    (Institut Pasteur, Université de Paris, Unité des bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella
    Harvard Medical School)

  • Corinne Ruckly

    (Institut Pasteur, Université de Paris, Unité des bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella)

  • Isabelle Carle

    (Institut Pasteur, Université de Paris, Unité des bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella)

  • Monique Lejay-Collin

    (Institut Pasteur, Université de Paris, Unité des bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella)

  • Laëtitia Fabre

    (Institut Pasteur, Université de Paris, Unité des bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella)

  • Rayane Rafei

    (Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University)

  • Dominique Clermont

    (Institut Pasteur, Université de Paris, Collection de l’Institut Pasteur)

  • Maria Pardos Gandara

    (Institut Pasteur, Université de Paris, Unité des bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella)

  • Fouad Dabboussi

    (Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University)

  • Nicholas R. Thomson

    (Wellcome Sanger Institute
    London School of Hygiene and Tropical Medicine)

  • François-Xavier Weill

    (Institut Pasteur, Université de Paris, Unité des bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella)

Abstract

The laboratory surveillance of bacillary dysentery is based on a standardised Shigella typing scheme that classifies Shigella strains into four serogroups and more than 50 serotypes on the basis of biochemical tests and lipopolysaccharide O-antigen serotyping. Real-time genomic surveillance of Shigella infections has been implemented in several countries, but without the use of a standardised typing scheme. Here, we study over 4000 reference strains and clinical isolates of Shigella, covering all serotypes, with both the current serotyping scheme and the standardised EnteroBase core-genome multilocus sequence typing scheme (cgMLST). The Shigella genomes are grouped into eight phylogenetically distinct clusters, within the E. coli species. The cgMLST hierarchical clustering (HC) analysis at different levels of resolution (HC2000 to HC400) recognises the natural population structure of Shigella. By contrast, the serotyping scheme is affected by horizontal gene transfer, leading to a conflation of genetically unrelated Shigella strains and a separation of genetically related strains. The use of this cgMLST scheme will facilitate the transition from traditional phenotypic typing to routine whole-genome sequencing for the laboratory surveillance of Shigella infections.

Suggested Citation

  • Iman Yassine & Sophie Lefèvre & Elisabeth E. Hansen & Corinne Ruckly & Isabelle Carle & Monique Lejay-Collin & Laëtitia Fabre & Rayane Rafei & Dominique Clermont & Maria Pardos Gandara & Fouad Dabbous, 2022. "Population structure analysis and laboratory monitoring of Shigella by core-genome multilocus sequence typing," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-28121-1
    DOI: 10.1038/s41467-022-28121-1
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    References listed on IDEAS

    as
    1. Jane Hawkey & Kalani Paranagama & Kate S. Baker & Rebecca J. Bengtsson & François-Xavier Weill & Nicholas R. Thomson & Stephen Baker & Louise Cerdeira & Zamin Iqbal & Martin Hunt & Danielle J. Ingle &, 2021. "Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    2. Kate S. Baker & Timothy J. Dallman & Nigel Field & Tristan Childs & Holly Mitchell & Martin Day & François-Xavier Weill & Sophie Lefèvre & Mathieu Tourdjman & Gwenda Hughes & Claire Jenkins & Nicholas, 2018. "Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
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    Cited by:

    1. Sophie Lefèvre & Elisabeth Njamkepo & Sarah Feldman & Corinne Ruckly & Isabelle Carle & Monique Lejay-Collin & Laëtitia Fabre & Iman Yassine & Lise Frézal & Maria Pardos de la Gandara & Arnaud Fontane, 2023. "Rapid emergence of extensively drug-resistant Shigella sonnei in France," Nature Communications, Nature, vol. 14(1), pages 1-10, December.

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