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

Iman Yassine, Sophie Lefèvre, Elisabeth E. Hansen, Corinne Ruckly, Isabelle Carle, Monique Lejay-Collin, Laëtitia Fabre, Rayane Rafei, Dominique Clermont, Maria Pardos Gandara, Fouad Dabboussi, Nicholas R. Thomson and François-Xavier Weill ()
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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
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
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
François-Xavier Weill: Institut Pasteur, Université de Paris, Unité des bactéries pathogènes entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella

Nature Communications, 2022, vol. 13, issue 1, 1-14

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-022-28121-1

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